2025-05-06 06:13
ftp://ftp.de.debian.org/debian/pool/main/m/metaeuk/metaeuk_7-bba0d80+ds.orig.tar.xz
cppcheck-options: --library=posix --library=gnu --library=bsd --library=openmp --library=zlib  --inconclusive --enable=style,information --inline-suppr --template=daca2 --disable=missingInclude --suppress=unmatchedSuppression --check-library --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning --suppress=normalCheckLevelConditionExpressions -D__GNUC__ --platform=unix64 -j3
platform: Linux-6.8.0-1022-oracle-aarch64-with-glibc2.39
python: 3.12.3
client-version: 1.3.67
compiler: g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
cppcheck: head 2.17.0
head-info: 581f101 (2025-05-05 21:13:30 +0200)
count: 2671 2428
elapsed-time: 328.8 327.5
head-timing-info:

old-timing-info:

head results:
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_ioutil.hpp:120:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable skipws [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_ioutil.cpp:94:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_ioutil.cpp:151:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_ioutil.hpp:114:25: style: Unused variable: line [unusedVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_ioutil.cpp:108:21: style: Variable 'pbuf' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_ioutil.cpp:147:58: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:144:29: style: Virtual function 'setValueFct' is called from constructor 'DynProgProb(ValueFct*valueFct_=0,long dimInputProb_=0,const double*inputProb_=0,long valueLower_=0,long valueUpper_=0,const double*prob_=0)' at line 84. Dynamic binding is not used. [virtualCallInConstructor]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:84:13: note: Calling setValueFct
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:144:29: note: setValueFct is a virtual function
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:149:22: style: Virtual function 'setInput' is called from constructor 'DynProgProb(ValueFct*valueFct_=0,long dimInputProb_=0,const double*inputProb_=0,long valueLower_=0,long valueUpper_=0,const double*prob_=0)' at line 85. Dynamic binding is not used. [virtualCallInConstructor]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:85:13: note: Calling setInput
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:149:22: note: setInput is a virtual function
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:135:22: style: Virtual function 'clear' is called from constructor 'DynProgProb(ValueFct*valueFct_=0,long dimInputProb_=0,const double*inputProb_=0,long valueLower_=0,long valueUpper_=0,const double*prob_=0)' at line 87. Dynamic binding is not used. [virtualCallInConstructor]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:87:13: note: Calling clear
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:135:22: note: clear is a virtual function
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:116:29: style: Virtual function 'copy' is called from copy constructor 'DynProgProb(const DynProgProb&dynProgProb_)' at line 95. Dynamic binding is not used. [virtualCallInConstructor]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:95:13: note: Calling copy
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:116:29: note: copy is a virtual function
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:202:22: style: Virtual function 'free2' is called from destructor '~DynProgProb()' at line 100. Dynamic binding is not used. [virtualCallInConstructor]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:100:13: note: Calling free2
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:202:22: note: free2 is a virtual function
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:195:22: style: Virtual function 'freeInput' is called from destructor '~DynProgProb()' at line 101. Dynamic binding is not used. [virtualCallInConstructor]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:101:13: note: Calling freeInput
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:195:22: note: freeInput is a virtual function
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:67:16: style: Class 'DynProgProb' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogproblim.hpp:67:16: style: Class 'DynProgProbLim' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:98:25: style: The destructor '~DynProgProb' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprobproto.hpp:65:18: note: Virtual destructor in base class
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:98:25: note: Destructor in derived class
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:104:24: style: The function 'operatorbool' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprobproto.hpp:67:24: note: Virtual function in base class
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:104:24: note: Function in derived class
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:142:29: style: The function 'clear' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprobproto.hpp:69:22: note: Virtual function in base class
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:142:29: note: Function in derived class
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:153:22: style: The function 'update' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprobproto.hpp:71:22: note: Virtual function in base class
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:153:22: note: Function in derived class
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:158:31: style: The function 'getProb' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprobproto.hpp:73:31: note: Virtual function in base class
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:158:31: note: Function in derived class
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:167:31: style: The function 'getStep' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprobproto.hpp:75:31: note: Virtual function in base class
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:167:31: note: Function in derived class
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:172:33: style: The function 'getValueLower' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprobproto.hpp:77:33: note: Virtual function in base class
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:172:33: note: Function in derived class
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:173:33: style: The function 'getValueUpper' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprobproto.hpp:78:33: note: Virtual function in base class
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:173:33: note: Function in derived class
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogproblim.hpp:88:25: style: The destructor '~DynProgProbLim' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:98:25: note: Virtual destructor in base class
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogproblim.hpp:88:25: note: Destructor in derived class
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogproblim.hpp:114:22: style: The function 'update' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:153:22: note: Virtual function in base class
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogproblim.hpp:114:22: note: Function in derived class
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogproblim.hpp:119:29: style: The function 'clear' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:135:22: note: Virtual function in base class
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogproblim.hpp:119:29: note: Function in derived class
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogproblim.hpp:130:29: style: The function 'clear' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:142:29: note: Virtual function in base class
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogproblim.hpp:130:29: note: Function in derived class
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogproblim.hpp:155:22: style: The function 'setValueBegin' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:223:22: note: Virtual function in base class
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogproblim.hpp:155:22: note: Function in derived class
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogproblim.cpp:104:28: style: Variable 'array' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogproblim.cpp:134:28: style: Variable 'array' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.cpp:131:11: style:inconclusive: Function 'copy' argument 7 names different: declaration 'valueFct_' definition 'newStateFct_'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.hpp:131:19: note: Function 'copy' argument 7 names different: declaration 'valueFct_' definition 'newStateFct_'.
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.cpp:131:11: note: Function 'copy' argument 7 names different: declaration 'valueFct_' definition 'newStateFct_'.
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.cpp:268:28: style: Variable 'array' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_dynprogprob.cpp:291:28: style: Variable 'array' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_basic.hpp:179:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_function.hpp:79:74: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LN_2 [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_function.hpp:80:74: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LN_2 [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_function.hpp:81:78: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LN_10 [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_function.hpp:82:78: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LN_10 [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_function.hpp:86:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LN_2 [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_function.hpp:87:74: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LN_2 [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_function.hpp:88:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LN_10 [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_function.hpp:89:75: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LN_10 [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_vector.hpp:203:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_matrix.hpp:150:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_matrix.hpp:294:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_root.hpp:262:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_root.hpp:350:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_root.hpp:402:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_localmaxstatutil.cpp:74:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REL_TOL [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_localmaxstatutil.cpp:242:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REL_TOL [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_localmaxstatutil.cpp:282:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REL_TOL [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_localmaxstatutil.cpp:396:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REL_TOL [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_localmaxstatutil.cpp:507:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REL_TOL [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_basic.hpp:65:47: performance: Variable 'st' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_localmaxstat.hpp:135:28: performance:inconclusive: Technically the member function 'Njn::LocalMaxStat::out' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_vector.hpp:57:27: style: Virtual function 'copy' is called from constructor 'Vector(const T*begin_,const T*end_)' at line 112. Dynamic binding is not used. [virtualCallInConstructor]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_vector.hpp:112:7: note: Calling copy
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_vector.hpp:57:27: note: copy is a virtual function
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_vector.hpp:58:27: style: Virtual function 'copy' is called from constructor 'Vector(long m_,const T&a_)' at line 121. Dynamic binding is not used. [virtualCallInConstructor]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_vector.hpp:121:7: note: Calling copy
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_vector.hpp:58:27: note: copy is a virtual function
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_vector.hpp:80:27: style: Virtual function 'free2' is called from destructor '~Vector()' at line 125. Dynamic binding is not used. [virtualCallInConstructor]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_vector.hpp:125:28: note: Calling free2
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_vector.hpp:80:27: note: free2 is a virtual function
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_matrix.hpp:101:29: style: Virtual function 'free2' is called from destructor '~Matrix()' at line 250. Dynamic binding is not used. [virtualCallInConstructor]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_matrix.hpp:250:29: note: Calling free2
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_matrix.hpp:101:29: note: free2 is a virtual function
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_localmaxstat.hpp:66:14: style: Class 'LocalMaxStat' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_localmaxstatmatrix.hpp:60:16: style: Class 'LocalMaxStatMatrix' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_matrix.hpp:284:16: style: The scope of the variable 'j' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_vector.hpp:285:22: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_vector.hpp:235:14: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_vector.hpp:285:22: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_vector.hpp:290:30: style: Local variable 'sstream' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_vector.hpp:248:20: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_vector.hpp:290:30: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_matrix.hpp:266:17: style: Local variable 'matrix' shadows outer function [shadowFunction]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_matrix.hpp:54:35: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_matrix.hpp:266:17: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_matrix.hpp:296:37: style: Local variable 'j' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_matrix.hpp:284:16: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_matrix.hpp:296:37: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_matrix.hpp:335:29: style: Local variable 'j' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_matrix.hpp:284:16: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_matrix.hpp:335:29: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_matrix.hpp:410:24: style: Local variable 's' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_matrix.hpp:365:16: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_matrix.hpp:410:24: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_matrix.hpp:411:30: style: Local variable 'sstream' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_matrix.hpp:366:22: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_matrix.hpp:411:30: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_localmaxstatmatrix.cpp:128:14: performance: Function parameter 'localMaxStat_' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_localmaxstat.cpp:105:8: style:inconclusive: Function 'copy' argument 15 names different: declaration 'meanDLE_' definition 'meanLength_'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_localmaxstat.hpp:132:14: note: Function 'copy' argument 15 names different: declaration 'meanDLE_' definition 'meanLength_'.
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_localmaxstat.cpp:105:8: note: Function 'copy' argument 15 names different: declaration 'meanDLE_' definition 'meanLength_'.
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_basic.hpp:65:21: performance: Function parameter 'st_' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_basic.hpp:175:39: style: Parameter 'pointer_' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_vector.hpp:235:14: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_localmaxstatmatrix.cpp:92:14: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_random.cpp:68:25: style:inconclusive: Function 'seed' argument 1 names different: declaration 'n' definition 'x'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_random.hpp:46:23: note: Function 'seed' argument 1 names different: declaration 'n' definition 'x'.
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_random.cpp:68:25: note: Function 'seed' argument 1 names different: declaration 'n' definition 'x'.
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_integer.hpp:75:28: style: Condition 'i>=0' is always false [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_integer.hpp:73:19: note: Assuming that condition 'i<0' is not redundant
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_integer.hpp:75:28: note: Condition 'i>=0' is always false
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_root.hpp:292:15: style: The scope of the variable 'fx' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_root.hpp:293:15: style: The scope of the variable 'dfx' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_root.hpp:369:17: style: The scope of the variable 'fx' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_root.hpp:418:17: style: The scope of the variable 'x' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_integer.hpp:91:17: style: The scope of the variable 'remainder' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_localmaxstatutil.cpp:127:8: style:inconclusive: Function 'lambda' argument 1 names different: declaration 'dimMatrix_' definition 'dimension_'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_localmaxstatutil.hpp:59:16: note: Function 'lambda' argument 1 names different: declaration 'dimMatrix_' definition 'dimension_'.
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_localmaxstatutil.cpp:127:8: note: Function 'lambda' argument 1 names different: declaration 'dimMatrix_' definition 'dimension_'.
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_root.hpp:369:20: style: Variable 'fx' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_root.hpp:418:19: style: Variable 'x' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_root.hpp:419:20: style: Variable 'fx' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_localmaxstatutil.cpp:61:14: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_localmaxstatutil.cpp:123:20: style: Variable 'p' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_localmaxstatutil.cpp:132:14: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_integer.hpp:91:27: style: Variable 'remainder' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:257:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAND_MAX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:473:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:513:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.hpp:195:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.hpp:212:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:720:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:757:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:778:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:807:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:854:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:916:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:108:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:418:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable struct_for_randomization [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:575:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable struct_for_randomization [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:693:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable struct_for_randomization [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:710:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:820:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:894:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_EPSILON [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:1023:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:1179:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MIN [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:1400:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable q_elem [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:1523:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:2025:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable state [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:1253:14: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:372:11: warning: Member variable 'alp_data::d_realizations_number2' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:372:11: warning: Member variable 'alp_data::d_time_before1' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:478:11: warning: Member variable 'alp_data::d_realizations_number2' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:478:11: warning: Member variable 'alp_data::d_time_before1' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:386:17: performance:inconclusive: Technically the member function 'Sls::alp_data::ran2' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:702:16: style:inconclusive: Technically the member function 'Sls::alp_data::check_out_file' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:396:8: note: Technically the member function 'Sls::alp_data::check_out_file' can be const.
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:702:16: note: Technically the member function 'Sls::alp_data::check_out_file' can be const.
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:1289:3: warning: Class 'importance_sampling' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:1289:3: warning: Class 'importance_sampling' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:532:3: warning: Class 'alp_data' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:532:3: warning: Class 'alp_data' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:103:3: style: Class 'array_positive' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:169:3: style: Class 'array' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:596:15: style: Condition 'v2_minus<0' is always true [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:581:15: note: Assuming that condition 'v2_minus>=0' is not redundant
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:589:21: note: Assuming condition is false
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:596:15: note: Condition 'v2_minus<0' is always true
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:863:3: style: Exception should be caught by reference. [catchExceptionByValue]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:789:33: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:1234:49: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:1262:4: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:1347:27: style: Redundant assignment of 'd_elements_values[ind]' to itself. [selfAssignment]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:501:13: style: The scope of the variable 'i' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:990:13: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:950:12: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:990:13: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:42:8: performance: Function parameter 'randout_' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:43:8: performance: Function parameter 'smatr_file_name_' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:44:8: performance: Function parameter 'RR1_file_name_' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:45:8: performance: Function parameter 'RR2_file_name_' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:209:8: performance: Function parameter 'randout_' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:374:8: performance: Function parameter 'randout_' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:384:8: performance: Function parameter 'smatr_file_name_' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:385:8: performance: Function parameter 'RR1_file_name_' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:386:8: performance: Function parameter 'RR2_file_name_' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:703:9: performance: Function parameter 'out_file_name_' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:810:8: performance: Function parameter 'smatr_file_name_' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:860:8: performance: Function parameter 'RR_file_name_' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:882:8: performance: Function parameter 'RR_file_name_' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:1011:8: performance: Function parameter 'RR_file_name_' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:1514:8: performance: Function parameter 'str_' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:53:10: style: Parameter 'letterFreqs1_' can be declared as pointer to const [constParameterReference]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:54:10: style: Parameter 'letterFreqs2_' can be declared as pointer to const [constParameterReference]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:480:27: style: Parameter 'randomization_parameters_' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:731:8: style: Variable 'str_for_test0' can be declared as const array [constVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:732:9: style: Variable 'test_flag0' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:739:8: style: Variable 'str_for_test' can be declared as const array [constVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:741:8: style: Variable 'test_flag' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:792:10: style: Variable 'd_RR1' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:793:10: style: Variable 'd_RR2' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:306:24: warning:inconclusive: Division of result of sizeof() on pointer type. [divideSizeof]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:686:23: warning:inconclusive: Division of result of sizeof() on pointer type. [divideSizeof]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:541:7: style: Variable 'v1' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::lambda' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::lambda_error' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::C' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::C_error' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::K' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::K_error' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::a_I' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::a_I_error' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::a_J' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::a_J_error' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::sigma' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::sigma_error' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::alpha_I' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::alpha_I_error' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::alpha_J' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::alpha_J_error' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::a' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::a_error' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::alpha' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::alpha_error' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::gapless_a' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::gapless_a_error' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::gapless_alpha' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::gapless_alpha_error' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::G' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::G1' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::G2' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::m_CalcTime' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::vi_y_thr' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::vj_y_thr' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::c_y_thr' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alignment_evaluer.hpp:60:3: warning: Member variable 'gapped_computation_parameters_struct::d_total_realizations_number_with_ALP' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alignment_evaluer.hpp:60:3: warning: Member variable 'gapped_computation_parameters_struct::d_total_realizations_number_with_killing' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.hpp:153:14: performance:inconclusive: Technically the member function 'Sls::alp::swap' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.hpp:94:2: style: Class 'alp' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.hpp:78:3: style: Class 'alp_sim' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:169:3: style: Class 'array < long >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:103:3: style: Class 'array_positive < long >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:103:3: style: Class 'array_positive < double >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:103:3: style: Class 'array_positive < state * >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:103:3: style: Class 'array_positive < alp * >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alignment_evaluer.cpp:1082:9: style: Local variable 'area' shadows outer function [shadowFunction]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alignment_evaluer.hpp:150:9: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alignment_evaluer.cpp:1082:9: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alignment_evaluer.cpp:101:14: performance: Function parameter 'function_name_' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_regression.cpp:300:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MAX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_regression.cpp:511:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MAX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_regression.cpp:699:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_regression.cpp:366:9: style: Parameter 'values_' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_regression.cpp:367:9: style: Parameter 'errors_' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_regression.cpp:568:9: style: Parameter 'values_' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_regression.cpp:569:9: style: Parameter 'errors_' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_regression.cpp:635:9: style: Parameter 'array_' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_regression.cpp:164:6: style: Variable 'y2' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_basic.cpp:136:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pi [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_basic.cpp:172:9: style: Parameter 'p_' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:751:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:1077:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MAX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2017:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable alp [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2148:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable alp [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2241:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable alp [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2337:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable alp [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1998:8: warning: Member variable 'state::d_HS_ij_next' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1998:8: warning: Member variable 'state::d_HI_ij_next' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1998:8: warning: Member variable 'state::d_HD_ij_next' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1998:8: warning: Member variable 'state::d_H_ij_next' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1998:8: warning: Member variable 'state::d_H_matr_len' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1998:8: warning: Member variable 'state::d_M' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1998:8: warning: Member variable 'state::d_sentinel_i_next' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1998:8: warning: Member variable 'state::d_sentinel_j_next' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:44:6: warning: Member variable 'alp::d_nalp_killing' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:44:6: warning: Member variable 'alp::d_diff_opt' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:44:6: warning: Member variable 'alp::d_sentinels_flag' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:44:6: warning: Member variable 'alp::d_IS_state' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:127:3: warning: Class 'alp' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:127:3: warning: Class 'alp' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:269:11: style: The scope of the variable 'i' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:386:11: style: The scope of the variable 'i' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1203:12: style: The scope of the variable 'i' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1389:12: style: The scope of the variable 'i' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1673:12: style: The scope of the variable 'i' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1906:12: style: The scope of the variable 'i' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1203:12: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1143:11: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1203:12: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1389:12: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1322:11: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1389:12: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1648:12: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1580:11: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1648:12: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1673:12: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1580:11: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1673:12: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1881:12: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1813:11: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1881:12: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1906:12: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1813:11: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1906:12: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:2108:11: style: Parameter 'M_upper_level_' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:2208:24: style: Variable 'd_is_tmp' can be declared as pointer to const [constVariableReference]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:2252:4: style: Variable 'UI' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:2255:4: style: Variable 'VD' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.cpp:901:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MAX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.cpp:1040:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/nrutil.cpp:9:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.cpp:819:15: style:inconclusive: Technically the member function 'Sls::pvalues::calculate_P_values' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:244:8: note: Technically the member function 'Sls::pvalues::calculate_P_values' can be const.
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.cpp:819:15: note: Technically the member function 'Sls::pvalues::calculate_P_values' can be const.
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.cpp:113:5: style: Condition 'blast_' is always false [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.cpp:67:9: note: Assignment 'blast_=false', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.cpp:113:5: note: Condition 'blast_' is always false
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.cpp:153:21: style: Condition 'blast_' is always false [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.cpp:67:9: note: Assignment 'blast_=false', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.cpp:153:21: note: Condition 'blast_' is always false
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.cpp:411:5: style: Condition 'blast_' is always false [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.cpp:383:9: note: Assignment 'blast_=false', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.cpp:411:5: note: Condition 'blast_' is always false
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.cpp:438:21: style: Condition 'blast_' is always false [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.cpp:383:9: note: Assignment 'blast_=false', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.cpp:438:21: note: Condition 'blast_' is always false
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.cpp:864:10: style: The scope of the variable 'P_tmp' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.cpp:864:16: style: The scope of the variable 'E_tmp' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/nrutil.cpp:20:5: error: Memory leak: v [memleak]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/nrutil.cpp:28:5: error: Memory leak: v [memleak]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/nrutil.cpp:36:5: error: Memory leak: v [memleak]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/nrutil.cpp:18:9: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/nrutil.cpp:26:9: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/nrutil.cpp:34:9: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/nrutil.cpp:43:9: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/nrutil.cpp:48:16: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/nrutil.cpp:59:9: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/nrutil.cpp:64:16: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/nrutil.cpp:75:9: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/nrutil.cpp:85:10: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/nrutil.cpp:89:10: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/nrutil.cpp:95:39: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/nrutil.cpp:96:10: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/lambda_calculator.cpp:294:17: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/nrutil.cpp:89:10: portability:inconclusive: Casting from double * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/nrutil.cpp:95:39: portability:inconclusive: Casting from double * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/nrutil.cpp:96:10: portability:inconclusive: Casting from double * * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/lubksb.cpp:4:20: style: The scope of the variable 'ip' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/lambda_calculator.cpp:61:9: style: The scope of the variable 'k' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/lambda_calculator.cpp:126:9: style: The scope of the variable 'pos_flag_r' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/lambda_calculator.cpp:126:21: style: The scope of the variable 'neg_flag_r' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/lambda_calculator.cpp:127:9: style: The scope of the variable 'pos_flag_c' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/lambda_calculator.cpp:127:21: style: The scope of the variable 'neg_flag_c' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/lambda_calculator.cpp:128:12: style: The scope of the variable 'r_max' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/lambda_calculator.cpp:128:19: style: The scope of the variable 'c_max' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/lambda_calculator.cpp:242:12: style: The scope of the variable 'lambda' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/lambda_calculator.cpp:317:12: style: The scope of the variable 'j' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/lambda_calculator.cpp:319:12: style: The scope of the variable 'lambda' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/lambda_calculator.cpp:327:9: style: The scope of the variable 'j_monitor' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/lambda_calculator.cpp:418:25: style:inconclusive: Function 'Nail_lambda' argument 7 names different: declaration 'la_add' definition 'lam_add'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/lambda_calculator.cpp:49:25: note: Function 'Nail_lambda' argument 7 names different: declaration 'la_add' definition 'lam_add'.
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/lambda_calculator.cpp:418:25: note: Function 'Nail_lambda' argument 7 names different: declaration 'la_add' definition 'lam_add'.
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/nrutil.cpp:16:12: style: Variable 'v' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/nrutil.cpp:24:10: style: Variable 'v' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/nrutil.cpp:32:13: style: Variable 'v' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/lib/cacode/lubksb.cpp:3:37: style: Parameter 'indx' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/lib/microtar/microtar.c:50:18: style: Variable 'p' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/lib/omptl/Example.cpp:23:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/tinyexpr/benchmark.c:56:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CLOCKS_PER_SEC [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/tinyexpr/example2.c:4:26: style: Parameter 'argv' can be declared as const array [constParameter]
metaeuk-7-bba0d80/lib/mmseqs/lib/tinyexpr/test.c:622:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/tinyexpr/test.c:771:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CLOCKS_PER_SEC [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/tinyexpr/test.c:364:9: warning: Invalid acos() argument nr 1. The value is -5 but the valid values are '-1.0:1.0'. [invalidFunctionArg]
metaeuk-7-bba0d80/lib/mmseqs/lib/tinyexpr/test.c:365:9: warning: Invalid asin() argument nr 1. The value is -5 but the valid values are '-1.0:1.0'. [invalidFunctionArg]
metaeuk-7-bba0d80/lib/mmseqs/lib/tinyexpr/test.c:372:9: warning: Invalid log() argument nr 1. The value is -5 but the valid values are '4.94066e-324:'. [invalidFunctionArg]
metaeuk-7-bba0d80/lib/mmseqs/lib/tinyexpr/test.c:373:9: warning: Invalid log10() argument nr 1. The value is -5 but the valid values are '4.94066e-324:'. [invalidFunctionArg]
metaeuk-7-bba0d80/lib/mmseqs/lib/tinyexpr/test.c:376:9: warning: Invalid sqrt() argument nr 1. The value is -5 but the valid values are '0.0:'. [invalidFunctionArg]
metaeuk-7-bba0d80/lib/mmseqs/lib/tinyexpr/test.c:567:9: warning: Either the condition '!ex' is redundant or there is possible null pointer dereference: ex. [nullPointerRedundantCheck]
metaeuk-7-bba0d80/lib/mmseqs/lib/tinyexpr/test.c:563:9: note: Assuming that condition '!ex' is not redundant
metaeuk-7-bba0d80/lib/mmseqs/lib/tinyexpr/test.c:567:9: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/lib/tinyexpr/test.c:195:18: style: Variable 'n' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/lib/tinyexpr/test.c:327:14: style: Variable 'expr5' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/lib/tinyexpr/test.c:331:14: style: Variable 'expr6' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/lib/tinyexpr/test.c:335:14: style: Variable 'expr7' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/lib/tinyexpr/test.c:339:14: style: Variable 'expr8' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/lib/tinyexpr/test.c:487:13: style: Variable 'c' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/lib/tinyexpr/test.c:769:26: style: Parameter 'argv' can be declared as const array [constParameter]
metaeuk-7-bba0d80/lib/mmseqs/lib/tinyexpr/tinyexpr.c:695:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable type [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/tinyexpr/tinyexpr.c:89:12: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
metaeuk-7-bba0d80/lib/mmseqs/lib/tinyexpr/tinyexpr.c:88:26: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/lib/tinyexpr/tinyexpr.c:88:26: note: Assignment 'ret=malloc(size)', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/lib/tinyexpr/tinyexpr.c:89:12: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/lib/tinyexpr/tinyexpr.c:93:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
metaeuk-7-bba0d80/lib/mmseqs/lib/tinyexpr/tinyexpr.c:88:26: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/lib/tinyexpr/tinyexpr.c:88:26: note: Assignment 'ret=malloc(size)', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/lib/tinyexpr/tinyexpr.c:93:5: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/lib/tinyexpr/tinyexpr.c:94:5: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
metaeuk-7-bba0d80/lib/mmseqs/lib/tinyexpr/tinyexpr.c:88:26: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/lib/tinyexpr/tinyexpr.c:88:26: note: Assignment 'ret=malloc(size)', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/lib/tinyexpr/tinyexpr.c:94:5: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:109:36: warning: If memory allocation fails, then there is a possible null pointer dereference: H [nullPointerOutOfMemory]
metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:108:17: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:108:7: note: Assignment 'H=(int32_t*)malloc(tlen_*16*4)', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:109:36: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:106:8: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:104:18: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:104:8: note: Assignment 'mem=(uint8_t*)calloc(tlen_*6+qlen_+1,16)', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:105:4: note: u is assigned '(__m128i*)(((unsigned long)mem+15)>>4<<4)' here.
metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:106:8: note: Null pointer addition
metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:115:17: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:114:15: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:114:9: note: Assignment 'off=(int*)malloc((qlen+tlen-1)*sizeof(int)*2)', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:115:17: note: Null pointer addition
metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2.h:134:12: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:104:8: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:106:67: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:108:7: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:112:10: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:114:9: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:124:45: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:124:64: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:140:11: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:143:17: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:148:26: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:149:26: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:154:33: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:158:6: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:226:27: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:230:23: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:236:22: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:237:22: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:280:39: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:282:39: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:147:17: style: Local variable 'st' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:122:7: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:147:17: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/EvalueComputation.h:23:73: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable lambda [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/EvalueComputation.h:28:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable K [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/EvalueComputation.h:149:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ERROR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Alignment.cpp:30:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALIGNMENT_MODE_UNGAPPED [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Alignment.cpp:225:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFO [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Alignment.cpp:249:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_ALIGNMENT_RES [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Alignment.cpp:581:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ERROR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/DistanceCalculator.h:126:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RESCORE_MODE_HAMMING [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/DistanceCalculator.h:278:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VECSIZE_INT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/BandedNucleotideAligner.cpp:104:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RESCORE_MODE_ALIGNMENT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.h:183:24: style: Comparison of a variable having boolean value using relational (<, >, <= or >=) operator. [comparisonOfBoolWithBoolError]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.h:185:23: style: Comparison of a variable having boolean value using relational (<, >, <= or >=) operator. [comparisonOfBoolWithBoolError]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.h:189:25: style: Comparison of a variable having boolean value using relational (<, >, <= or >=) operator. [comparisonOfBoolWithBoolError]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.h:191:24: style: Comparison of a variable having boolean value using relational (<, >, <= or >=) operator. [comparisonOfBoolWithBoolError]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.h:91:9: warning:inconclusive: Member variable 'result_t::dbKey' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.h:91:9: warning:inconclusive: Member variable 'result_t::score' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.h:91:9: warning:inconclusive: Member variable 'result_t::qcov' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.h:91:9: warning:inconclusive: Member variable 'result_t::dbcov' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.h:91:9: warning:inconclusive: Member variable 'result_t::seqId' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.h:91:9: warning:inconclusive: Member variable 'result_t::eval' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.h:91:9: warning:inconclusive: Member variable 'result_t::alnLength' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.h:91:9: warning:inconclusive: Member variable 'result_t::qStartPos' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.h:91:9: warning:inconclusive: Member variable 'result_t::qEndPos' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.h:91:9: warning:inconclusive: Member variable 'result_t::qLen' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.h:91:9: warning:inconclusive: Member variable 'result_t::dbStartPos' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.h:91:9: warning:inconclusive: Member variable 'result_t::dbEndPos' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.h:91:9: warning:inconclusive: Member variable 'result_t::dbLen' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.h:91:9: warning:inconclusive: Member variable 'result_t::queryOrfStartPos' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.h:91:9: warning:inconclusive: Member variable 'result_t::queryOrfEndPos' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.h:91:9: warning:inconclusive: Member variable 'result_t::dbOrfStartPos' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.h:91:9: warning:inconclusive: Member variable 'result_t::dbOrfEndPos' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Alignment.cpp:544:19: style: Unused private function: 'Alignment::estimateHDDMemoryConsumption' [unusedPrivateFunction]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Alignment.h:123:19: note: Unused private function: 'Alignment::estimateHDDMemoryConsumption'
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Alignment.cpp:544:19: note: Unused private function: 'Alignment::estimateHDDMemoryConsumption'
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Alignment.cpp:152:9: warning: Class 'Alignment' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Alignment.cpp:152:9: warning: Class 'Alignment' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/EvalueComputation.h:85:27: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/EvalueComputation.h:105:56: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/EvalueComputation.h:126:56: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Alignment.cpp:335:40: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Alignment.cpp:569:119: style:inconclusive: Function 'computeAlternativeAlignment' argument 3 names different: declaration 'vector' definition 'swResults'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Alignment.h:126:70: note: Function 'computeAlternativeAlignment' argument 3 names different: declaration 'vector' definition 'swResults'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Alignment.cpp:569:119: note: Function 'computeAlternativeAlignment' argument 3 names different: declaration 'vector' definition 'swResults'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Alignment.cpp:460:34: style: Local variable 'rejected' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Alignment.cpp:345:30: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Alignment.cpp:460:34: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Alignment.cpp:61:85: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Alignment.cpp:73:89: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.h:65:30: performance: Function parameter 'backtrace' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.h:83:30: performance: Function parameter 'backtrace' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.h:117:48: style: Parameter 'backtrace' can be declared as reference to const [constParameterReference]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.h:136:27: style: Variable 'buffNext' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/BandedNucleotideAligner.cpp:18:26: warning: Member variable 'BandedNucleotideAligner::querySeq' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/BandedNucleotideAligner.cpp:18:26: warning: Member variable 'BandedNucleotideAligner::querySeqObj' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/BandedNucleotideAligner.cpp:28:5: warning: Class 'BandedNucleotideAligner' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/BandedNucleotideAligner.cpp:28:5: warning: Class 'BandedNucleotideAligner' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/DistanceCalculator.h:279:31: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/DistanceCalculator.h:280:31: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/BandedNucleotideAligner.cpp:29:20: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/BandedNucleotideAligner.cpp:61:32: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/BandedNucleotideAligner.cpp:61:55: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/BandedNucleotideAligner.cpp:68:32: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/BandedNucleotideAligner.cpp:68:62: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/BandedNucleotideAligner.cpp:78:32: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/BandedNucleotideAligner.cpp:93:32: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/BandedNucleotideAligner.cpp:93:56: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/BandedNucleotideAligner.cpp:51:52: style:inconclusive: Function 'initQuery' argument 1 names different: declaration 'q' definition 'query'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/BandedNucleotideAligner.h:24:30: note: Function 'initQuery' argument 1 names different: declaration 'q' definition 'query'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/BandedNucleotideAligner.cpp:51:52: note: Function 'initQuery' argument 1 names different: declaration 'q' definition 'query'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/DistanceCalculator.h:366:26: style: Local variable 's1' shadows outer argument [shadowArgument]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/DistanceCalculator.h:351:54: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/DistanceCalculator.h:366:26: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/DistanceCalculator.h:367:30: style: Local variable 's2' shadows outer argument [shadowArgument]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/DistanceCalculator.h:351:77: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/DistanceCalculator.h:367:30: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/DistanceCalculator.h:366:26: performance: Range variable 's1' should be declared as const reference. [iterateByValue]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/DistanceCalculator.h:367:30: performance: Range variable 's2' should be declared as const reference. [iterateByValue]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/BandedNucleotideAligner.cpp:78:12: style: Variable 'queryCharSeqAlign' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/DistanceCalculator.h:368:58: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/BandedNucleotideAligner.cpp:158:16: error: Uninitialized variables: result.score2, result.ref_end2 [uninitvar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/BandedNucleotideAligner.cpp:260:12: error: Uninitialized variables: result.score2, result.ref_end2 [uninitvar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/BandedNucleotideAligner.cpp:260:12: error: Uninitialized struct member: result.score2 [uninitStructMember]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/BandedNucleotideAligner.cpp:260:12: error: Uninitialized struct member: result.ref_end2 [uninitStructMember]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/BandedNucleotideAligner.cpp:158:16: error: Uninitialized struct member: result.score2 [uninitStructMember]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/BandedNucleotideAligner.cpp:158:16: error: Uninitialized struct member: result.ref_end2 [uninitStructMember]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/BandedNucleotideAligner.cpp:195:28: style: Variable 'letterCode' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/BandedNucleotideAligner.cpp:195:17: style: Variable 'letterCode' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Main.cpp:17:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMMAND_ALIGN [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Main.cpp:39:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMMAND_ALIGN [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/CompressedA3M.cpp:59:19: style: Variable 'last_char' is reassigned a value before the old one has been used. [redundantAssignment]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/CompressedA3M.cpp:53:23: note: last_char is assigned
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/CompressedA3M.cpp:59:19: note: last_char is overwritten
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.cpp:14:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_NUCLEOTIDES [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.cpp:50:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_NUCLEOTIDES [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.cpp:70:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_NUCLEOTIDES [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.cpp:206:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ERROR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:215:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.cpp:9:10: warning: Member variable 'Matcher::currentQuery' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.cpp:19:9: warning: Class 'Matcher' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.cpp:19:9: warning: Class 'Matcher' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.cpp:64:13: style: The scope of the variable 'maskLen' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.cpp:60:119: style:inconclusive: Function 'getSWResult' argument 9 names different: declaration 'isIdentical' definition 'isIdentity'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.h:154:83: note: Function 'getSWResult' argument 9 names different: declaration 'isIdentical' definition 'isIdentity'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.cpp:60:119: note: Function 'getSWResult' argument 9 names different: declaration 'isIdentical' definition 'isIdentity'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.cpp:155:35: warning: Function 'computeAlnLength' argument order different: declaration 'anEnd, start, dbEnd, dbStart' definition 'qStart, qEnd, dbStart, dbEnd' [funcArgOrderDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.h:221:37: note: Function 'computeAlnLength' argument order different: declaration 'anEnd, start, dbEnd, dbStart' definition 'qStart, qEnd, dbStart, dbEnd'
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.cpp:155:35: note: Function 'computeAlnLength' argument order different: declaration 'anEnd, start, dbEnd, dbStart' definition 'qStart, qEnd, dbStart, dbEnd'
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.cpp:277:39: style:inconclusive: Function 'resultToBuffer' argument 1 names different: declaration 'buffer' definition 'buff1'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.h:219:41: note: Function 'resultToBuffer' argument 1 names different: declaration 'buffer' definition 'buff1'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Matcher.cpp:277:39: note: Function 'resultToBuffer' argument 1 names different: declaration 'buffer' definition 'buff1'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:570:17: style:inconclusive: Technically the member function 'MsaFilter::getKept' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.h:42:10: note: Technically the member function 'MsaFilter::getKept' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:570:17: note: Technically the member function 'MsaFilter::getKept' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:627:16: style:inconclusive: Technically the member function 'MsaFilter::prune' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.h:55:9: note: Technically the member function 'MsaFilter::prune' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:627:16: note: Technically the member function 'MsaFilter::prune' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:18:11: warning: Class 'MsaFilter' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:18:11: warning: Class 'MsaFilter' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:54:9: error: Common realloc mistake: 'in' nulled but not freed upon failure [memleakOnRealloc]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:55:9: error: Common realloc mistake: 'inkk' nulled but not freed upon failure [memleakOnRealloc]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:56:9: error: Common realloc mistake: 'seqid_prev' nulled but not freed upon failure [memleakOnRealloc]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:57:9: error: Common realloc mistake: 'first' nulled but not freed upon failure [memleakOnRealloc]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:58:9: error: Common realloc mistake: 'last' nulled but not freed upon failure [memleakOnRealloc]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:59:9: error: Common realloc mistake: 'nres' nulled but not freed upon failure [memleakOnRealloc]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:60:9: error: Common realloc mistake: 'ksort' nulled but not freed upon failure [memleakOnRealloc]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:61:9: error: Common realloc mistake: 'display' nulled but not freed upon failure [memleakOnRealloc]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:62:9: error: Common realloc mistake: 'keep' nulled but not freed upon failure [memleakOnRealloc]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:63:9: error: Common realloc mistake: 'X' nulled but not freed upon failure [memleakOnRealloc]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:64:9: error: Common realloc mistake: 'keep_local' nulled but not freed upon failure [memleakOnRealloc]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:21:16: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:22:18: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:23:24: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:24:19: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:25:18: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:26:18: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:27:19: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:28:21: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:29:18: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:30:16: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:31:24: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:54:14: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:55:16: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:56:22: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:57:17: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:58:16: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:59:16: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:60:17: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:61:19: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:62:16: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:63:14: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:64:22: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:69:125: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:445:42: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:446:42: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:154:13: style: The scope of the variable 'diffNmax_prev' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:262:19: style: The scope of the variable 'qsc_sum' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:85:36: style:inconclusive: Function 'filter' argument 1 names different: declaration 'N_in' definition 'N_in_total'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.h:39:29: note: Function 'filter' argument 1 names different: declaration 'N_in' definition 'N_in_total'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:85:36: note: Function 'filter' argument 1 names different: declaration 'N_in' definition 'N_in_total'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:85:106: style:inconclusive: Function 'filter' argument 4 names different: declaration 'qid' definition 'qid_vec'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.h:39:93: note: Function 'filter' argument 4 names different: declaration 'qid' definition 'qid_vec'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:85:106: note: Function 'filter' argument 4 names different: declaration 'qid' definition 'qid_vec'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:86:109: style:inconclusive: Function 'filter' argument 9 names different: declaration 'X' definition 'X_in'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.h:40:102: note: Function 'filter' argument 9 names different: declaration 'X' definition 'X_in'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:86:109: note: Function 'filter' argument 9 names different: declaration 'X' definition 'X_in'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:570:31: style:inconclusive: Function 'getKept' argument 1 names different: declaration 'offsets' definition 'kept'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.h:42:24: note: Function 'getKept' argument 1 names different: declaration 'offsets' definition 'kept'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:570:31: note: Function 'getKept' argument 1 names different: declaration 'offsets' definition 'kept'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:269:26: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:168:13: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:269:26: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:306:26: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:168:13: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:306:26: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:461:30: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:168:13: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:461:30: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:627:58: style: Parameter 'query' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:627:71: style: Parameter 'target' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.cpp:18:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VECSIZE_INT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.cpp:80:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ERROR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.cpp:123:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ERROR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.cpp:187:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ERROR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.cpp:226:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ERROR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:26:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PCMODE_CONTEXT_SPECIFIC [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:174:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PROFILE_AA_SIZE [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:210:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PROFILE_AA_SIZE [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:226:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PROFILE_AA_SIZE [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:244:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PROFILE_AA_SIZE [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:260:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PROFILE_AA_SIZE [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:271:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PROFILE_AA_SIZE [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:311:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PROFILE_AA_SIZE [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:369:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PROFILE_AA_SIZE [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:381:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PROFILE_AA_SIZE [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:408:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VECSIZE_FLOAT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:639:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PROFILE_AA_SIZE [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:656:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PROFILE_AA_SIZE [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:683:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PROFILE_AA_SIZE [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.cpp:76:27: style:inconclusive: Technically the member function 'MultipleAlignment::updateGapsInCenterSequence' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.h:53:12: note: Technically the member function 'MultipleAlignment::updateGapsInCenterSequence' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.cpp:76:27: note: Technically the member function 'MultipleAlignment::updateGapsInCenterSequence' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.cpp:95:25: style:inconclusive: Technically the member function 'MultipleAlignment::updateGapsInSequenceSet' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.h:55:10: note: Technically the member function 'MultipleAlignment::updateGapsInSequenceSet' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.cpp:95:25: note: Technically the member function 'MultipleAlignment::updateGapsInSequenceSet' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.cpp:221:49: style:inconclusive: Technically the member function 'MultipleAlignment::singleSequenceMSA' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.h:59:15: note: Technically the member function 'MultipleAlignment::singleSequenceMSA' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.cpp:221:49: note: Technically the member function 'MultipleAlignment::singleSequenceMSA' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.cpp:10:5: warning: Class 'MultipleAlignment' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.cpp:10:5: warning: Class 'MultipleAlignment' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.cpp:20:17: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.cpp:34:41: performance: Function parameter 'msaResult' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.cpp:34:73: style: Parameter 'subMat' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.cpp:44:77: style: Parameter 'centerSeq' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.cpp:96:119: style: Parameter 'queryGaps' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:13:17: warning: Member variable 'PSSMCalculator::seqWeightTotal' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:634:22: performance:inconclusive: Technically the member function 'PSSMCalculator::computeConsensusSequence' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.h:158:10: note: Technically the member function 'PSSMCalculator::computeConsensusSequence' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:634:22: note: Technically the member function 'PSSMCalculator::computeConsensusSequence' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:27:9: warning: Class 'PSSMCalculator' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:27:9: warning: Class 'PSSMCalculator' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:675:9: error: Common realloc mistake: 'seqWeight' nulled but not freed upon failure [memleakOnRealloc]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:676:9: error: Common realloc mistake: 'wi' nulled but not freed upon failure [memleakOnRealloc]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:33:32: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:36:32: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:37:32: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:38:32: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:44:25: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:46:24: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:48:10: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:52:17: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:54:16: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:174:103: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:415:14: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:417:14: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:491:43: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:567:14: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:569:14: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:675:21: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:676:14: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:46:24: portability: Casting between unsigned char * and float * which have an incompatible binary data representation. [invalidPointerCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:360:65: style:inconclusive: Function 'computePseudoCounts' argument 6 names different: declaration 'length' definition 'queryLength'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.h:62:147: note: Function 'computePseudoCounts' argument 6 names different: declaration 'length' definition 'queryLength'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:360:65: note: Function 'computePseudoCounts' argument 6 names different: declaration 'length' definition 'queryLength'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:395:80: style:inconclusive: Function 'computeContextSpecificWeights' argument 2 names different: declaration 'seqWeight' definition 'wg'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.h:152:68: note: Function 'computeContextSpecificWeights' argument 2 names different: declaration 'seqWeight' definition 'wg'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:395:80: note: Function 'computeContextSpecificWeights' argument 2 names different: declaration 'seqWeight' definition 'wg'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:396:65: style:inconclusive: Function 'computeContextSpecificWeights' argument 6 names different: declaration 'msaSeqs' definition 'X'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.h:152:144: note: Function 'computeContextSpecificWeights' argument 6 names different: declaration 'msaSeqs' definition 'X'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:396:65: note: Function 'computeContextSpecificWeights' argument 6 names different: declaration 'msaSeqs' definition 'X'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:634:123: style:inconclusive: Function 'computeConsensusSequence' argument 4 names different: declaration 'back' definition 'pBack'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.h:158:111: note: Function 'computeConsensusSequence' argument 4 names different: declaration 'back' definition 'pBack'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:634:123: note: Function 'computeConsensusSequence' argument 4 names different: declaration 'back' definition 'pBack'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:650:50: style: Parameter 'centerSequence' can be declared as reference to const [constParameterReference]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:654:110: style: Parameter 'subMat' can be declared as reference to const [constParameterReference]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:179:17: style: Variable 'csprofile' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:266:43: style: Parameter 'frequency' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:266:61: style: Parameter 'seqWeight' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:358:65: style: Parameter 'frequency' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:359:49: style: Parameter 'frequency_with_pseudocounts' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:360:50: style: Parameter 'Neff_M' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:379:71: style: Parameter 'seqWeight' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:634:84: style: Parameter 'frequency' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:634:123: style: Parameter 'pBack' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:634:136: style: Parameter 'num2aa' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:680:62: style: Parameter 'matchWeight' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:680:82: style: Parameter 'Neff_M' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:43:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALIGN_INT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1240:82: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_HMM_PROFILE [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1410:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1661:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1667:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1681:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1694:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1743:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VECSIZE_INT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:370:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:976:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VECSIZE_INT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:665:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VECSIZE_INT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/rescorediagonal.cpp:39:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WARNING [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/rescorediagonal.cpp:54:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRELOAD_MODE_MMAP [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/rescorediagonal.cpp:394:117: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:45:10: warning: Member variable 'alp_sim::m_GaplessAlpha' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:45:10: warning: Member variable 'alp_sim::m_GaplessAlphaError' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:45:10: warning: Member variable 'alp_sim::m_GaplessA' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:45:10: warning: Member variable 'alp_sim::m_GaplessAError' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:45:10: warning: Member variable 'alp_sim::m_G' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:45:10: warning: Member variable 'alp_sim::m_G1' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:45:10: warning: Member variable 'alp_sim::m_G2' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2593:15: performance:inconclusive: Technically the member function 'Sls::alp_sim::memory_release_for_get_minimal_simulation' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.hpp:102:8: note: Technically the member function 'Sls::alp_sim::memory_release_for_get_minimal_simulation' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2593:15: note: Technically the member function 'Sls::alp_sim::memory_release_for_get_minimal_simulation' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3534:15: performance:inconclusive: Technically the member function 'Sls::alp_sim::calculate_C' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.hpp:136:8: note: Technically the member function 'Sls::alp_sim::calculate_C' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3534:15: note: Technically the member function 'Sls::alp_sim::calculate_C' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2773:15: performance:inconclusive: Technically the member function 'Sls::alp_sim::memory_release_for_calculate_FSC' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.hpp:148:8: note: Technically the member function 'Sls::alp_sim::memory_release_for_calculate_FSC' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2773:15: note: Technically the member function 'Sls::alp_sim::memory_release_for_calculate_FSC' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3493:15: performance:inconclusive: Technically the member function 'Sls::alp_sim::sigma_calculation' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.hpp:206:8: note: Technically the member function 'Sls::alp_sim::sigma_calculation' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3493:15: note: Technically the member function 'Sls::alp_sim::sigma_calculation' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:1104:15: style:inconclusive: Technically the member function 'Sls::alp_sim::memory_release_for_calculate_main_parameters2m' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.hpp:354:8: note: Technically the member function 'Sls::alp_sim::memory_release_for_calculate_main_parameters2m' can be const.
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:1104:15: note: Technically the member function 'Sls::alp_sim::memory_release_for_calculate_main_parameters2m' can be const.
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:72:3: warning: Class 'alp_sim' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:72:3: warning: Class 'alp_sim' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:372:9: style: Condition '!loop_break_flag' is always true [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:329:7: note: Assuming that condition 'loop_break_flag' is not redundant
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:372:9: note: Condition '!loop_break_flag' is always true
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:475:9: style: Condition '!loop_break_flag' is always true [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:432:7: note: Assuming that condition 'loop_break_flag' is not redundant
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:475:9: note: Condition '!loop_break_flag' is always true
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:660:5: style: Exception should be caught by reference. [catchExceptionByValue]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2908:32: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3585:33: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3586:40: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3686:33: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3687:40: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3951:5: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3952:5: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3957:32: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3958:39: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:4410:45: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:4430:33: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:4431:40: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:570:6: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:575:6: note: Found duplicate branches for 'if' and 'else'.
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:570:6: note: Found duplicate branches for 'if' and 'else'.
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:4314:35: style: Variable 'tmp_struct.d_calculate_alp_number' is reassigned a value before the old one has been used. [redundantAssignment]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:4311:35: note: tmp_struct.d_calculate_alp_number is assigned
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:4314:35: note: tmp_struct.d_calculate_alp_number is overwritten
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:277:12: style: The scope of the variable 'number_of_realizations_with_ALP_pred' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:383:12: style: The scope of the variable 'number_of_realizations_with_killing_pred' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:590:10: style: The scope of the variable 'sucess_flag' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2006:11: style: The scope of the variable 'i' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2302:12: style: The scope of the variable 'alp_number' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:4354:9: style: The scope of the variable 'sum2_error' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:1469:13: style: Local variable 'j' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:1336:12: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:1469:13: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:1487:11: style: Local variable 'test_difference' shadows outer argument [shadowArgument]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:1250:9: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:1487:11: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:1488:11: style: Local variable 'test_difference_error' shadows outer argument [shadowArgument]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:1251:9: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:1488:11: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2062:12: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2049:11: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2062:12: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2066:9: style: Local variable 'flag' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2043:7: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2066:9: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2090:11: style: Local variable 'flag' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2066:9: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2090:11: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2363:13: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2326:12: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2363:13: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2477:14: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2363:13: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2477:14: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2918:11: style: Local variable 'tmp' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2908:27: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2918:11: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3028:13: style: Local variable 'j' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2988:12: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3028:13: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3731:13: style: Local variable 'number_of_elements' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3620:12: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3731:13: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3733:9: style: Local variable 'cut_left_tail' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3622:8: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3733:9: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3734:9: style: Local variable 'cut_right_tail' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3623:8: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3734:9: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3738:11: style: Local variable 'beta1' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3617:10: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3738:11: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3740:11: style: Local variable 'beta1_error' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3618:10: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3740:11: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3742:9: style: Local variable 'res_was_calculated' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3634:8: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3742:9: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:4460:13: style: Local variable 'k' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:4427:12: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:4460:13: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2762:11: style: Parameter 'i_' can be declared as reference to const [constParameterReference]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3947:14: style: Variable 'alp_tmp' can be declared as reference to const [constVariableReference]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3948:12: style: Variable 'weight_tmp' can be declared as reference to const [constVariableReference]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:4042:14: style: Variable 'alp_tmp' can be declared as reference to const [constVariableReference]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:4043:12: style: Variable 'weight_tmp' can be declared as reference to const [constVariableReference]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:4146:14: style: Variable 'alp_tmp' can be declared as reference to const [constVariableReference]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:4147:12: style: Variable 'weight_tmp' can be declared as reference to const [constVariableReference]
metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2763:10: style: Parameter 'exp_array_' can be declared as pointer to const [constParameterReference]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/AlignmentSymmetry.h:36:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ERROR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/AlignmentSymmetry.cpp:48:76: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_ALIGNMENT_RES [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/AlignmentSymmetry.cpp:125:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nothrow [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/AlignmentSymmetry.cpp:179:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ERROR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/rescorediagonal.cpp:102:52: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/rescorediagonal.cpp:103:52: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/rescorediagonal.cpp:165:36: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/rescorediagonal.cpp:174:56: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/rescorediagonal.cpp:183:36: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/rescorediagonal.cpp:121:16: style: The scope of the variable 'start' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/rescorediagonal.cpp:239:34: style: The scope of the variable 'distanceToDiagonal' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/rescorediagonal.cpp:286:42: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/rescorediagonal.cpp:120:17: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/rescorediagonal.cpp:286:42: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/rescorediagonal.cpp:347:29: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/rescorediagonal.cpp:120:17: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/rescorediagonal.cpp:347:29: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/rescorediagonal.cpp:355:29: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/rescorediagonal.cpp:120:17: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/rescorediagonal.cpp:355:29: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/rescorediagonal.cpp:195:27: style: Variable 'querySeqToAlign' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/rescorediagonal.cpp:206:27: style: Variable 'targetSeq' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/rescorediagonal.cpp:293:35: style: Variable 'end' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/AlignmentSymmetry.cpp:29:16: style: The scope of the variable 'start' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/AlignmentSymmetry.cpp:75:26: style: The scope of the variable 'similarity' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/AlignmentSymmetry.cpp:20:59: style:inconclusive: Function 'readInData' argument 1 names different: declaration 'pReader' definition 'alnDbr'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/AlignmentSymmetry.h:16:51: note: Function 'readInData' argument 1 names different: declaration 'pReader' definition 'alnDbr'.
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/AlignmentSymmetry.cpp:20:59: note: Function 'readInData' argument 1 names different: declaration 'pReader' definition 'alnDbr'.
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/AlignmentSymmetry.cpp:20:90: style:inconclusive: Function 'readInData' argument 2 names different: declaration 'pDBReader' definition 'seqDbr'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/AlignmentSymmetry.h:16:83: note: Function 'readInData' argument 2 names different: declaration 'pDBReader' definition 'seqDbr'.
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/AlignmentSymmetry.cpp:20:90: note: Function 'readInData' argument 2 names different: declaration 'pDBReader' definition 'seqDbr'.
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/AlignmentSymmetry.cpp:21:51: style:inconclusive: Function 'readInData' argument 3 names different: declaration 'pInt' definition 'elementLookupTable'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/AlignmentSymmetry.h:16:109: note: Function 'readInData' argument 3 names different: declaration 'pInt' definition 'elementLookupTable'.
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/AlignmentSymmetry.cpp:21:51: note: Function 'readInData' argument 3 names different: declaration 'pInt' definition 'elementLookupTable'.
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/AlignmentSymmetry.cpp:168:50: style:inconclusive: Function 'addMissingLinks' argument 2 names different: declaration 'offsetTable' definition 'offsetTableWithOutNewLinks'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/AlignmentSymmetry.h:28:76: note: Function 'addMissingLinks' argument 2 names different: declaration 'offsetTable' definition 'offsetTableWithOutNewLinks'.
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/AlignmentSymmetry.cpp:168:50: note: Function 'addMissingLinks' argument 2 names different: declaration 'offsetTable' definition 'offsetTableWithOutNewLinks'.
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/AlignmentSymmetry.cpp:168:87: style:inconclusive: Function 'addMissingLinks' argument 3 names different: declaration 'newOffset' definition 'offsetTableWithNewLinks'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/AlignmentSymmetry.h:28:98: note: Function 'addMissingLinks' argument 3 names different: declaration 'newOffset' definition 'offsetTableWithNewLinks'.
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/AlignmentSymmetry.cpp:168:87: note: Function 'addMissingLinks' argument 3 names different: declaration 'newOffset' definition 'offsetTableWithNewLinks'.
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/AlignmentSymmetry.cpp:218:81: style:inconclusive: Function 'sortElements' argument 2 names different: declaration 'offsets' definition 'elementOffsets'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/AlignmentSymmetry.h:29:73: note: Function 'sortElements' argument 2 names different: declaration 'offsets' definition 'elementOffsets'.
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/AlignmentSymmetry.cpp:218:81: note: Function 'sortElements' argument 2 names different: declaration 'offsets' definition 'elementOffsets'.
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/AlignmentSymmetry.cpp:22:59: style: Parameter 'offsets' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/AlignmentSymmetry.cpp:168:50: style: Parameter 'offsetTableWithOutNewLinks' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/AlignmentSymmetry.cpp:168:87: style: Parameter 'offsetTableWithNewLinks' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/AlignmentSymmetry.cpp:218:81: style: Parameter 'elementOffsets' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/Clustering.cpp:20:109: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/Clustering.cpp:52:96: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_CLUSTER_RES [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/Clustering.cpp:109:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/Clustering.cpp:103:18: performance:inconclusive: Technically the member function 'Clustering::writeData' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/Clustering.h:24:10: note: Technically the member function 'Clustering::writeData' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/Clustering.cpp:103:18: note: Technically the member function 'Clustering::writeData' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/Clustering.cpp:20:5: warning: Class 'Clustering' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/Clustering.cpp:20:5: warning: Class 'Clustering' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/Clustering.cpp:10:43: style:inconclusive: Function 'Clustering' argument 3 names different: declaration 'alnResultsDB' definition 'alnDB'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/Clustering.h:12:35: note: Function 'Clustering' argument 3 names different: declaration 'alnResultsDB' definition 'alnDB'.
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/Clustering.cpp:10:43: note: Function 'Clustering' argument 3 names different: declaration 'alnResultsDB' definition 'alnDB'.
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/Clustering.cpp:10:69: style:inconclusive: Function 'Clustering' argument 4 names different: declaration 'alnResultsDBIndex' definition 'alnDBIndex'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/Clustering.h:12:68: note: Function 'Clustering' argument 4 names different: declaration 'alnResultsDBIndex' definition 'alnDBIndex'.
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/Clustering.cpp:10:69: note: Function 'Clustering' argument 4 names different: declaration 'alnResultsDBIndex' definition 'alnDBIndex'.
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/Clustering.cpp:12:43: style:inconclusive: Function 'Clustering' argument 7 names different: declaration 'weightFileName' definition 'sequenceWeightFile'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/Clustering.h:14:35: note: Function 'Clustering' argument 7 names different: declaration 'weightFileName' definition 'sequenceWeightFile'.
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/Clustering.cpp:12:43: note: Function 'Clustering' argument 7 names different: declaration 'weightFileName' definition 'sequenceWeightFile'.
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/Clustering.cpp:116:19: style: Variable 'outpos' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/Clustering.cpp:122:20: style: Variable 'outpos' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/ClusteringAlgorithms.cpp:21:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ERROR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/ClusteringAlgorithms.cpp:41:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nothrow [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/ClusteringAlgorithms.cpp:163:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nothrow [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/ClusteringAlgorithms.cpp:256:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ERROR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/ClusteringAlgorithms.cpp:295:65: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/ClusteringAlgorithms.cpp:367:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFO [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/A3MReader.cpp:35:1: error: There is an unknown macro here somewhere. Configuration is required. If KSEQ_INIT is a macro then please configure it. [unknownMacro]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/ClusteringAlgorithms.cpp:17:23: warning: Member variable 'ClusteringAlgorithms::maxClustersize' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/ClusteringAlgorithms.cpp:17:23: warning: Member variable 'ClusteringAlgorithms::sorted_clustersizes' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/ClusteringAlgorithms.cpp:17:23: warning: Member variable 'ClusteringAlgorithms::clusterid_to_arrayposition' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/ClusteringAlgorithms.cpp:17:23: warning: Member variable 'ClusteringAlgorithms::borders_of_set' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/ClusteringAlgorithms.cpp:30:11: warning: Class 'ClusteringAlgorithms' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/ClusteringAlgorithms.cpp:30:11: warning: Class 'ClusteringAlgorithms' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/ClusteringAlgorithms.cpp:204:52: style:inconclusive: Function 'setCover' argument 1 names different: declaration 'elementLookup' definition 'elementLookupTable'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/ClusteringAlgorithms.h:47:34: note: Function 'setCover' argument 1 names different: declaration 'elementLookup' definition 'elementLookupTable'.
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/ClusteringAlgorithms.cpp:204:52: note: Function 'setCover' argument 1 names different: declaration 'elementLookup' definition 'elementLookupTable'.
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/ClusteringAlgorithms.cpp:205:94: style:inconclusive: Function 'setCover' argument 5 names different: declaration 'offsets' definition 'newElementOffsets'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/ClusteringAlgorithms.h:48:76: note: Function 'setCover' argument 5 names different: declaration 'offsets' definition 'newElementOffsets'.
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/ClusteringAlgorithms.cpp:205:94: note: Function 'setCover' argument 5 names different: declaration 'offsets' definition 'newElementOffsets'.
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/ClusteringAlgorithms.cpp:205:94: style: Parameter 'newElementOffsets' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/clustering/AlignmentSymmetry.h:32:76: style: Parameter 'elementOffset' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Util.h:27:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Util.h:103:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable is_signed [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Util.h:300:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MathUtil.h:122:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FLT_MAX_EXP [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Debug.h:19:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Debug.h:73:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Debug.h:185:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Application.cpp:107:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable left [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Application.cpp:209:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:212:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:223:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ScoreMatrix.h:45:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAX_ALIGN_INT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ScoreMatrix.h:54:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAX_ALIGN_INT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.cpp:62:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.cpp:80:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:161:5: warning:inconclusive: Member variable 'PseudoCounts::first' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:161:5: warning:inconclusive: Member variable 'PseudoCounts::second' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:98:5: warning:inconclusive: Member variable 'SeqProf < int >::first' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:98:5: warning:inconclusive: Member variable 'SeqProf < int >::second' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:33:5: warning:inconclusive: Member variable 'NuclAA < int >::first' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:33:5: warning:inconclusive: Member variable 'NuclAA < int >::second' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:33:5: warning:inconclusive: Member variable 'NuclAA < float >::first' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:33:5: warning:inconclusive: Member variable 'NuclAA < float >::second' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Timer.h:14:17: style:inconclusive: Technically the member function 'Timer::lapProgress' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Timer.h:32:17: style:inconclusive: Technically the member function 'Timer::lap' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Timer.h:43:12: style:inconclusive: Technically the member function 'Timer::getTimediff' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Debug.h:126:21: performance:inconclusive: Technically the member function 'Debug::Progress::buildItemString' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:205:10: performance:inconclusive: Technically the member function 'MultiParam < NuclAA < std :: string > >::assign' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:210:10: performance:inconclusive: Technically the member function 'MultiParam < NuclAA < std :: string > >::assign' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:221:10: performance:inconclusive: Technically the member function 'MultiParam < NuclAA < std :: string > >::assign' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:205:10: performance:inconclusive: Technically the member function 'MultiParam < SeqProf < int > >::assign' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:210:10: performance:inconclusive: Technically the member function 'MultiParam < SeqProf < int > >::assign' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:221:10: performance:inconclusive: Technically the member function 'MultiParam < SeqProf < int > >::assign' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:205:10: performance:inconclusive: Technically the member function 'MultiParam < NuclAA < int > >::assign' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:210:10: performance:inconclusive: Technically the member function 'MultiParam < NuclAA < int > >::assign' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:221:10: performance:inconclusive: Technically the member function 'MultiParam < NuclAA < int > >::assign' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:205:10: performance:inconclusive: Technically the member function 'MultiParam < PseudoCounts >::assign' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:210:10: performance:inconclusive: Technically the member function 'MultiParam < PseudoCounts >::assign' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:221:10: performance:inconclusive: Technically the member function 'MultiParam < PseudoCounts >::assign' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:205:10: performance:inconclusive: Technically the member function 'MultiParam < NuclAA < float > >::assign' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:210:10: performance:inconclusive: Technically the member function 'MultiParam < NuclAA < float > >::assign' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:221:10: performance:inconclusive: Technically the member function 'MultiParam < NuclAA < float > >::assign' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Debug.h:164:9: style: Class 'Progress' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:163:5: style: Class 'PseudoCounts' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:200:5: style: Class 'MultiParam < NuclAA < std :: string > >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:232:5: style: Class 'MultiParam < NuclAA < std :: string > >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:200:5: style: Class 'MultiParam < SeqProf < int > >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:232:5: style: Class 'MultiParam < SeqProf < int > >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:200:5: style: Class 'MultiParam < NuclAA < int > >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:232:5: style: Class 'MultiParam < NuclAA < int > >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:200:5: style: Class 'MultiParam < PseudoCounts >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:232:5: style: Class 'MultiParam < PseudoCounts >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:200:5: style: Class 'MultiParam < NuclAA < float > >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:232:5: style: Class 'MultiParam < NuclAA < float > >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:100:5: style: Class 'SeqProf < int >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:35:5: style: Class 'NuclAA < std :: string >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:35:5: style: Class 'NuclAA < int >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:35:5: style: Class 'NuclAA < float >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:57:7: performance: Function 'nucleotide()' should return member 'second' by const reference. [returnByReference]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:65:7: performance: Function 'aminoacid()' should return member 'first' by const reference. [returnByReference]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Util.h:194:13: style: Condition 'counter' is always true [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Util.h:191:13: note: Assuming that condition '!counter' is not redundant
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Util.h:194:13: note: Condition 'counter' is always true
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MathUtil.h:110:30: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MathUtil.h:125:30: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MathUtil.h:129:30: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MathUtil.h:110:30: portability: Casting from float * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MathUtil.h:125:30: portability: Casting from float * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MathUtil.h:129:30: portability: Casting from float * to signed int * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Debug.h:247:30: style: Local variable 'buffer' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Debug.h:293:17: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Debug.h:247:30: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/commons/FileUtil.h:27:65: performance: Function parameter 'path' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/FileUtil.h:29:61: performance: Function parameter 'path' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:200:18: performance: Function parameter 'type' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:236:32: performance: Function parameter 'value' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:35:17: performance: Function parameter 'first' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:40:17: performance: Function parameter 'first' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:40:26: performance: Function parameter 'second' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:45:36: performance: Function parameter 'value' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:51:28: performance: Function parameter 'value' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:61:23: performance: Function parameter 'val' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.h:69:22: performance: Function parameter 'val' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Debug.h:30:15: style: Variable 'ttyEnv' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Util.h:188:54: style: Parameter 'data' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MathUtil.h:129:25: style: Variable 'ix' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.cpp:12:13: warning: Member variable 'BaseMatrix::alphabetSize' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.cpp:12:13: warning: Member variable 'BaseMatrix::allocatedAlphabetSize' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.cpp:12:13: warning: Member variable 'BaseMatrix::subMatrix' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.cpp:12:13: warning: Member variable 'BaseMatrix::subMatrixPseudoCounts' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.cpp:12:13: warning: Member variable 'BaseMatrix::probMatrix' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.cpp:12:13: warning: Member variable 'BaseMatrix::lambda' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.cpp:12:13: warning: Member variable 'BaseMatrix::pBack' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.cpp:12:13: warning: Member variable 'BaseMatrix::scoreBias' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.cpp:161:25: style:inconclusive: Technically the member function 'BaseMatrix::getMatrixName' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.h:66:17: note: Technically the member function 'BaseMatrix::getMatrixName' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.cpp:161:25: note: Technically the member function 'BaseMatrix::getMatrixName' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.h:70:19: style:inconclusive: Technically the member function 'BaseMatrix::getLambda' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ScoreMatrix.h:22:10: style:inconclusive: Technically the member function 'ScoreMatrix::isValid' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.h:92:10: style:inconclusive: Technically the member function 'Sequence::hasNextKmer' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.h:97:17: style:inconclusive: Technically the member function 'Sequence::kmerContainsX' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.h:425:9: style:inconclusive: Technically the member function 'Sequence::getCurrentPosition' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.h:427:18: style:inconclusive: Technically the member function 'Sequence::getDbKey' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.h:429:9: style:inconclusive: Technically the member function 'Sequence::getSeqType' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.h:431:12: style:inconclusive: Technically the member function 'Sequence::getMaxLen' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.h:432:18: style:inconclusive: Technically the member function 'Sequence::getKmerSize' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.h:433:10: style:inconclusive: Technically the member function 'Sequence::isSpaced' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.h:485:26: style:inconclusive: Technically the member function 'Sequence::getAAPosInSpacedPattern' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.h:499:18: style:inconclusive: Technically the member function 'Sequence::getEffectiveKmerSize' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.h:528:17: style:inconclusive: Technically the member function 'Sequence::getSeqData' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.cpp:16:5: warning: Class 'BaseMatrix' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.cpp:16:5: warning: Class 'BaseMatrix' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.h:87:9: warning: Class 'ProbabilityMatrix' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.h:87:9: warning: Class 'ProbabilityMatrix' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.h:85:5: style: Class 'ProbabilityMatrix' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.h:66:17: performance: Function 'getMatrixName()' should return member 'matrixName' by const reference. [returnByReference]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ScoreMatrix.h:35:16: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ScoreMatrix.h:32:37: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ScoreMatrix.h:32:22: note: Assignment 'data=(char*)malloc(size(mat))', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ScoreMatrix.h:33:17: note: p is assigned 'data' here.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ScoreMatrix.h:35:16: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.cpp:179:12: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.cpp:177:32: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.cpp:177:18: note: Assignment 'data=(char*)malloc(memorySize(matrixName,matrixData)+1)', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.cpp:178:13: note: p is assigned 'data' here.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.cpp:179:12: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ScoreMatrix.h:32:22: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ScoreMatrix.h:49:28: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ScoreMatrix.h:49:44: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ScoreMatrix.h:58:25: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ScoreMatrix.h:59:32: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.h:401:42: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.cpp:51:37: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.cpp:177:18: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.h:525:32: style: Floating-point cast causes loss of precision. [suspiciousFloatingPointCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.cpp:37:39: style:inconclusive: Function 'initMatrixMemory' argument 1 names different: declaration 'alphSize' definition 'alphabetSize'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.h:52:31: note: Function 'initMatrixMemory' argument 1 names different: declaration 'alphSize' definition 'alphabetSize'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.cpp:37:39: note: Function 'initMatrixMemory' argument 1 names different: declaration 'alphSize' definition 'alphabetSize'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ScoreMatrix.h:44:16: style: Local variable 'size' shadows outer function [shadowFunction]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ScoreMatrix.h:26:19: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ScoreMatrix.h:44:16: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ScoreMatrix.h:53:16: style: Local variable 'size' shadows outer function [shadowFunction]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ScoreMatrix.h:26:19: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ScoreMatrix.h:53:16: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.cpp:170:45: style: Parameter 'matrixName' can be declared as reference to const [constParameterReference]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.cpp:170:71: style: Parameter 'matrixData' can be declared as reference to const [constParameterReference]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.cpp:61:46: style: Parameter 'num2aa' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.cpp:79:47: style: Parameter 'num2aa' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.h:65:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALIGN_FLOAT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.cpp:51:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALIGN_FLOAT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.cpp:137:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MAX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.cpp:182:71: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VECSIZE_FLOAT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.cpp:366:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FLT_MAX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:35:16: warning: Member variable 'SmithWaterman::query_id' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:35:16: warning: Member variable 'SmithWaterman::target_id' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:249:21: style: Unused private function: 'SmithWaterman::reverseMat' [unusedPrivateFunction]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:411:10: note: Unused private function: 'SmithWaterman::reverseMat'
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:249:21: note: Unused private function: 'SmithWaterman::reverseMat'
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1691:24: style:inconclusive: Technically the member function 'SmithWaterman::scoreIdentical' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:248:13: note: Technically the member function 'SmithWaterman::scoreIdentical' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1691:24: note: Technically the member function 'SmithWaterman::scoreIdentical' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1618:25: performance:inconclusive: Technically the member function 'SmithWaterman::to_cigar_int' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:383:21: note: Technically the member function 'SmithWaterman::to_cigar_int' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1618:25: note: Technically the member function 'SmithWaterman::to_cigar_int' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:238:24: performance:inconclusive: Technically the member function 'SmithWaterman::computeBias' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:409:13: note: Technically the member function 'SmithWaterman::computeBias' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:238:24: note: Technically the member function 'SmithWaterman::computeBias' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:249:21: performance:inconclusive: Technically the member function 'SmithWaterman::reverseMat' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:411:10: note: Technically the member function 'SmithWaterman::reverseMat' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:249:21: note: Technically the member function 'SmithWaterman::reverseMat' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:100:2: warning: Class 'SmithWaterman' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:100:2: warning: Class 'SmithWaterman' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:467:9: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:467:9: portability: %lu in format string (no. 3) requires 'unsigned long' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_uint]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:467:9: portability: %lu in format string (no. 4) requires 'unsigned long' but the argument type is 'size_t {aka unsigned long}'. [invalidPrintfArgType_uint]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1401:4: error: Common realloc mistake: 'h_b' nulled but not freed upon failure [memleakOnRealloc]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1402:4: error: Common realloc mistake: 'e_b' nulled but not freed upon failure [memleakOnRealloc]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1403:4: error: Common realloc mistake: 'h_c' nulled but not freed upon failure [memleakOnRealloc]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1413:4: error: Common realloc mistake: 'direction' nulled but not freed upon failure [memleakOnRealloc]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1568:5: error: Common realloc mistake: 'c' nulled but not freed upon failure [memleakOnRealloc]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1580:4: error: Common realloc mistake: 'c' nulled but not freed upon failure [memleakOnRealloc]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1588:4: error: Common realloc mistake: 'c' nulled but not freed upon failure [memleakOnRealloc]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CommandCaller.cpp:39:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CommandCaller.cpp:84:85: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:43:12: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:44:12: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:45:12: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:46:12: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:49:24: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:58:26: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:59:26: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:60:33: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:61:33: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:82:26: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:83:26: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:84:30: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:85:33: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:209:17: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1382:19: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1390:11: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1391:11: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1392:11: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1393:17: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1401:10: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1402:10: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1403:10: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1413:16: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1568:9: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1580:8: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1588:8: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1595:7: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1754:34: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1792:27: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:221:12: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:192:12: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:166:9: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:980:25: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1192:16: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:669:24: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:913:15: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:345:18: style: The comparison 'SmithWaterman::PROFILE_PROFILE == PROFILE_PROFILE' is always true because 'SmithWaterman::PROFILE_PROFILE' and 'PROFILE_PROFILE' represent the same value. [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:276:49: note: '::' is assigned value '6' here.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:276:49: note: 'PROFILE_PROFILE' is assigned value '6' here.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:345:18: note: The comparison 'SmithWaterman::PROFILE_PROFILE == PROFILE_PROFILE' is always true because 'SmithWaterman::PROFILE_PROFILE' and 'PROFILE_PROFILE' represent the same value.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:401:38: style: The comparison 'SmithWaterman::PROFILE_PROFILE == PROFILE_PROFILE' is always true because 'SmithWaterman::PROFILE_PROFILE' and 'PROFILE_PROFILE' represent the same value. [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:276:49: note: '::' is assigned value '6' here.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:276:49: note: 'PROFILE_PROFILE' is assigned value '6' here.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:401:38: note: The comparison 'SmithWaterman::PROFILE_PROFILE == PROFILE_PROFILE' is always true because 'SmithWaterman::PROFILE_PROFILE' and 'PROFILE_PROFILE' represent the same value.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:410:19: style: The comparison 'SmithWaterman::PROFILE_PROFILE == PROFILE_PROFILE' is always true because 'SmithWaterman::PROFILE_PROFILE' and 'PROFILE_PROFILE' represent the same value. [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:276:49: note: '::' is assigned value '6' here.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:276:49: note: 'PROFILE_PROFILE' is assigned value '6' here.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:410:19: note: The comparison 'SmithWaterman::PROFILE_PROFILE == PROFILE_PROFILE' is always true because 'SmithWaterman::PROFILE_PROFILE' and 'PROFILE_PROFILE' represent the same value.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:429:41: style: The comparison 'SmithWaterman::PROFILE_PROFILE == PROFILE_PROFILE' is always true because 'SmithWaterman::PROFILE_PROFILE' and 'PROFILE_PROFILE' represent the same value. [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:276:49: note: '::' is assigned value '6' here.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:276:49: note: 'PROFILE_PROFILE' is assigned value '6' here.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:429:41: note: The comparison 'SmithWaterman::PROFILE_PROFILE == PROFILE_PROFILE' is always true because 'SmithWaterman::PROFILE_PROFILE' and 'PROFILE_PROFILE' represent the same value.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:443:22: style: The comparison 'SmithWaterman::PROFILE_PROFILE == PROFILE_PROFILE' is always true because 'SmithWaterman::PROFILE_PROFILE' and 'PROFILE_PROFILE' represent the same value. [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:276:49: note: '::' is assigned value '6' here.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:276:49: note: 'PROFILE_PROFILE' is assigned value '6' here.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:443:22: note: The comparison 'SmithWaterman::PROFILE_PROFILE == PROFILE_PROFILE' is always true because 'SmithWaterman::PROFILE_PROFILE' and 'PROFILE_PROFILE' represent the same value.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:470:46: style: The comparison 'SmithWaterman::PROFILE_PROFILE == PROFILE_PROFILE' is always true because 'SmithWaterman::PROFILE_PROFILE' and 'PROFILE_PROFILE' represent the same value. [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:276:49: note: '::' is assigned value '6' here.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:276:49: note: 'PROFILE_PROFILE' is assigned value '6' here.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:470:46: note: The comparison 'SmithWaterman::PROFILE_PROFILE == PROFILE_PROFILE' is always true because 'SmithWaterman::PROFILE_PROFILE' and 'PROFILE_PROFILE' represent the same value.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:499:11: style: The comparison 'SmithWaterman::PROFILE_PROFILE == PROFILE_PROFILE' is always true because 'SmithWaterman::PROFILE_PROFILE' and 'PROFILE_PROFILE' represent the same value. [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:276:49: note: '::' is assigned value '6' here.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:276:49: note: 'PROFILE_PROFILE' is assigned value '6' here.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:499:11: note: The comparison 'SmithWaterman::PROFILE_PROFILE == PROFILE_PROFILE' is always true because 'SmithWaterman::PROFILE_PROFILE' and 'PROFILE_PROFILE' represent the same value.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:533:14: style: The comparison 'SmithWaterman::PROFILE_PROFILE == PROFILE_PROFILE' is always true because 'SmithWaterman::PROFILE_PROFILE' and 'PROFILE_PROFILE' represent the same value. [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:276:49: note: '::' is assigned value '6' here.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:276:49: note: 'PROFILE_PROFILE' is assigned value '6' here.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:533:14: note: The comparison 'SmithWaterman::PROFILE_PROFILE == PROFILE_PROFILE' is always true because 'SmithWaterman::PROFILE_PROFILE' and 'PROFILE_PROFILE' represent the same value.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:401:15: style: The comparison 'SmithWaterman::PROFILE_SEQ == PROFILE_SEQ' is always true because 'SmithWaterman::PROFILE_SEQ' and 'PROFILE_SEQ' represent the same value. [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:275:45: note: '::' is assigned value '5' here.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:275:45: note: 'PROFILE_SEQ' is assigned value '5' here.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:401:15: note: The comparison 'SmithWaterman::PROFILE_SEQ == PROFILE_SEQ' is always true because 'SmithWaterman::PROFILE_SEQ' and 'PROFILE_SEQ' represent the same value.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:429:18: style: The comparison 'SmithWaterman::PROFILE_SEQ == PROFILE_SEQ' is always true because 'SmithWaterman::PROFILE_SEQ' and 'PROFILE_SEQ' represent the same value. [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:275:45: note: '::' is assigned value '5' here.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:275:45: note: 'PROFILE_SEQ' is assigned value '5' here.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:429:18: note: The comparison 'SmithWaterman::PROFILE_SEQ == PROFILE_SEQ' is always true because 'SmithWaterman::PROFILE_SEQ' and 'PROFILE_SEQ' represent the same value.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:470:20: style: The comparison 'SmithWaterman::PROFILE_SEQ == PROFILE_SEQ' is always true because 'SmithWaterman::PROFILE_SEQ' and 'PROFILE_SEQ' represent the same value. [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:275:45: note: '::' is assigned value '5' here.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:275:45: note: 'PROFILE_SEQ' is assigned value '5' here.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:470:20: note: The comparison 'SmithWaterman::PROFILE_SEQ == PROFILE_SEQ' is always true because 'SmithWaterman::PROFILE_SEQ' and 'PROFILE_SEQ' represent the same value.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:506:18: style: The comparison 'SmithWaterman::PROFILE_SEQ == PROFILE_SEQ' is always true because 'SmithWaterman::PROFILE_SEQ' and 'PROFILE_SEQ' represent the same value. [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:275:45: note: '::' is assigned value '5' here.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:275:45: note: 'PROFILE_SEQ' is assigned value '5' here.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:506:18: note: The comparison 'SmithWaterman::PROFILE_SEQ == PROFILE_SEQ' is always true because 'SmithWaterman::PROFILE_SEQ' and 'PROFILE_SEQ' represent the same value.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1043:18: style: The comparison 'SmithWaterman::PROFILE_PROFILE == PROFILE_PROFILE' is always true because 'SmithWaterman::PROFILE_PROFILE' and 'PROFILE_PROFILE' represent the same value. [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:276:49: note: '::' is assigned value '6' here.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:276:49: note: 'PROFILE_PROFILE' is assigned value '6' here.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1043:18: note: The comparison 'SmithWaterman::PROFILE_PROFILE == PROFILE_PROFILE' is always true because 'SmithWaterman::PROFILE_PROFILE' and 'PROFILE_PROFILE' represent the same value.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1057:16: style: The comparison 'SmithWaterman::PROFILE_PROFILE == PROFILE_PROFILE' is always true because 'SmithWaterman::PROFILE_PROFILE' and 'PROFILE_PROFILE' represent the same value. [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:276:49: note: '::' is assigned value '6' here.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:276:49: note: 'PROFILE_PROFILE' is assigned value '6' here.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1057:16: note: The comparison 'SmithWaterman::PROFILE_PROFILE == PROFILE_PROFILE' is always true because 'SmithWaterman::PROFILE_PROFILE' and 'PROFILE_PROFILE' represent the same value.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:732:18: style: The comparison 'SmithWaterman::PROFILE_PROFILE == PROFILE_PROFILE' is always true because 'SmithWaterman::PROFILE_PROFILE' and 'PROFILE_PROFILE' represent the same value. [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:276:49: note: '::' is assigned value '6' here.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:276:49: note: 'PROFILE_PROFILE' is assigned value '6' here.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:732:18: note: The comparison 'SmithWaterman::PROFILE_PROFILE == PROFILE_PROFILE' is always true because 'SmithWaterman::PROFILE_PROFILE' and 'PROFILE_PROFILE' represent the same value.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:746:16: style: The comparison 'SmithWaterman::PROFILE_PROFILE == PROFILE_PROFILE' is always true because 'SmithWaterman::PROFILE_PROFILE' and 'PROFILE_PROFILE' represent the same value. [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:276:49: note: '::' is assigned value '6' here.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:276:49: note: 'PROFILE_PROFILE' is assigned value '6' here.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:746:16: note: The comparison 'SmithWaterman::PROFILE_PROFILE == PROFILE_PROFILE' is always true because 'SmithWaterman::PROFILE_PROFILE' and 'PROFILE_PROFILE' represent the same value.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1071:23: style: Redundant initialization for 'score'. The initialized value is overwritten before it is read. [redundantInitialization]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1056:22: note: score is initialized
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1071:23: note: score is overwritten
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:760:23: style: Redundant initialization for 'score'. The initialized value is overwritten before it is read. [redundantInitialization]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:745:22: note: score is initialized
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:760:23: note: score is overwritten
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1386:13: style: The scope of the variable 'width' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1752:15: style: The scope of the variable 'qji' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1753:15: style: The scope of the variable 's_prev_it' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1753:27: style: The scope of the variable 's_curr_it' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:341:19: style: The scope of the variable 'db_matrix' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1195:11: style: The scope of the variable 'temp' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:916:11: style: The scope of the variable 'temp' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:249:40: style:inconclusive: Function 'reverseMat' argument 1 names different: declaration 'rev_mat' definition 'mat_rev'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:411:29: note: Function 'reverseMat' argument 1 names different: declaration 'rev_mat' definition 'mat_rev'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:249:40: note: Function 'reverseMat' argument 1 names different: declaration 'rev_mat' definition 'mat_rev'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:281:23: style:inconclusive: Function 'ssw_align' argument 3 names different: declaration 'db_profile' definition 'db_mat'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:197:39: note: Function 'ssw_align' argument 3 names different: declaration 'db_profile' definition 'db_mat'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:281:23: note: Function 'ssw_align' argument 3 names different: declaration 'db_profile' definition 'db_mat'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:287:23: style:inconclusive: Function 'ssw_align' argument 9 names different: declaration 'filters' definition 'evalueThr'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:203:38: note: Function 'ssw_align' argument 9 names different: declaration 'filters' definition 'evalueThr'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:287:23: note: Function 'ssw_align' argument 9 names different: declaration 'filters' definition 'evalueThr'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:288:29: style:inconclusive: Function 'ssw_align' argument 10 names different: declaration 'filterd' definition 'evaluer'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:204:45: note: Function 'ssw_align' argument 10 names different: declaration 'filterd' definition 'evaluer'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:288:29: note: Function 'ssw_align' argument 10 names different: declaration 'filterd' definition 'evaluer'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1372:66: style:inconclusive: Function 'banded_sw' argument 14 names different: declaration 'target_mat' definition 'db_mat'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:375:90: note: Function 'banded_sw' argument 14 names different: declaration 'target_mat' definition 'db_mat'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1372:66: note: Function 'banded_sw' argument 14 names different: declaration 'target_mat' definition 'db_mat'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:312:17: style:inconclusive: Function 'ssw_align_private < SmithWaterman :: PROFILE_PROFILE , true >' argument 2 names different: declaration 'db_profile' definition 'db_mat'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:308:39: note: Function 'ssw_align_private < SmithWaterman :: PROFILE_PROFILE , true >' argument 2 names different: declaration 'db_profile' definition 'db_mat'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:312:17: note: Function 'ssw_align_private < SmithWaterman :: PROFILE_PROFILE , true >' argument 2 names different: declaration 'db_profile' definition 'db_mat'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:318:17: style:inconclusive: Function 'ssw_align_private < SmithWaterman :: PROFILE_PROFILE , true >' argument 8 names different: declaration 'filters' definition 'evalueThr'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:314:38: note: Function 'ssw_align_private < SmithWaterman :: PROFILE_PROFILE , true >' argument 8 names different: declaration 'filters' definition 'evalueThr'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:318:17: note: Function 'ssw_align_private < SmithWaterman :: PROFILE_PROFILE , true >' argument 8 names different: declaration 'filters' definition 'evalueThr'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:319:23: style:inconclusive: Function 'ssw_align_private < SmithWaterman :: PROFILE_PROFILE , true >' argument 9 names different: declaration 'filterd' definition 'evaluer'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:315:45: note: Function 'ssw_align_private < SmithWaterman :: PROFILE_PROFILE , true >' argument 9 names different: declaration 'filterd' definition 'evaluer'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:319:23: note: Function 'ssw_align_private < SmithWaterman :: PROFILE_PROFILE , true >' argument 9 names different: declaration 'filterd' definition 'evaluer'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:312:17: style:inconclusive: Function 'ssw_align_private < SmithWaterman :: PROFILE_SEQ , true >' argument 2 names different: declaration 'db_profile' definition 'db_mat'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:308:39: note: Function 'ssw_align_private < SmithWaterman :: PROFILE_SEQ , true >' argument 2 names different: declaration 'db_profile' definition 'db_mat'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:312:17: note: Function 'ssw_align_private < SmithWaterman :: PROFILE_SEQ , true >' argument 2 names different: declaration 'db_profile' definition 'db_mat'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:318:17: style:inconclusive: Function 'ssw_align_private < SmithWaterman :: PROFILE_SEQ , true >' argument 8 names different: declaration 'filters' definition 'evalueThr'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:314:38: note: Function 'ssw_align_private < SmithWaterman :: PROFILE_SEQ , true >' argument 8 names different: declaration 'filters' definition 'evalueThr'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:318:17: note: Function 'ssw_align_private < SmithWaterman :: PROFILE_SEQ , true >' argument 8 names different: declaration 'filters' definition 'evalueThr'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:319:23: style:inconclusive: Function 'ssw_align_private < SmithWaterman :: PROFILE_SEQ , true >' argument 9 names different: declaration 'filterd' definition 'evaluer'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:315:45: note: Function 'ssw_align_private < SmithWaterman :: PROFILE_SEQ , true >' argument 9 names different: declaration 'filterd' definition 'evaluer'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:319:23: note: Function 'ssw_align_private < SmithWaterman :: PROFILE_SEQ , true >' argument 9 names different: declaration 'filterd' definition 'evaluer'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:312:17: style:inconclusive: Function 'ssw_align_private < SmithWaterman :: SEQ_PROFILE , false >' argument 2 names different: declaration 'db_profile' definition 'db_mat'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:308:39: note: Function 'ssw_align_private < SmithWaterman :: SEQ_PROFILE , false >' argument 2 names different: declaration 'db_profile' definition 'db_mat'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:312:17: note: Function 'ssw_align_private < SmithWaterman :: SEQ_PROFILE , false >' argument 2 names different: declaration 'db_profile' definition 'db_mat'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:318:17: style:inconclusive: Function 'ssw_align_private < SmithWaterman :: SEQ_PROFILE , false >' argument 8 names different: declaration 'filters' definition 'evalueThr'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:314:38: note: Function 'ssw_align_private < SmithWaterman :: SEQ_PROFILE , false >' argument 8 names different: declaration 'filters' definition 'evalueThr'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:318:17: note: Function 'ssw_align_private < SmithWaterman :: SEQ_PROFILE , false >' argument 8 names different: declaration 'filters' definition 'evalueThr'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:319:23: style:inconclusive: Function 'ssw_align_private < SmithWaterman :: SEQ_PROFILE , false >' argument 9 names different: declaration 'filterd' definition 'evaluer'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:315:45: note: Function 'ssw_align_private < SmithWaterman :: SEQ_PROFILE , false >' argument 9 names different: declaration 'filterd' definition 'evaluer'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:319:23: note: Function 'ssw_align_private < SmithWaterman :: SEQ_PROFILE , false >' argument 9 names different: declaration 'filterd' definition 'evaluer'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:312:17: style:inconclusive: Function 'ssw_align_private < SmithWaterman :: SEQ_SEQ , false >' argument 2 names different: declaration 'db_profile' definition 'db_mat'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:308:39: note: Function 'ssw_align_private < SmithWaterman :: SEQ_SEQ , false >' argument 2 names different: declaration 'db_profile' definition 'db_mat'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:312:17: note: Function 'ssw_align_private < SmithWaterman :: SEQ_SEQ , false >' argument 2 names different: declaration 'db_profile' definition 'db_mat'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:318:17: style:inconclusive: Function 'ssw_align_private < SmithWaterman :: SEQ_SEQ , false >' argument 8 names different: declaration 'filters' definition 'evalueThr'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:314:38: note: Function 'ssw_align_private < SmithWaterman :: SEQ_SEQ , false >' argument 8 names different: declaration 'filters' definition 'evalueThr'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:318:17: note: Function 'ssw_align_private < SmithWaterman :: SEQ_SEQ , false >' argument 8 names different: declaration 'filters' definition 'evalueThr'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:319:23: style:inconclusive: Function 'ssw_align_private < SmithWaterman :: SEQ_SEQ , false >' argument 9 names different: declaration 'filterd' definition 'evaluer'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:315:45: note: Function 'ssw_align_private < SmithWaterman :: SEQ_SEQ , false >' argument 9 names different: declaration 'filterd' definition 'evaluer'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:319:23: note: Function 'ssw_align_private < SmithWaterman :: SEQ_SEQ , false >' argument 9 names different: declaration 'filterd' definition 'evaluer'.
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:208:19: style: Local variable 'segSize' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:288:9: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:208:19: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:980:13: style: Local variable 'maxColumn' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:284:15: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:980:13: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:669:12: style: Local variable 'maxColumn' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:284:15: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:669:12: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:549:49: style: Parameter 'alignment' can be declared as reference to const [constParameterReference]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:611:53: style: Parameter 'scorePreCol' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1691:54: style: Parameter 'dbSeq' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1725:9: error: Uninitialized variables: r.score2, r.ref_end2 [uninitvar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:387:16: error: Uninitialized variables: r.qCov, r.tCov, r.evalue, r.identicalAACnt [uninitvar]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1725:9: error: Uninitialized struct member: r.score2 [uninitStructMember]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1725:9: error: Uninitialized struct member: r.ref_end2 [uninitStructMember]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:387:16: error: Uninitialized struct member: r.qCov [uninitStructMember]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:387:16: error: Uninitialized struct member: r.tCov [uninitStructMember]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:387:16: error: Uninitialized struct member: r.evalue [uninitStructMember]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:387:16: error: Uninitialized struct member: r.identicalAACnt [uninitStructMember]
metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:522:14: style: Variable 'band_width' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CommandCaller.cpp:48:21: performance:inconclusive: Technically the member function 'CommandCaller::addVariable' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CommandCaller.h:12:10: note: Technically the member function 'CommandCaller::addVariable' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CommandCaller.cpp:48:21: note: Technically the member function 'CommandCaller::addVariable' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CommandCaller.cpp:56:20: performance:inconclusive: Technically the member function 'CommandCaller::callProgram' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CommandCaller.h:14:9: note: Technically the member function 'CommandCaller::callProgram' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CommandCaller.cpp:56:20: note: Technically the member function 'CommandCaller::callProgram' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CommandCaller.cpp:70:21: performance:inconclusive: Technically the member function 'CommandCaller::execProgram' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CommandCaller.h:19:10: note: Technically the member function 'CommandCaller::execProgram' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CommandCaller.cpp:70:21: note: Technically the member function 'CommandCaller::execProgram' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CommandCaller.cpp:81:32: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CommandCaller.cpp:33:11: style: Variable 'currentCallDepth' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.h:61:11: performance:inconclusive: Technically the member function 'ProfileStates::score' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.h:105:12: style:inconclusive: Technically the member function 'ProfileStates::getAlphSize' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.cpp:202:25: performance:inconclusive: Technically the member function 'CSProfile::computeSeqContextScore' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.h:79:11: note: Technically the member function 'CSProfile::computeSeqContextScore' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.cpp:202:25: note: Technically the member function 'CSProfile::computeSeqContextScore' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.cpp:158:25: performance:inconclusive: Technically the member function 'CSProfile::computeProfileContextScore' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.h:83:11: note: Technically the member function 'CSProfile::computeProfileContextScore' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.cpp:158:25: note: Technically the member function 'CSProfile::computeProfileContextScore' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.h:16:5: style: Struct 'Color' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.h:19:5: style: Struct 'Color' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.h:63:5: style: Class 'CSProfile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.h:19:14: style: The destructor '~SubstitutionMatrix' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.h:10:14: note: Virtual destructor in base class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.h:19:14: note: Destructor in derived class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.h:21:19: style: The function 'getBitFactor' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.h:64:19: note: Virtual function in base class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.h:21:19: note: Function in derived class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.h:23:20: style: The function 'getBackgroundProb' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.h:60:20: note: Virtual function in base class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.h:23:20: note: Function in derived class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.h:43:10: style: The function 'setupLetterMapping' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.h:62:18: note: Virtual function in base class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.h:43:10: note: Function in derived class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.h:69:28: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.h:70:28: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.h:65:25: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.h:67:20: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.h:68:26: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.h:69:22: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.cpp:10:22: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.cpp:51:37: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.cpp:53:25: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.cpp:54:17: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.cpp:103:22: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.cpp:98:10: style: Variable 'line' is reassigned a value before the old one has been used. [redundantAssignment]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.cpp:97:10: note: line is assigned
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.cpp:98:10: note: line is overwritten
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.cpp:353:80: style:inconclusive: Function 'computeSequenceCs' argument 3 names different: declaration 'tau' definition 'pTau'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.h:88:73: note: Function 'computeSequenceCs' argument 3 names different: declaration 'tau' definition 'pTau'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.cpp:353:80: note: Function 'computeSequenceCs' argument 3 names different: declaration 'tau' definition 'pTau'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.h:19:23: performance: Function parameter 'coldef' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.h:55:54: style: Parameter 'submat' can be declared as reference to const [constParameterReference]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.cpp:359:51: style: Parameter 'numSeq' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.cpp:360:43: style: Parameter 'count' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.cpp:360:58: style: Parameter 'Neff_M' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.h:61:24: style: Parameter 'profileColA' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.h:61:44: style: Parameter 'avgProfColA' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.h:61:64: style: Parameter 'profileColB' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.h:109:13: style: Variable 'order' can be declared as const array [constVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBConcat.cpp:162:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:231:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable compareById [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:243:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable accessType [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:268:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable accessType [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:919:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Index [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:940:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Index [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:959:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Index [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:1124:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:44:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dataFileName [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:55:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dataMode [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:67:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dataMode [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:80:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable magicBytes [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:103:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable accessType [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:222:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sortedByOffset [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:430:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:471:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dataMode [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:491:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dataMode [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:530:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable compareByIdOnly [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:545:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable compressedBuffers [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:566:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dataSize [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:574:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable compression [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:583:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dataMode [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:602:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable totalDataSize [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:618:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dataMode [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:629:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable compression [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:638:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable lookupSize [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:643:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable size [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:648:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable size [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:660:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dataMode [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:672:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dataMode [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:684:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable lookupSize [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:693:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable lookupSize [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:702:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable lookupSize [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:732:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable id2local [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:742:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable compression [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:788:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable closed [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:822:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable size [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:859:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable lastKey [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:882:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dataMapped [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:909:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable offset [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:966:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dataFiles [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:982:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dataMode [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:987:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable size [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:1001:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:1016:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNCOMPRESSED [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:1038:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable lookupSize [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:1218:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable length [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:148:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nothrow [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:668:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:680:85: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Concat.h:41:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Concat.h:94:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Concat.h:102:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Concat.h:153:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:125:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:459:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:547:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.h:48:12: style:inconclusive: Technically the member function 'DBWriter::getStart' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.h:52:12: style:inconclusive: Technically the member function 'DBWriter::getOffset' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.h:64:10: style:inconclusive: Technically the member function 'DBWriter::isClosed' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:164:17: style:inconclusive: Technically the member function 'DBReader < unsigned int >::getDataFileName' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:166:17: style:inconclusive: Technically the member function 'DBReader < unsigned int >::getIndexFileName' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:170:12: style:inconclusive: Technically the member function 'DBReader < unsigned int >::getDataSize' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:187:18: style:inconclusive: Technically the member function 'DBReader < unsigned int >::getMaxSeqLen' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:196:12: style:inconclusive: Technically the member function 'DBReader < unsigned int >::getSeqLen' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:218:12: style:inconclusive: Technically the member function 'DBReader < unsigned int >::getEntryLen' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:279:12: style:inconclusive: Technically the member function 'DBReader < unsigned int >::getDataFileCnt' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:283:12: style:inconclusive: Technically the member function 'DBReader < unsigned int >::getDataSizeForFile' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:287:30: style:inconclusive: Technically the member function 'DBReader < unsigned int >::getDataFileNames' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:291:12: style:inconclusive: Technically the member function 'DBReader < unsigned int >::getTotalDataSize' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:440:9: style:inconclusive: Technically the member function 'DBReader < unsigned int >::isCompressed' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBConcat.cpp:52:5: warning: Class 'DBConcat' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBConcat.cpp:52:5: warning: Class 'DBConcat' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:185:12: warning: The class 'DBReader < unsigned int >' defines member function with name 'getSize' also defined in its parent class 'MemoryTracker'. [duplInheritedMember]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MemoryTracker.h:10:19: note: Parent function 'MemoryTracker::getSize'
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:185:12: note: Derived function 'DBReader < unsigned int >::getSize'
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:370:9: style: Struct 'sortIndecesById' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:287:30: performance: Function 'getDataFileNames()' should return member 'dataFileNames' by const reference. [returnByReference]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBConcat.cpp:173:64: warning: If resource allocation fails, then there is a possible null pointer dereference: mappingFilePtr [nullPointerOutOfResources]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBConcat.cpp:159:37: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBConcat.cpp:159:37: note: Assignment 'mappingFilePtr=fopen((dataFileNameC+"_mapping").c_str(),"w")', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBConcat.cpp:173:64: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBConcat.cpp:235:75: warning: If resource allocation fails, then there is a possible null pointer dereference: lookupFilePtr [nullPointerOutOfResources]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBConcat.cpp:211:36: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBConcat.cpp:211:36: note: Assignment 'lookupFilePtr=fopen((dataFileNameC+".lookup").c_str(),"w")', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBConcat.cpp:235:75: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBConcat.cpp:303:75: warning: If resource allocation fails, then there is a possible null pointer dereference: sourceFilePtr [nullPointerOutOfResources]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBConcat.cpp:289:36: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBConcat.cpp:289:36: note: Assignment 'sourceFilePtr=fopen((dataFileNameC+".source").c_str(),"w")', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBConcat.cpp:303:75: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBConcat.cpp:83:23: style: Variable 'data' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBConcat.cpp:122:23: style: Variable 'data' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBConcat.cpp:226:19: style: Variable 'tmpBuff' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBConcat.cpp:256:19: style: Variable 'tmpBuff' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBConcat.cpp:297:19: style: Variable 'tmpBuff' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBConcat.cpp:326:19: style: Variable 'tmpBuff' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBConcat.cpp:350:44: style: Variable 'originalMap' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBConcat.cpp:358:44: style: Variable 'originalMap' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBConcat.cpp:290:65: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBConcat.cpp:320:65: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:25:14: warning: Member variable 'DBReader < std :: string >::maxSeqLen' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:25:14: warning: Member variable 'DBReader < std :: string >::compression' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:25:14: warning: Member variable 'DBReader < std :: string >::dstream' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:25:14: warning: Member variable 'DBReader < std :: string >::lookupSize' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:25:14: warning: Member variable 'DBReader < std :: string >::lookup' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:25:14: warning: Member variable 'DBReader < std :: string >::sortedByOffset' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:25:14: warning: Member variable 'DBReader < std :: string >::magicBytes' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:34:14: warning: Member variable 'DBReader < std :: string >::compression' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:34:14: warning: Member variable 'DBReader < std :: string >::dstream' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:34:14: warning: Member variable 'DBReader < std :: string >::lookupSize' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:34:14: warning: Member variable 'DBReader < std :: string >::lookup' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:34:14: warning: Member variable 'DBReader < std :: string >::magicBytes' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:164:17: style:inconclusive: Technically the member function 'DBReader < std :: string >::getDataFileName' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:166:17: style:inconclusive: Technically the member function 'DBReader < std :: string >::getIndexFileName' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:562:43: style:inconclusive: Technically the member function 'DBReader < std :: string >::getAminoAcidDBSize' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:168:12: note: Technically the member function 'DBReader < std :: string >::getAminoAcidDBSize' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:562:43: note: Technically the member function 'DBReader < std :: string >::getAminoAcidDBSize' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:170:12: style:inconclusive: Technically the member function 'DBReader < std :: string >::getDataSize' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:187:18: style:inconclusive: Technically the member function 'DBReader < std :: string >::getMaxSeqLen' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:646:38: style:inconclusive: Technically the member function 'DBReader < std :: string >::getDbKey' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:193:7: note: Technically the member function 'DBReader < std :: string >::getDbKey' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:646:38: note: Technically the member function 'DBReader < std :: string >::getDbKey' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:196:12: style:inconclusive: Technically the member function 'DBReader < std :: string >::getSeqLen' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:218:12: style:inconclusive: Technically the member function 'DBReader < std :: string >::getEntryLen' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:683:38: style:inconclusive: Technically the member function 'DBReader < std :: string >::getLookupKey' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:245:7: note: Technically the member function 'DBReader < std :: string >::getLookupKey' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:683:38: note: Technically the member function 'DBReader < std :: string >::getLookupKey' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:692:48: style:inconclusive: Technically the member function 'DBReader < std :: string >::getLookupEntryName' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:246:17: note: Technically the member function 'DBReader < std :: string >::getLookupEntryName' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:692:48: note: Technically the member function 'DBReader < std :: string >::getLookupEntryName' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:701:49: style:inconclusive: Technically the member function 'DBReader < std :: string >::getLookupFileNumber' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:247:18: note: Technically the member function 'DBReader < std :: string >::getLookupFileNumber' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:701:49: note: Technically the member function 'DBReader < std :: string >::getLookupFileNumber' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:279:12: style:inconclusive: Technically the member function 'DBReader < std :: string >::getDataFileCnt' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:283:12: style:inconclusive: Technically the member function 'DBReader < std :: string >::getDataSizeForFile' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:287:30: style:inconclusive: Technically the member function 'DBReader < std :: string >::getDataFileNames' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:291:12: style:inconclusive: Technically the member function 'DBReader < std :: string >::getTotalDataSize' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:214:19: performance:inconclusive: Technically the member function 'DBReader < std :: string >::sortIndex' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:320:10: note: Technically the member function 'DBReader < std :: string >::sortIndex' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:214:19: note: Technically the member function 'DBReader < std :: string >::sortIndex' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:217:19: performance:inconclusive: Technically the member function 'DBReader < std :: string >::sortIndex' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:321:10: note: Technically the member function 'DBReader < std :: string >::sortIndex' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:217:19: note: Technically the member function 'DBReader < std :: string >::sortIndex' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:221:19: style:inconclusive: Technically the member function 'DBReader < std :: string >::isSortedByOffset' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:322:10: note: Technically the member function 'DBReader < std :: string >::isSortedByOffset' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:221:19: note: Technically the member function 'DBReader < std :: string >::isSortedByOffset' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:79:19: style:inconclusive: Technically the member function 'DBReader < std :: string >::printMagicNumber' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:341:10: note: Technically the member function 'DBReader < std :: string >::printMagicNumber' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:79:19: note: Technically the member function 'DBReader < std :: string >::printMagicNumber' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:858:37: style:inconclusive: Technically the member function 'DBReader < std :: string >::getLastKey' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:343:7: note: Technically the member function 'DBReader < std :: string >::getLastKey' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:858:37: note: Technically the member function 'DBReader < std :: string >::getLastKey' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:986:21: style:inconclusive: Technically the member function 'DBReader < std :: string >::getOffset' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:436:12: note: Technically the member function 'DBReader < std :: string >::getOffset' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:986:21: note: Technically the member function 'DBReader < std :: string >::getOffset' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:440:9: style:inconclusive: Technically the member function 'DBReader < std :: string >::isCompressed' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:1020:19: performance:inconclusive: Technically the member function 'DBReader < std :: string >::setSequentialAdvice' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:446:10: note: Technically the member function 'DBReader < std :: string >::setSequentialAdvice' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:1020:19: note: Technically the member function 'DBReader < std :: string >::setSequentialAdvice' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:26:39: warning: Class 'DBReader < std :: string >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:26:39: warning: Class 'DBReader < std :: string >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:641:43: warning: The class 'DBReader < std :: string >' defines member function with name 'getSize' also defined in its parent class 'MemoryTracker'. [duplInheritedMember]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MemoryTracker.h:10:19: note: Parent function 'MemoryTracker::getSize'
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:641:43: note: Derived function 'DBReader < std :: string >::getSize'
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MemoryMapped.h:48:3: style: Class 'MemoryMapped' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:343:7: performance: Function 'getLastKey()' should return member 'lastKey' by const reference. [returnByReference]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:930:12: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:928:32: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:928:18: note: Assignment 'data=(char*)malloc(indexMemorySize(idx))', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:929:13: note: p is assigned 'data' here.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:930:12: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:458:35: warning: If memory allocation fails, then there is a possible null pointer dereference: ret [nullPointerOutOfMemory]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:454:44: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:454:37: note: Assignment 'ret=static_cast<char*>(malloc(*dataSize))', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:458:35: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:1219:9: warning: If memory allocation fails, then there is a possible null pointer dereference: entriesPerWorker [nullPointerOutOfMemory]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:1209:47: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:1209:32: note: Assignment 'entriesPerWorker=(unsigned long*)calloc(worldSize,sizeof(unsigned long))', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:1219:9: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:1223:19: warning: If memory allocation fails, then there is a possible null pointer dereference: entriesPerWorker [nullPointerOutOfMemory]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:1209:47: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:1209:32: note: Assignment 'entriesPerWorker=(unsigned long*)calloc(worldSize,sizeof(unsigned long))', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:1223:19: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:1225:24: warning: If memory allocation fails, then there is a possible null pointer dereference: entriesPerWorker [nullPointerOutOfMemory]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:1209:47: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:1209:32: note: Assignment 'entriesPerWorker=(unsigned long*)calloc(worldSize,sizeof(unsigned long))', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:1225:24: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:201:13: warning: Either the condition 'dstream==NULL' is redundant or there is possible null pointer dereference: dstream. [nullPointerRedundantCheck]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:202:24: note: Assuming that condition 'dstream==NULL' is not redundant
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:201:13: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:931:7: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:928:32: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:928:18: note: Assignment 'data=(char*)malloc(indexMemorySize(idx))', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:929:13: note: p is assigned 'data' here.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:931:7: note: Null pointer addition
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:928:18: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:948:21: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:950:25: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:952:30: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:954:20: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:956:32: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:958:42: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:145:32: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:165:31: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:195:36: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:815:31: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:838:47: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:846:43: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:1035:24: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:1048:32: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:1209:32: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:438:11: style: The scope of the variable 'ret' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:538:12: style: The scope of the variable 'totalSize' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:806:12: style: The scope of the variable 'globalIdOffset' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:25:35: style:inconclusive: Function 'DBReader < std :: string >' argument 1 names different: declaration 'dataFileName' definition 'dataFileName_'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:151:26: note: Function 'DBReader < std :: string >' argument 1 names different: declaration 'dataFileName' definition 'dataFileName_'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:25:35: note: Function 'DBReader < std :: string >' argument 1 names different: declaration 'dataFileName' definition 'dataFileName_'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:25:62: style:inconclusive: Function 'DBReader < std :: string >' argument 2 names different: declaration 'indexFileName' definition 'indexFileName_'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:151:52: note: Function 'DBReader < std :: string >' argument 2 names different: declaration 'indexFileName' definition 'indexFileName_'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:25:62: note: Function 'DBReader < std :: string >' argument 2 names different: declaration 'indexFileName' definition 'indexFileName_'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:25:95: style:inconclusive: Function 'DBReader < std :: string >' argument 4 names different: declaration 'mode' definition 'dataMode'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:151:84: note: Function 'DBReader < std :: string >' argument 4 names different: declaration 'mode' definition 'dataMode'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:25:95: note: Function 'DBReader < std :: string >' argument 4 names different: declaration 'mode' definition 'dataMode'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:34:70: style:inconclusive: Function 'DBReader < std :: string >' argument 3 names different: declaration 'aaDbSize' definition 'dataSize'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:153:48: note: Function 'DBReader < std :: string >' argument 3 names different: declaration 'aaDbSize' definition 'dataSize'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:34:70: note: Function 'DBReader < std :: string >' argument 3 names different: declaration 'aaDbSize' definition 'dataSize'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:43:43: style:inconclusive: Function 'setDataFile' argument 1 names different: declaration 'dataFileName' definition 'dataFileName_'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:156:34: note: Function 'setDataFile' argument 1 names different: declaration 'dataFileName' definition 'dataFileName_'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:43:43: note: Function 'setDataFile' argument 1 names different: declaration 'dataFileName' definition 'dataFileName_'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:101:50: style:inconclusive: Function 'open' argument 1 names different: declaration 'sort' definition 'accessType'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:160:19: note: Function 'open' argument 1 names different: declaration 'sort' definition 'accessType'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:101:50: note: Function 'open' argument 1 names different: declaration 'sort' definition 'accessType'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:526:79: style:inconclusive: Function 'bsearch' argument 2 names different: declaration 'size' definition 'N'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:235:48: note: Function 'bsearch' argument 2 names different: declaration 'size' definition 'N'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:526:79: note: Function 'bsearch' argument 2 names different: declaration 'size' definition 'N'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:627:59: style:inconclusive: Function 'getDataByDBKey' argument 1 names different: declaration 'key' definition 'dbKey'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:181:28: note: Function 'getDataByDBKey' argument 1 names different: declaration 'key' definition 'dbKey'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:627:59: note: Function 'getDataByDBKey' argument 1 names different: declaration 'key' definition 'dbKey'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:173:14: style: Local variable 'isSortedById' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:158:10: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:173:14: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:58:20: style: Local variable 'dataSize' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:472:12: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:58:20: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:70:24: style: Local variable 'dataSize' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:472:12: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:70:24: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:123:20: style: Local variable 'dataSize' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:472:12: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:123:20: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:479:20: style: Local variable 'dataSize' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:472:12: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:479:20: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:541:10: style: Local variable 'isCompressed' shadows outer function [shadowFunction]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:440:9: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:541:10: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:622:16: style: Local variable 'dataSize' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:472:12: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:622:16: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:770:16: style: Local variable 'dataSize' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:472:12: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:770:16: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:1187:18: style: Local variable 'dataSize' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:472:12: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:1187:18: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:526:84: performance: Function parameter 'value' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:627:59: performance: Function parameter 'dbKey' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:659:62: performance: Function parameter 'dbKey' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:730:52: performance: Function parameter 'dbKey' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:907:60: performance: Function parameter 'i' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:755:23: style: Variable 'data' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:771:16: style: Variable 'data' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:1016:25: portability: Shifting signed 32-bit value by 31 bits is implementation-defined behaviour [shiftTooManyBitsSigned]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:959:7: style: Variable 'p' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:23:11: warning: Member variable 'DBWriter::bufferSize' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:437:16: style:inconclusive: Technically the member function 'DBWriter::checkClosed' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.h:73:10: note: Technically the member function 'DBWriter::checkClosed' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:437:16: note: Technically the member function 'DBWriter::checkClosed' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:25:5: warning: Class 'DBWriter' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:25:5: warning: Class 'DBWriter' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:185:12: warning: The class 'DBReader < std :: string >' defines member function with name 'getSize' also defined in its parent class 'MemoryTracker'. [duplInheritedMember]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MemoryTracker.h:10:19: note: Parent function 'MemoryTracker::getSize'
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:185:12: note: Derived function 'DBReader < std :: string >::getSize'
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ExpressionParser.cpp:53:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TE_FUNCTION0 [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Concat.h:69:21: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Concat.h:92:31: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Concat.h:132:27: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:66:35: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:182:36: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:184:31: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:240:48: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:240:79: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:491:22: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:491:36: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:491:50: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ExpressionParser.cpp:5:19: warning: Member variable 'ExpressionParser::variables' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ExpressionParser.cpp:8:19: warning: Member variable 'ExpressionParser::variables' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ExpressionParser.h:18:10: style:inconclusive: Technically the member function 'ExpressionParser::isOk' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ExpressionParser.cpp:42:24: performance:inconclusive: Technically the member function 'ExpressionParser::findBound' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ExpressionParser.h:36:10: note: Technically the member function 'ExpressionParser::findBound' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ExpressionParser.cpp:42:24: note: Technically the member function 'ExpressionParser::findBound' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ExpressionParser.h:9:5: style: Class 'ExpressionParser' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ExpressionParser.cpp:55:28: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ExpressionParser.cpp:31:13: style: Variable 'base' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Concat.h:51:17: style: The scope of the variable 'cc' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:23:32: style:inconclusive: Function 'DBWriter' argument 1 names different: declaration 'dataFileName' definition 'dataFileName_'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.h:16:26: note: Function 'DBWriter' argument 1 names different: declaration 'dataFileName' definition 'dataFileName_'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:23:32: note: Function 'DBWriter' argument 1 names different: declaration 'dataFileName' definition 'dataFileName_'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:23:59: style:inconclusive: Function 'DBWriter' argument 2 names different: declaration 'indexFileName' definition 'indexFileName_'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.h:16:52: note: Function 'DBWriter' argument 2 names different: declaration 'indexFileName' definition 'indexFileName_'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:23:59: note: Function 'DBWriter' argument 2 names different: declaration 'indexFileName' definition 'indexFileName_'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:98:62: style:inconclusive: Function 'sortDatafileByIdOrder' argument 1 names different: declaration 'qdbr' definition 'dbr'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.h:38:56: note: Function 'sortDatafileByIdOrder' argument 1 names different: declaration 'qdbr' definition 'dbr'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:98:62: note: Function 'sortDatafileByIdOrder' argument 1 names different: declaration 'qdbr' definition 'dbr'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:403:92: style:inconclusive: Function 'writeData' argument 4 names different: declaration 'threadIdx' definition 'thrIdx'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.h:32:86: note: Function 'writeData' argument 4 names different: declaration 'threadIdx' definition 'thrIdx'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:403:92: note: Function 'writeData' argument 4 names different: declaration 'threadIdx' definition 'thrIdx'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:537:39: style: Variable 'filenames' can be declared as reference to const [constVariableReference]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:575:43: style: Variable 'filenames' can be declared as reference to const [constVariableReference]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:585:35: style: Variable 'filenames' can be declared as reference to const [constVariableReference]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:108:19: style: Variable 'data' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:698:42: style: Variable 'lookup' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:703:40: style: Variable 'idx' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:200:41: portability: Shifting signed 32-bit value by 31 bits is implementation-defined behaviour [shiftTooManyBitsSigned]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:200:63: portability: Shifting signed 32-bit value by 31 bits is implementation-defined behaviour [shiftTooManyBitsSigned]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/PatternCompiler.h:10:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REG_EXTENDED [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/HeaderSummarizer.cpp:98:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/HeaderSummarizer.cpp:211:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/FileUtil.cpp:39:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/FileUtil.cpp:66:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/FileUtil.cpp:105:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_WRONLY [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/FileUtil.cpp:125:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/FileUtil.cpp:132:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/FileUtil.cpp:141:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/FileUtil.cpp:220:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/FileUtil.cpp:285:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BUFSIZ [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/FileUtil.cpp:359:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/FileUtil.cpp:451:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RLIMIT_NOFILE [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.cpp:15:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KSEQ_FILE [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.cpp:48:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KSEQ_STREAM [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.cpp:203:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KSEQ_BUFFER [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/HeaderSummarizer.cpp:30:22: performance:inconclusive: Technically the member function 'UniprotHeader::isUninformative' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/PatternCompiler.h:9:5: style: Class 'PatternCompiler' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/HeaderSummarizer.h:15:17: style: The function 'summarize' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/HeaderSummarizer.h:9:25: note: Virtual function in base class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/HeaderSummarizer.h:15:17: note: Function in derived class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/HeaderSummarizer.h:16:6: style: The destructor '~UniprotHeaderSummarizer' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/HeaderSummarizer.h:10:14: note: Virtual destructor in base class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/HeaderSummarizer.h:16:6: note: Destructor in derived class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/HeaderSummarizer.h:21:17: style: The function 'summarize' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/HeaderSummarizer.h:9:25: note: Virtual function in base class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/HeaderSummarizer.h:21:17: note: Function in derived class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/HeaderSummarizer.h:22:6: style: The destructor '~MetaclustHeaderSummarizer' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/HeaderSummarizer.h:10:14: note: Virtual destructor in base class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/HeaderSummarizer.h:22:6: note: Destructor in derived class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/HeaderSummarizer.h:16:6: style: The destructor '~UniprotHeaderSummarizer' overrides a destructor in a base class but is identical to the overridden function [uselessOverride]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/HeaderSummarizer.h:10:14: note: Virtual destructor in base class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/HeaderSummarizer.h:16:6: note: Destructor in derived class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/HeaderSummarizer.h:22:6: style: The destructor '~MetaclustHeaderSummarizer' overrides a destructor in a base class but is identical to the overridden function [uselessOverride]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/HeaderSummarizer.h:10:14: note: Virtual destructor in base class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/HeaderSummarizer.h:22:6: note: Destructor in derived class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/HeaderSummarizer.cpp:154:43: performance: Passing the result of c_str() to a stream is slow and redundant. [stlcstrStream]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/HeaderSummarizer.cpp:228:43: performance: Passing the result of c_str() to a stream is slow and redundant. [stlcstrStream]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/FileUtil.cpp:32:36: style:inconclusive: Function 'makeDir' argument 1 names different: declaration 'dirName' definition 'directoryName'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/FileUtil.h:23:37: note: Function 'makeDir' argument 1 names different: declaration 'dirName' definition 'directoryName'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/FileUtil.cpp:32:36: note: Function 'makeDir' argument 1 names different: declaration 'dirName' definition 'directoryName'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/FileUtil.cpp:104:78: style:inconclusive: Function 'writeFile' argument 2 names different: declaration 'sh' definition 'data'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/FileUtil.h:35:79: note: Function 'writeFile' argument 2 names different: declaration 'sh' definition 'data'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/FileUtil.cpp:104:78: note: Function 'writeFile' argument 2 names different: declaration 'sh' definition 'data'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/FileUtil.cpp:137:43: style:inconclusive: Function 'getFreeSpace' argument 1 names different: declaration 'dir' definition 'path'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/FileUtil.h:41:44: note: Function 'getFreeSpace' argument 1 names different: declaration 'dir' definition 'path'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/FileUtil.cpp:137:43: note: Function 'getFreeSpace' argument 1 names different: declaration 'dir' definition 'path'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/FileUtil.cpp:331:17: style: Local variable 'baseName' shadows outer function [shadowFunction]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/FileUtil.h:39:24: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/commons/FileUtil.cpp:331:17: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/commons/FileUtil.cpp:364:17: style: Local variable 'dirName' shadows outer function [shadowFunction]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/FileUtil.h:37:24: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/commons/FileUtil.cpp:364:17: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/commons/FileUtil.cpp:149:64: performance: Function parameter 'path' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/FileUtil.cpp:161:60: performance: Function parameter 'path' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/FileUtil.cpp:56:34: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.cpp:12:11: warning: Member variable 'KSeqWrapper::entry' is not initialized in the constructor. Maybe it should be initialized directly in the class KSeqWrapper? [uninitDerivedMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.cpp:46:13: warning: Member variable 'KSeqWrapper::entry' is not initialized in the constructor. Maybe it should be initialized directly in the class KSeqWrapper? [uninitDerivedMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.cpp:198:13: warning: Member variable 'KSeqWrapper::entry' is not initialized in the constructor. Maybe it should be initialized directly in the class KSeqWrapper? [uninitDerivedMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.h:39:5: style: Class 'KSeqFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.h:40:10: style: The function 'ReadEntry' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.h:30:18: note: Virtual function in base class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.h:40:10: note: Function in derived class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.h:41:6: style: The destructor '~KSeqFile' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.h:31:14: note: Virtual destructor in base class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.h:41:6: note: Destructor in derived class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.h:50:10: style: The function 'ReadEntry' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.h:30:18: note: Virtual function in base class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.h:50:10: note: Function in derived class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.h:51:6: style: The destructor '~KSeqStream' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.h:31:14: note: Virtual destructor in base class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.h:51:6: note: Destructor in derived class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.h:83:10: style: The function 'ReadEntry' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.h:30:18: note: Virtual function in base class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.h:83:10: note: Function in derived class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.h:84:6: style: The destructor '~KSeqBuffer' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.h:31:14: note: Virtual destructor in base class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.h:84:6: note: Destructor in derived class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/FileUtil.cpp:97:94: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.cpp:14:11: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.cpp:19:27: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.cpp:34:18: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.cpp:47:11: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.cpp:52:29: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.cpp:65:18: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.cpp:199:16: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.cpp:202:11: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.cpp:207:29: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.cpp:222:18: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.cpp:12:32: style:inconclusive: Function 'KSeqFile' argument 1 names different: declaration 'file' definition 'fileName'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.h:39:26: note: Function 'KSeqFile' argument 1 names different: declaration 'file' definition 'fileName'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/KSeqWrapper.cpp:12:32: note: Function 'KSeqFile' argument 1 names different: declaration 'file' definition 'fileName'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.cpp:18:21: performance:inconclusive: Technically the member function 'LibraryReader::StreamStartsWith' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.h:14:10: note: Technically the member function 'LibraryReader::StreamStartsWith' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.cpp:18:21: note: Technically the member function 'LibraryReader::StreamStartsWith' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.cpp:31:20: performance:inconclusive: Technically the member function 'LibraryReader::ReadInt' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.h:15:9: note: Technically the member function 'LibraryReader::ReadInt' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.cpp:31:20: note: Technically the member function 'LibraryReader::ReadInt' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.cpp:46:23: performance:inconclusive: Technically the member function 'LibraryReader::ReadDouble' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.h:16:12: note: Technically the member function 'LibraryReader::ReadDouble' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.cpp:46:23: note: Technically the member function 'LibraryReader::ReadDouble' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.cpp:86:21: performance:inconclusive: Technically the member function 'LibraryReader::ReadBool' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.h:18:10: note: Technically the member function 'LibraryReader::ReadBool' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.cpp:86:21: note: Technically the member function 'LibraryReader::ReadBool' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.cpp:10:28: performance:inconclusive: Technically the member function 'LibraryReader::strscn' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.h:19:17: note: Technically the member function 'LibraryReader::strscn' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.cpp:10:28: note: Technically the member function 'LibraryReader::strscn' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.cpp:74:28: performance:inconclusive: Technically the member function 'LibraryReader::getline' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.h:21:17: note: Technically the member function 'LibraryReader::getline' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.cpp:74:28: note: Technically the member function 'LibraryReader::getline' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MemoryMapped.cpp:129:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_RDONLY [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MemoryMapped.cpp:311:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MADV_NORMAL [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MemoryMapped.cpp:336:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _SC_PAGESIZE [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MemoryMapped.cpp:196:13: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MemoryMapped.cpp:270:23: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.cpp:8:53: style: Condition 'assign(parametercstring,values.second)==false' is always false [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.cpp:8:19: note: Calling function 'assign' returns 1
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.cpp:8:53: note: Condition 'assign(parametercstring,values.second)==false' is always false
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.cpp:22:67: style: Condition 'assign(pair[1],values.first)==false' is always false [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.cpp:22:43: note: Calling function 'assign' returns 1
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.cpp:22:67: note: Condition 'assign(pair[1],values.first)==false' is always false
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.cpp:28:68: style: Condition 'assign(pair[1],values.second)==false' is always false [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.cpp:28:43: note: Calling function 'assign' returns 1
metaeuk-7-bba0d80/lib/mmseqs/src/commons/MultiParam.cpp:28:68: note: Condition 'assign(pair[1],values.second)==false' is always false
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.cpp:58:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALIGN_INT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.cpp:132:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VECSIZE_INT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/NucleotideMatrix.h:16:9: style:inconclusive: Technically the member function 'NucleotideMatrix::reverseResidue' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/NucleotideMatrix.cpp:7:5: warning: Class 'NucleotideMatrix' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/NucleotideMatrix.cpp:7:5: warning: Class 'NucleotideMatrix' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/NucleotideMatrix.h:10:14: style: The destructor '~NucleotideMatrix' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.h:19:14: note: Virtual destructor in base class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/NucleotideMatrix.h:10:14: note: Destructor in derived class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/NucleotideMatrix.h:14:10: style: The function 'setupLetterMapping' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.h:43:10: note: Virtual function in base class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/NucleotideMatrix.h:14:10: note: Function in derived class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ByteParser.h:42:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:1455:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fixed [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:1582:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REG_EXTENDED [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:1604:94: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:1729:98: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable values [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2196:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable boolalpha [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2718:77: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.cpp:197:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALIGN_FLOAT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.cpp:288:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FLT_MIN [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.cpp:314:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALIGN_FLOAT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.cpp:405:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALIGN_FLOAT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.cpp:269:22: performance:inconclusive: Technically the member function 'ProfileStates::entropy' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.h:117:11: note: Technically the member function 'ProfileStates::entropy' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.cpp:269:22: note: Technically the member function 'ProfileStates::entropy' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.cpp:59:5: warning: Class 'ProfileStates' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.cpp:59:5: warning: Class 'ProfileStates' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.cpp:36:40: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.cpp:40:40: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.cpp:45:40: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.cpp:50:40: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.cpp:132:21: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.cpp:197:13: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.cpp:204:33: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.cpp:205:33: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.cpp:252:29: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.cpp:314:23: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.cpp:319:22: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.cpp:373:43: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.cpp:405:23: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.cpp:410:22: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.cpp:26:35: style:inconclusive: Function 'ProfileStates' argument 1 names different: declaration 'alphSize' definition 'pAlphSize'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.h:38:23: note: Function 'ProfileStates' argument 1 names different: declaration 'alphSize' definition 'pAlphSize'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.cpp:26:35: note: Function 'ProfileStates' argument 1 names different: declaration 'alphSize' definition 'pAlphSize'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.cpp:427:35: style:inconclusive: Function 'score' argument 1 names different: declaration 'profile' definition 'profileCol'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.h:51:24: note: Function 'score' argument 1 names different: declaration 'profile' definition 'profileCol'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.cpp:427:35: note: Function 'score' argument 1 names different: declaration 'profile' definition 'profileCol'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.cpp:143:19: style: Local variable 'score' shadows outer function [shadowFunction]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.h:51:11: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.cpp:143:19: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.cpp:26:55: style: Parameter 'pBack' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.cpp:269:37: style: Parameter 'distribution' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.cpp:373:21: style: Variable 'curDiffScoreSimdFlt' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/TranslateNucl.h:494:29: style:inconclusive: Boolean expression 'isLowerCase' is used in bitwise operation. [bitwiseOnBoolean]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.cpp:55:6: warning: Member variable 'Orf::sequenceLength' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.h:66:9: warning:inconclusive: Member variable 'SequenceLocation::id' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.h:66:9: warning:inconclusive: Member variable 'SequenceLocation::from' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.h:66:9: warning:inconclusive: Member variable 'SequenceLocation::to' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.h:66:9: warning:inconclusive: Member variable 'SequenceLocation::hasIncompleteStart' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.h:66:9: warning:inconclusive: Member variable 'SequenceLocation::hasIncompleteEnd' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.h:66:9: warning:inconclusive: Member variable 'SequenceLocation::strand' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.cpp:161:38: style:inconclusive: Technically the member function 'Orf::getSequence' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.h:91:37: note: Technically the member function 'Orf::getSequence' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.cpp:161:38: note: Technically the member function 'Orf::getSequence' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/TranslateNucl.h:287:30: performance:inconclusive: Technically the member function 'TranslateNucl::getCodons' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/TranslateNucl.h:110:5: style: Class 'TranslateNucl' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.cpp:373:83: style: Condition 'hasNumericStart==true' is always true [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.cpp:372:31: note: Assignment 'hasNumericStart=true', assigned value is 1
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.cpp:373:83: note: Condition 'hasNumericStart==true' is always true
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.cpp:373:107: style: Condition 'hasPlusMinus==false' is always true [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.cpp:364:29: note: Assignment 'hasPlusMinus=false', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.cpp:373:107: note: Condition 'hasPlusMinus==false' is always true
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.cpp:58:18: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.cpp:59:18: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.cpp:80:19: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.cpp:93:16: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.cpp:94:25: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.cpp:135:20: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.cpp:136:29: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.cpp:253:41: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.cpp:254:41: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.cpp:259:42: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.cpp:260:42: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.cpp:209:31: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/TranslateNucl.h:336:22: style: The scope of the variable 'ch' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.cpp:127:35: style:inconclusive: Function 'setSequence' argument 1 names different: declaration 'sequence' definition 'seq'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.h:72:34: note: Function 'setSequence' argument 1 names different: declaration 'sequence' definition 'seq'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.cpp:127:35: note: Function 'setSequence' argument 1 names different: declaration 'sequence' definition 'seq'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.cpp:127:47: style:inconclusive: Function 'setSequence' argument 2 names different: declaration 'sequenceLength' definition 'length'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.h:72:51: note: Function 'setSequence' argument 2 names different: declaration 'sequenceLength' definition 'length'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.cpp:127:47: note: Function 'setSequence' argument 2 names different: declaration 'sequenceLength' definition 'length'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.h:17:47: performance: Function parameter 'frames' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.cpp:107:12: style: Variable 'orfHeader' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/TranslateNucl.h:338:22: style: Variable 'charToBase' can be declared as const array [constVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/TranslateNucl.h:339:22: style: Variable 'baseToComp' can be declared as const array [constVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/TranslateNucl.h:389:21: style: Variable 'expansions' can be declared as const array [constVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/TranslateNucl.h:391:21: style: Variable 'codonIdx' can be declared as const array [constVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:36:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VECSIZE_INT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:382:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SequenceWeights.cpp:28:11: warning: Class 'SequenceWeights' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SequenceWeights.cpp:28:11: warning: Class 'SequenceWeights' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SequenceWeights.h:22:5: style: Class 'SequenceWeights' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SequenceWeights.cpp:34:25: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:14:11: warning: Member variable 'Sequence::L' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:14:11: warning: Member variable 'Sequence::id' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:14:11: warning: Member variable 'Sequence::dbKey' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:14:11: warning: Member variable 'Sequence::seqData' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:14:11: warning: Member variable 'Sequence::kmerHasX' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrixProfileStates.h:96:11: style:inconclusive: Technically the member function 'SubstitutionMatrixProfileStates::getScoreNormalization' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:65:15: warning: Class 'Sequence' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:65:15: warning: Class 'Sequence' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrixProfileStates.h:72:9: warning: Class 'SubstitutionMatrixProfileStates' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrixProfileStates.h:72:9: warning: Class 'SubstitutionMatrixProfileStates' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrixProfileStates.h:107:11: warning: The class 'SubstitutionMatrixProfileStates' defines member variable with name 'scoreBias' also defined in its parent class 'BaseMatrix'. [duplInheritedMember]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.h:45:11: note: Parent variable 'BaseMatrix::scoreBias'
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrixProfileStates.h:107:11: note: Derived variable 'SubstitutionMatrixProfileStates::scoreBias'
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrixProfileStates.h:86:6: style: The destructor '~SubstitutionMatrixProfileStates' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.h:10:14: note: Virtual destructor in base class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrixProfileStates.h:86:6: note: Destructor in derived class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrixProfileStates.h:95:19: style: The function 'getBitFactor' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.h:64:19: note: Virtual function in base class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrixProfileStates.h:95:19: note: Function in derived class
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:320:5: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:337:5: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:16:25: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:17:34: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:19:20: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:38:28: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:70:39: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:71:39: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:72:39: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:126:13: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:127:13: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:128:13: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:129:13: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:130:13: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:131:13: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:132:13: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:133:13: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:134:13: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:135:13: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:136:13: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:137:13: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:138:13: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:139:13: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:140:13: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:141:13: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:142:13: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:143:13: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:144:13: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:145:13: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:146:13: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:147:13: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:148:13: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:149:13: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:150:13: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:151:13: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:152:13: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:201:56: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:239:19: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:285:74: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:240:12: style: The scope of the variable 'currPos' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:204:71: style:inconclusive: Function 'mapSequence' argument 3 names different: declaration 'seq' definition 'sequence'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.h:83:65: note: Function 'mapSequence' argument 3 names different: declaration 'seq' definition 'sequence'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:204:71: note: Function 'mapSequence' argument 3 names different: declaration 'seq' definition 'sequence'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:304:41: style:inconclusive: Function 'mapSequence' argument 1 names different: declaration 'seq' definition 'sequence'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.h:537:34: note: Function 'mapSequence' argument 1 names different: declaration 'seq' definition 'sequence'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:304:41: note: Function 'mapSequence' argument 1 names different: declaration 'seq' definition 'sequence'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrixProfileStates.h:9:49: performance: Function parameter 'matrixName' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Sequence.cpp:239:12: style: Variable 'data' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrixProfileStates.h:10:67: style: Parameter 'pBack' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/UniprotKB.h:11:9: warning: Class 'UniprotKB' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/UniprotKB.h:11:9: warning: Class 'UniprotKB' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.cpp:313:25: style: Unused private function: 'SubstitutionMatrix::parseAlphabet' [unusedPrivateFunction]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.h:75:9: note: Unused private function: 'SubstitutionMatrix::parseAlphabet'
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.cpp:313:25: note: Unused private function: 'SubstitutionMatrix::parseAlphabet'
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.cpp:261:26: style:inconclusive: Technically the member function 'SubstitutionMatrix::mappingHasAminoAcidLetters' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.h:41:10: note: Technically the member function 'SubstitutionMatrix::mappingHasAminoAcidLetters' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.cpp:261:26: note: Technically the member function 'SubstitutionMatrix::mappingHasAminoAcidLetters' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.cpp:348:47: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.cpp:429:47: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.cpp:61:69: style:inconclusive: Function 'estimateLambdaAndBackground' argument 1 names different: declaration 'mat' definition 'scoreMatrix'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.h:39:54: note: Function 'estimateLambdaAndBackground' argument 1 names different: declaration 'mat' definition 'scoreMatrix'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.cpp:61:69: note: Function 'estimateLambdaAndBackground' argument 1 names different: declaration 'mat' definition 'scoreMatrix'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.cpp:105:16: style: Variable 'subMat' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.cpp:314:11: style: Variable 'charReader' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.cpp:351:17: performance: Inefficient usage of string::find() in condition; string::starts_with() could be faster. [stlIfStrFind]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.cpp:358:17: performance: Inefficient usage of string::find() in condition; string::starts_with() could be faster. [stlIfStrFind]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.cpp:265:13: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Util.cpp:154:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Util.cpp:287:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _SC_PAGE_SIZE [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Util.cpp:297:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _SC_PHYS_PAGES [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Util.cpp:457:79: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/tantan.cpp:35:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/tantan.cpp:73:9: warning: Member variable 'Tantan::backgroundProb' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/tantan.cpp:251:14: style:inconclusive: Technically the member function 'tantan::Tantan::addEndCounts' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/tantan.cpp:258:14: style:inconclusive: Technically the member function 'tantan::Tantan::addTransitionCounts' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/tantan.cpp:273:14: style:inconclusive: Technically the member function 'tantan::Tantan::isNearSeqBeg' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/tantan.cpp:474:36: style: Parameter 'seqEnd' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/KmerIndex.h:87:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TYPE [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/KmerIndex.h:146:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ERROR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/KmerIndex.h:211:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFO [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.cpp:239:71: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VERSION [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.cpp:251:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ERROR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.cpp:263:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_NUCLEOTIDES [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.cpp:284:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WARNING [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.cpp:183:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFO [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.cpp:71:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFO [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.cpp:24:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_NUCLEOTIDES [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.h:167:5: warning:inconclusive: Member variable 'FileKmerPosition::repSeq' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.h:167:5: warning:inconclusive: Member variable 'FileKmerPosition::id' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.h:167:5: warning:inconclusive: Member variable 'FileKmerPosition::pos' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.h:167:5: warning:inconclusive: Member variable 'FileKmerPosition::score' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.h:167:5: warning:inconclusive: Member variable 'FileKmerPosition::file' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.h:167:5: warning:inconclusive: Member variable 'FileKmerPosition::reverse' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.h:14:5: warning:inconclusive: Member variable 'FileKmer::kmer' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.h:14:5: warning:inconclusive: Member variable 'FileKmer::id' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.h:14:5: warning:inconclusive: Member variable 'FileKmer::file' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.h:14:5: warning:inconclusive: Member variable 'FileKmer::seqLen' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.h:14:5: warning:inconclusive: Member variable 'FileKmer::pos' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.h:14:5: warning:inconclusive: Member variable 'FileKmer::reverse' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/KmerIndex.h:53:5: warning:inconclusive: Member variable 'KmerIndex::indexGridSize' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/KmerIndex.h:53:5: warning:inconclusive: Member variable 'KmerIndex::entryOffsets' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/KmerIndex.h:53:5: warning:inconclusive: Member variable 'KmerIndex::prevKmerStartRange' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/KmerIndex.h:53:5: warning:inconclusive: Member variable 'KmerIndex::iteratorPos' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/KmerIndex.h:53:5: warning:inconclusive: Member variable 'KmerIndex::entryOffsetPos' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/KmerIndex.h:53:5: warning:inconclusive: Member variable 'KmerIndex::writingPosition' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/KmerIndex.h:53:5: warning:inconclusive: Member variable 'KmerIndex::entryCount' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/KmerIndex.h:53:5: warning:inconclusive: Member variable 'KmerIndex::maxWriteEntries' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/KmerIndex.h:53:5: warning:inconclusive: Member variable 'KmerIndex::isMmaped' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/KmerIndex.h:53:5: warning:inconclusive: Member variable 'KmerIndex::alphabetSize' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/KmerIndex.h:53:5: warning:inconclusive: Member variable 'KmerIndex::kmerSize' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/KmerIndex.h:53:5: warning:inconclusive: Member variable 'KmerIndex::entries' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/KmerIndex.h:69:5: warning: Member variable 'KmerIndex::iteratorPos' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/KmerIndex.h:69:5: warning: Member variable 'KmerIndex::entryOffsetPos' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/KmerIndex.h:176:5: warning: Member variable 'KmerIndex::writingPosition' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/KmerIndex.h:176:5: warning: Member variable 'KmerIndex::maxWriteEntries' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/KmerIndex.h:48:9: warning:inconclusive: Member variable 'KmerEntry::kmer' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/KmerIndex.h:48:9: warning:inconclusive: Member variable 'KmerEntry::id' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/KmerIndex.h:48:9: warning:inconclusive: Member variable 'KmerEntry::pos' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/KmerIndex.h:48:9: warning:inconclusive: Member variable 'KmerEntry::seqLen' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.h:139:10: performance:inconclusive: Technically the member function 'KmerEntry::setReverse' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.h:142:19: performance:inconclusive: Technically the member function 'KmerEntry::getRev' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.h:155:19: style:inconclusive: Technically the member function 'KmerEntryRev::getRev' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/KmerIndex.h:75:10: style:inconclusive: Technically the member function 'KmerIndex::hasNextEntry' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/KmerIndex.h:100:12: style:inconclusive: Technically the member function 'KmerIndex::getGridPosition' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/KmerIndex.h:104:12: style:inconclusive: Technically the member function 'KmerIndex::getKmerStartRange' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/KmerIndex.h:108:12: style:inconclusive: Technically the member function 'KmerIndex::getGridResolution' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/KmerIndex.h:164:20: style:inconclusive: Technically the member function 'KmerIndex::getOffsets' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/KmerIndex.h:168:12: style:inconclusive: Technically the member function 'KmerIndex::getOffsetsSize' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/KmerIndex.h:172:14: style:inconclusive: Technically the member function 'KmerIndex::getTableEntriesNum' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.cpp:249:66: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: filePtr [nullPointerOutOfResources]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.cpp:247:26: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.cpp:247:26: note: Assignment 'filePtr=fopen(fileName.c_str(),"wb")', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.cpp:249:66: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.cpp:250:16: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: filePtr [nullPointerOutOfResources]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.cpp:247:26: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.cpp:247:26: note: Assignment 'filePtr=fopen(fileName.c_str(),"wb")', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.cpp:250:16: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/KmerIndex.h:136:25: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/KmerIndex.h:181:26: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/KmerIndex.h:184:30: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.cpp:206:19: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.cpp:212:32: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.cpp:220:27: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.cpp:82:28: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.cpp:143:30: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.cpp:154:19: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.cpp:160:32: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.cpp:167:27: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.cpp:257:105: style:inconclusive: Function 'findIncompatibleParameter' argument 2 names different: declaration 'parameters' definition 'par'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.h:61:94: note: Function 'findIncompatibleParameter' argument 2 names different: declaration 'parameters' definition 'par'.
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.cpp:257:105: note: Function 'findIncompatibleParameter' argument 2 names different: declaration 'parameters' definition 'par'.
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.cpp:21:66: style:inconclusive: Function 'pickCenterKmer < 0 >' argument 1 names different: declaration 'kmers' definition 'hashSeqPair'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.h:45:55: note: Function 'pickCenterKmer < 0 >' argument 1 names different: declaration 'kmers' definition 'hashSeqPair'.
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.cpp:21:66: note: Function 'pickCenterKmer < 0 >' argument 1 names different: declaration 'kmers' definition 'hashSeqPair'.
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.cpp:21:66: style:inconclusive: Function 'pickCenterKmer < 1 >' argument 1 names different: declaration 'kmers' definition 'hashSeqPair'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.h:45:55: note: Function 'pickCenterKmer < 1 >' argument 1 names different: declaration 'kmers' definition 'hashSeqPair'.
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.cpp:21:66: note: Function 'pickCenterKmer < 1 >' argument 1 names different: declaration 'kmers' definition 'hashSeqPair'.
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.cpp:232:57: performance: Function parameter 'baseName' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.cpp:246:61: performance: Function parameter 'fileName' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.h:176:41: style: Parameter 'first' can be declared as reference to const [constParameterReference]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.h:176:67: style: Parameter 'second' can be declared as reference to const [constParameterReference]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.h:22:33: style: Parameter 'first' can be declared as reference to const [constParameterReference]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.h:22:51: style: Parameter 'second' can be declared as reference to const [constParameterReference]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.cpp:239:12: style: Variable 'version' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/LinsearchIndexReader.cpp:246:92: style: Parameter 'kmers' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Util.cpp:36:27: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Util.cpp:47:35: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmerindexdb.cpp:24:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMMAND_CLUSTLINEAR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Util.cpp:189:49: style:inconclusive: Function 'parseFastaHeader' argument 1 names different: declaration 'header' definition 'headerPtr'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Util.h:281:54: note: Function 'parseFastaHeader' argument 1 names different: declaration 'header' definition 'headerPtr'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Util.cpp:189:49: note: Function 'parseFastaHeader' argument 1 names different: declaration 'header' definition 'headerPtr'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Util.cpp:365:53: style:inconclusive: Function 'ompCountLines' argument 2 names different: declaration 'length' definition 'dataSize'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Util.h:94:58: note: Function 'ompCountLines' argument 2 names different: declaration 'length' definition 'dataSize'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Util.cpp:365:53: note: Function 'ompCountLines' argument 2 names different: declaration 'length' definition 'dataSize'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Util.cpp:440:73: style:inconclusive: Function 'readLookup' argument 1 names different: declaration 'lookupFile' definition 'file'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Util.h:350:78: note: Function 'readLookup' argument 1 names different: declaration 'lookupFile' definition 'file'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Util.cpp:440:73: note: Function 'readLookup' argument 1 names different: declaration 'lookupFile' definition 'file'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Util.cpp:451:38: style: Local variable 'split' shadows outer function [shadowFunction]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Util.h:140:37: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Util.cpp:451:38: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Util.cpp:28:35: performance: Function parameter 'mappingFilename' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Util.cpp:279:55: performance: Function parameter 'message' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Util.cpp:604:41: performance: Function parameter 'x' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Util.cpp:205:11: style: Variable 'endPosOfId' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Util.cpp:279:34: style: Parameter 'pointer' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Util.cpp:458:24: performance: Ineffective call of function 'substr' because a prefix of the string is assigned to itself. Use resize() or pop_back() instead. [uselessCallsSubstr]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmerindexdb.cpp:167:16: style: Condition 'mpiRank==0' is always true [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmerindexdb.cpp:96:22: note: Assignment 'mpiRank=0', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmerindexdb.cpp:167:16: note: Condition 'mpiRank==0' is always true
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmerindexdb.cpp:173:23: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmerindexdb.cpp:186:29: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmerindexdb.cpp:212:30: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmerindexdb.cpp:277:20: style: Local variable 'offsetIndex' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmerindexdb.cpp:234:16: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmerindexdb.cpp:277:20: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmerindexdb.cpp:281:20: style: Local variable 'offsetData' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmerindexdb.cpp:239:16: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmerindexdb.cpp:281:20: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmersearch.cpp:32:73: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_NUCLEOTIDES [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmersearch.cpp:137:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMMAND_CLUSTLINEAR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmersearch.cpp:299:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PARAM_RESULT_DIRECTION_TARGET [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmersearch.cpp:71:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_NUCLEOTIDES [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/KmerIndex.h:87:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_NUCLEOTIDES [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:69:92: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_AMINO_ACIDS [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:652:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CLUST_LINEAR_DEFAULT_K [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:867:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMMAND_CLUSTLINEAR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:899:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable kmer [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:1283:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_NUCLEOTIDES [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:822:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFO [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:680:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_NUCLEOTIDES [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:527:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_NUCLEOTIDES [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:447:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_NUCLEOTIDES [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:394:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_NUCLEOTIDES [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:92:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_HMM_PROFILE [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:43:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nothrow [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:1205:74: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable kmer [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:1032:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFO [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:1016:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_NUCLEOTIDES [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmersearch.cpp:97:33: style: Condition 'kmers[i].pos==prevDiagonal' is always true [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmersearch.cpp:95:26: note: prevDiagonal is assigned 'kmers[i].pos' here.
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmersearch.cpp:97:33: note: Condition 'kmers[i].pos==prevDiagonal' is always true
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmersearch.cpp:226:32: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmersearch.cpp:227:37: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmersearch.cpp:84:15: style: The scope of the variable 'prevDiagonal' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmersearch.cpp:23:76: style:inconclusive: Function 'extractKmerAndSort' argument 1 names different: declaration 'splitKmerCount' definition 'totalKmers'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmersearch.h:28:63: note: Function 'extractKmerAndSort' argument 1 names different: declaration 'splitKmerCount' definition 'totalKmers'.
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmersearch.cpp:23:76: note: Function 'extractKmerAndSort' argument 1 names different: declaration 'splitKmerCount' definition 'totalKmers'.
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmersearch.cpp:23:95: style:inconclusive: Function 'extractKmerAndSort' argument 2 names different: declaration 'split' definition 'hashStartRange'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmersearch.h:28:86: note: Function 'extractKmerAndSort' argument 2 names different: declaration 'split' definition 'hashStartRange'.
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmersearch.cpp:23:95: note: Function 'extractKmerAndSort' argument 2 names different: declaration 'split' definition 'hashStartRange'.
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmersearch.cpp:23:118: style:inconclusive: Function 'extractKmerAndSort' argument 3 names different: declaration 'splits' definition 'hashEndRange'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmersearch.h:28:100: note: Function 'extractKmerAndSort' argument 3 names different: declaration 'splits' definition 'hashEndRange'.
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmersearch.cpp:23:118: note: Function 'extractKmerAndSort' argument 3 names different: declaration 'splits' definition 'hashEndRange'.
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmersearch.cpp:337:39: style: Local variable 'currQueryKmer' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmersearch.cpp:320:31: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmersearch.cpp:337:39: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/Aggregation.cpp:14:124: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_DATA [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/Aggregation.cpp:38:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ERROR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/Aggregation.cpp:49:112: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_DATA [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/Aggregation.cpp:14:5: warning: Class 'Aggregation' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/Aggregation.cpp:14:5: warning: Class 'Aggregation' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/Aggregation.cpp:41:15: style: Local variable 'data' shadows outer argument [shadowArgument]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/Aggregation.cpp:24:34: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/Aggregation.cpp:41:15: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/MultiHitDb.cpp:23:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFO [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/MultiHitSearch.cpp:25:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALIGNMENT_MODE_SCORE_COV [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/MultiHitSearch.cpp:32:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMMAND_EXPERT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/besthitperset.cpp:17:129: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_DATA [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/besthitperset.cpp:30:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MAX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/besthitperset.cpp:17:9: warning: Class 'BestHitBySetFilter' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/besthitperset.cpp:17:9: warning: Class 'BestHitBySetFilter' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/besthitperset.cpp:21:6: style: The destructor '~BestHitBySetFilter' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/Aggregation.h:15:14: note: Virtual destructor in base class
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/besthitperset.cpp:21:6: note: Destructor in derived class
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/besthitperset.cpp:27:10: style: The function 'prepareInput' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/Aggregation.h:18:18: note: Virtual function in base class
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/besthitperset.cpp:27:10: note: Function in derived class
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/besthitperset.cpp:29:17: style: The function 'aggregateEntry' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/Aggregation.h:19:25: note: Virtual function in base class
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/besthitperset.cpp:29:17: note: Function in derived class
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/besthitperset.cpp:30:16: style:inconclusive: Same expression used in consecutive assignments of 'bestScore' and 'secondBestScore'. [duplicateAssignExpression]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/besthitperset.cpp:31:16: note: Same expression used in consecutive assignments of 'bestScore' and 'secondBestScore'.
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/besthitperset.cpp:30:16: note: Same expression used in consecutive assignments of 'bestScore' and 'secondBestScore'.
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/combinepvalperset.cpp:37:128: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_DATA [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/combinepvalperset.cpp:98:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AGGREGATION_MODE_MULTIHIT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/combinepvalperset.cpp:55:38: warning: Invalid lgamma() argument nr 1. The value is 0 but the valid values are '!0.0:'. [invalidFunctionArg]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/combinepvalperset.cpp:54:25: note: Assignment 'i=0', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/combinepvalperset.cpp:55:38: note: Invalid argument
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/combinepvalperset.cpp:24:33: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/combinepvalperset.cpp:37:9: warning: Class 'PvalueAggregator' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/combinepvalperset.cpp:37:9: warning: Class 'PvalueAggregator' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/combinepvalperset.cpp:64:6: style: The destructor '~PvalueAggregator' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/Aggregation.h:15:14: note: Virtual destructor in base class
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/combinepvalperset.cpp:64:6: note: Destructor in derived class
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/combinepvalperset.cpp:79:10: style: The function 'prepareInput' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/Aggregation.h:18:18: note: Virtual function in base class
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/combinepvalperset.cpp:79:10: note: Function in derived class
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/combinepvalperset.cpp:85:17: style: The function 'aggregateEntry' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/Aggregation.h:19:25: note: Virtual function in base class
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/combinepvalperset.cpp:85:17: note: Function in derived class
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/combinepvalperset.cpp:31:34: performance: Function parameter 'queryDbName' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/combinepvalperset.cpp:31:59: performance: Function parameter 'targetDbName' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/combinepvalperset.cpp:12:26: style: Parameter 'lookup' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/combinepvalperset.cpp:93:15: style: Variable 'tmpBuff' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/resultsbyset.cpp:63:116: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_DATA [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/resultsbyset.cpp:136:73: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/resultsbyset.cpp:63:9: warning: Class 'SetSummaryAggregator' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/resultsbyset.cpp:63:9: warning: Class 'SetSummaryAggregator' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/resultsbyset.cpp:77:6: style: The destructor '~SetSummaryAggregator' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/Aggregation.h:15:14: note: Virtual destructor in base class
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/resultsbyset.cpp:77:6: note: Destructor in derived class
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/resultsbyset.cpp:89:10: style: The function 'prepareInput' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/Aggregation.h:18:18: note: Virtual function in base class
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/resultsbyset.cpp:89:10: note: Function in derived class
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/resultsbyset.cpp:91:17: style: The function 'aggregateEntry' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/Aggregation.h:19:25: note: Virtual function in base class
metaeuk-7-bba0d80/lib/mmseqs/src/multihit/resultsbyset.cpp:91:17: note: Function in derived class
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Indexer.h:143:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:72:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nothrow [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:137:85: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_NUCLEOTIDES [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:215:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nothrow [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:244:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nothrow [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:262:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:322:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable kmer [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:354:85: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_NUCLEOTIDES [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:409:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFO [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:448:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:460:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE_MAX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:12:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nothrow [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:293:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nothrow [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:290:35: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:50:5: warning:inconclusive: Member variable 'IndexEntryLocalTmp::kmer' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:50:5: warning:inconclusive: Member variable 'IndexEntryLocalTmp::seqId' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:50:5: warning:inconclusive: Member variable 'IndexEntryLocalTmp::position_j' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:67:5: warning: Member variable 'IndexTable::sequenceLookup' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Indexer.h:93:17: style:inconclusive: Technically the member function 'Indexer::index2int' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:97:12: style:inconclusive: Technically the member function 'IndexTable::addSimilarKmerCount' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:133:12: style:inconclusive: Technically the member function 'IndexTable::addKmerCount' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:196:19: style:inconclusive: Technically the member function 'IndexTable::getOffset' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:419:12: style:inconclusive: Technically the member function 'IndexTable::getSize' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:422:14: style:inconclusive: Technically the member function 'IndexTable::getTableEntriesNum' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:425:12: style:inconclusive: Technically the member function 'IndexTable::getTableSize' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:428:12: performance:inconclusive: Technically the member function 'IndexTable::getSizeOfEntry' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:430:9: style:inconclusive: Technically the member function 'IndexTable::getKmerSize' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:434:9: style:inconclusive: Technically the member function 'IndexTable::getAlphabetSize' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:70:15: warning: Class 'IndexTable' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:70:15: warning: Class 'IndexTable' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:12:5: warning: Class 'CacheFriendlyOperations < 2048 >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:12:5: warning: Class 'CacheFriendlyOperations < 2048 >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:12:5: warning: Class 'CacheFriendlyOperations < 1024 >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:12:5: warning: Class 'CacheFriendlyOperations < 1024 >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:12:5: warning: Class 'CacheFriendlyOperations < 512 >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:12:5: warning: Class 'CacheFriendlyOperations < 512 >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:12:5: warning: Class 'CacheFriendlyOperations < 256 >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:12:5: warning: Class 'CacheFriendlyOperations < 256 >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:12:5: warning: Class 'CacheFriendlyOperations < 128 >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:12:5: warning: Class 'CacheFriendlyOperations < 128 >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:12:5: warning: Class 'CacheFriendlyOperations < 64 >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:12:5: warning: Class 'CacheFriendlyOperations < 64 >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:12:5: warning: Class 'CacheFriendlyOperations < 32 >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:12:5: warning: Class 'CacheFriendlyOperations < 32 >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:12:5: warning: Class 'CacheFriendlyOperations < 16 >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:12:5: warning: Class 'CacheFriendlyOperations < 16 >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:12:5: warning: Class 'CacheFriendlyOperations < 8 >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:12:5: warning: Class 'CacheFriendlyOperations < 8 >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:12:5: warning: Class 'CacheFriendlyOperations < 4 >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:12:5: warning: Class 'CacheFriendlyOperations < 4 >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:12:5: warning: Class 'CacheFriendlyOperations < 2 >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:12:5: warning: Class 'CacheFriendlyOperations < 2 >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.h:15:5: style: Class 'SequenceLookup' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:186:30: style: Local variable 'entries' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:484:22: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:186:30: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:206:16: style: Local variable 'tableEntriesNum' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:477:14: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:206:16: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:269:29: style: Local variable 'size' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:479:12: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:269:29: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:101:21: style: Local variable 'n' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:92:16: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:101:21: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:247:25: style: Local variable 'n' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:239:20: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:247:25: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:279:20: style: Variable 'lastPosition' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:322:68: style: Parameter 'inputArray' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:323:20: style: Variable 'lastPosition' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:337:99: style: Parameter 'inputArray' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/CacheFriendlyOperations.cpp:337:137: style: Parameter 'lastPosition' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:134:46: style: Parameter 'diagonalScore' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:240:118: style: Parameter 'entryOffsets' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexTable.h:349:45: style: Parameter 'diagonalScore' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Indexer.h:136:14: style: Variable 'nuclCode' can be declared as const array [constVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/ExtendedSubstitutionMatrix.cpp:24:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MAX_ALIGN_INT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/ExtendedSubstitutionMatrix.cpp:30:21: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/ExtendedSubstitutionMatrix.cpp:32:28: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/ExtendedSubstitutionMatrix.cpp:21:14: style: The scope of the variable 'subMatrix' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/ExtendedSubstitutionMatrix.cpp:49:25: style: Local variable 'score' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/ExtendedSubstitutionMatrix.cpp:30:13: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/ExtendedSubstitutionMatrix.cpp:49:25: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/ExtendedSubstitutionMatrix.cpp:76:61: style: Parameter 'i_seq' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/ExtendedSubstitutionMatrix.cpp:76:84: style: Parameter 'j_seq' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/ExtendedSubstitutionMatrix.cpp:121:87: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexBuilder.cpp:15:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WARNING [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexBuilder.cpp:59:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFO [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexBuilder.cpp:29:9: warning: Class 'DbInfo' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexBuilder.cpp:29:9: warning: Class 'DbInfo' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexBuilder.cpp:147:61: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexBuilder.cpp:148:61: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexBuilder.cpp:34:20: style: The scope of the variable 'idFromNull' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexBuilder.cpp:134:33: style: Local variable 'seq' shadows outer argument [shadowArgument]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexBuilder.cpp:56:83: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexBuilder.cpp:134:33: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/IndexBuilder.cpp:9:34: style: Parameter 'matrix' can be declared as reference to const [constParameterReference]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Indexer.cpp:38:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFO [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Indexer.cpp:43:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFO [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Indexer.cpp:41:15: performance:inconclusive: Technically the member function 'Indexer::printKmer' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Indexer.h:119:10: note: Technically the member function 'Indexer::printKmer' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Indexer.cpp:41:15: note: Technically the member function 'Indexer::printKmer' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Indexer.cpp:6:11: warning: Class 'Indexer' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Indexer.cpp:6:11: warning: Class 'Indexer' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Indexer.cpp:35:61: style: Parameter 'num2aa' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Indexer.cpp:41:72: style: Parameter 'num2aa' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/KmerGenerator.cpp:101:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALIGN_INT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/KmerGenerator.cpp:4:16: warning: Member variable 'KmerGenerator::divideStepCount' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/KmerGenerator.cpp:4:16: warning: Member variable 'KmerGenerator::divideStep' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/KmerGenerator.cpp:4:16: warning: Member variable 'KmerGenerator::kmerIndex' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/KmerGenerator.cpp:4:16: warning: Member variable 'KmerGenerator::stepMultiplicator' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/KmerGenerator.cpp:4:16: warning: Member variable 'KmerGenerator::highestScorePerArray' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/KmerGenerator.cpp:4:16: warning: Member variable 'KmerGenerator::possibleRest' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/KmerGenerator.cpp:4:16: warning: Member variable 'KmerGenerator::matrixLookup' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/KmerGenerator.cpp:4:16: warning: Member variable 'KmerGenerator::outputScoreArray' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/KmerGenerator.cpp:4:16: warning: Member variable 'KmerGenerator::outputIndexArray' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/KmerGenerator.cpp:7:11: warning: Class 'KmerGenerator' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/KmerGenerator.cpp:7:11: warning: Class 'KmerGenerator' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/KmerGenerator.cpp:101:31: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/KmerGenerator.cpp:102:31: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/KmerGenerator.cpp:107:83: style:inconclusive: Function 'generateKmerList' argument 1 names different: declaration 'intSeq' definition 'int_seq'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/KmerGenerator.h:16:76: note: Function 'generateKmerList' argument 1 names different: declaration 'intSeq' definition 'int_seq'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/KmerGenerator.cpp:107:83: note: Function 'generateKmerList' argument 1 names different: declaration 'intSeq' definition 'int_seq'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/KmerGenerator.cpp:143:22: style: Local variable 'index' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/KmerGenerator.cpp:132:18: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/KmerGenerator.cpp:143:22: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/KmerGenerator.cpp:172:26: style: Local variable 'index' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/KmerGenerator.cpp:132:18: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/KmerGenerator.cpp:172:26: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:218:25: error: Common realloc mistake: 'kmers' nulled but not freed upon failure [memleakOnRealloc]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:59:31: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:60:31: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:118:36: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:146:43: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:151:57: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:218:33: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:1047:32: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:1174:42: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:756:16: style: The comparison 'mpiRank == 0' is always true. [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:713:22: note: 'mpiRank' is assigned value '0' here.
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:756:16: note: The comparison 'mpiRank == 0' is always true.
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:355:28: style: The comparison 'thread_idx == 0' is always true. [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:351:39: note: 'thread_idx' is assigned value '0' here.
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:355:28: note: The comparison 'thread_idx == 0' is always true.
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:795:22: style: The scope of the variable 'buffer' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:94:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFO [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:1282:76: style:inconclusive: Function 'setKmerLengthAndAlphabet' argument 3 names different: declaration 'seqType' definition 'seqTyp'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.h:206:76: note: Function 'setKmerLengthAndAlphabet' argument 3 names different: declaration 'seqType' definition 'seqTyp'.
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:1282:76: note: Function 'setKmerLengthAndAlphabet' argument 3 names different: declaration 'seqType' definition 'seqTyp'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Main.cpp:17:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMMAND_PREFILTER [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:1190:70: style:inconclusive: Function 'writeKmersToDisk < Parameters :: DBTYPE_NUCLEOTIDES , KmerEntryRev , short >' argument 2 names different: declaration 'kmers' definition 'hashSeqPair'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.h:209:70: note: Function 'writeKmersToDisk < Parameters :: DBTYPE_NUCLEOTIDES , KmerEntryRev , short >' argument 2 names different: declaration 'kmers' definition 'hashSeqPair'.
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:1190:70: note: Function 'writeKmersToDisk < Parameters :: DBTYPE_NUCLEOTIDES , KmerEntryRev , short >' argument 2 names different: declaration 'kmers' definition 'hashSeqPair'.
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:1190:70: style:inconclusive: Function 'writeKmersToDisk < Parameters :: DBTYPE_AMINO_ACIDS , KmerEntry , short >' argument 2 names different: declaration 'kmers' definition 'hashSeqPair'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.h:209:70: note: Function 'writeKmersToDisk < Parameters :: DBTYPE_AMINO_ACIDS , KmerEntry , short >' argument 2 names different: declaration 'kmers' definition 'hashSeqPair'.
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:1190:70: note: Function 'writeKmersToDisk < Parameters :: DBTYPE_AMINO_ACIDS , KmerEntry , short >' argument 2 names different: declaration 'kmers' definition 'hashSeqPair'.
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:1190:70: style:inconclusive: Function 'writeKmersToDisk < Parameters :: DBTYPE_NUCLEOTIDES , KmerEntryRev , int >' argument 2 names different: declaration 'kmers' definition 'hashSeqPair'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.h:209:70: note: Function 'writeKmersToDisk < Parameters :: DBTYPE_NUCLEOTIDES , KmerEntryRev , int >' argument 2 names different: declaration 'kmers' definition 'hashSeqPair'.
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:1190:70: note: Function 'writeKmersToDisk < Parameters :: DBTYPE_NUCLEOTIDES , KmerEntryRev , int >' argument 2 names different: declaration 'kmers' definition 'hashSeqPair'.
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:1190:70: style:inconclusive: Function 'writeKmersToDisk < Parameters :: DBTYPE_AMINO_ACIDS , KmerEntry , int >' argument 2 names different: declaration 'kmers' definition 'hashSeqPair'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.h:209:70: note: Function 'writeKmersToDisk < Parameters :: DBTYPE_AMINO_ACIDS , KmerEntry , int >' argument 2 names different: declaration 'kmers' definition 'hashSeqPair'.
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:1190:70: note: Function 'writeKmersToDisk < Parameters :: DBTYPE_AMINO_ACIDS , KmerEntry , int >' argument 2 names different: declaration 'kmers' definition 'hashSeqPair'.
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:351:26: style: Local variable 'thread_idx' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:100:22: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:351:26: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:442:108: performance: Function parameter 'splitFile' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:1190:35: performance: Function parameter 'tmpFile' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:173:71: warning: Uninitialized variable: kmerToHash [uninitvar]
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:168:89: note: Assuming condition is false
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:171:46: note: Assignment 'kmerToHash=revKmer', assigned value is <Uninit>
metaeuk-7-bba0d80/lib/mmseqs/src/linclust/kmermatcher.cpp:173:71: note: Uninitialized variable: kmerToHash
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/UngappedAlignment.h:34:18: performance:inconclusive: Technically the member function 'UngappedAlignment::getQueryBias' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:81:25: style:inconclusive: Technically the member function 'QueryMatcher::getStatistics' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:206:62: style: Parameter 'scoreSizes' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/ReducedMatrix.h:38:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable aa2num [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:60:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_MASK [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:261:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRELOAD_MODE_FREAD [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:279:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TARGET_DB_SPLIT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:383:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:524:81: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_HMM_PROFILE [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:665:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ERROR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:726:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFO [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:963:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFO [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:1000:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TARGET_DB_SPLIT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:1014:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FLT_MAX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:1088:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Index [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:1114:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_NUCLEOTIDES [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:66:153: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_INDEX_DB [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:317:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NOSORT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:340:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NOSORT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:357:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ERROR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:398:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ERROR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:440:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFO [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:464:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFO [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:547:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRELOAD_MODE_FREAD [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:567:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRELOAD_MODE_FREAD [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:582:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WARNING [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:998:20: style:inconclusive: Technically the member function 'Prefiltering::mergePrefilterSplits' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.h:49:10: note: Technically the member function 'Prefiltering::mergePrefilterSplits' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:998:20: note: Technically the member function 'Prefiltering::mergePrefilterSplits' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:955:20: performance:inconclusive: Technically the member function 'Prefiltering::printStatistics' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.h:137:10: note: Technically the member function 'Prefiltering::printStatistics' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:955:20: note: Technically the member function 'Prefiltering::printStatistics' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:186:9: warning: Class 'Prefiltering' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:186:9: warning: Class 'Prefiltering' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcherTaxonomyHook.h:20:9: warning: Class 'QueryMatcherTaxonomyHook' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcherTaxonomyHook.h:20:9: warning: Class 'QueryMatcherTaxonomyHook' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcherTaxonomyHook.h:27:6: style: The destructor '~QueryMatcherTaxonomyHook' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:270:14: note: Virtual destructor in base class
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcherTaxonomyHook.h:27:6: note: Destructor in derived class
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcherTaxonomyHook.h:40:12: style: The function 'afterDiagonalMatchingHook' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:271:20: note: Virtual function in base class
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcherTaxonomyHook.h:40:12: note: Function in derived class
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:715:34: style: Condition 'splitProcessCount==0' is always true [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:711:34: note: Assuming that condition 'splitProcessCount==1' is not redundant
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:715:34: note: Condition 'splitProcessCount==0' is always true
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:908:5: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:915:7: note: Found duplicate branches for 'if' and 'else'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:908:5: note: Found duplicate branches for 'if' and 'else'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:418:12: style: The scope of the variable 'globalIdOffset' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:765:12: style: The scope of the variable 'realResSize' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:272:55: style:inconclusive: Function 'setupSplit' argument 1 names different: declaration 'dbr' definition 'tdbr'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.h:55:52: note: Function 'setupSplit' argument 1 names different: declaration 'dbr' definition 'tdbr'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:272:55: note: Function 'setupSplit' argument 1 names different: declaration 'dbr' definition 'tdbr'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:272:104: style:inconclusive: Function 'setupSplit' argument 3 names different: declaration 'querySeqType' definition 'querySeqTyp'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.h:55:100: note: Function 'setupSplit' argument 3 names different: declaration 'querySeqType' definition 'querySeqTyp'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:272:104: note: Function 'setupSplit' argument 3 names different: declaration 'querySeqType' definition 'querySeqTyp'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:998:60: style:inconclusive: Function 'mergePrefilterSplits' argument 1 names different: declaration 'outDb' definition 'outDB'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.h:49:50: note: Function 'mergePrefilterSplits' argument 1 names different: declaration 'outDb' definition 'outDB'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:998:60: note: Function 'mergePrefilterSplits' argument 1 names different: declaration 'outDb' definition 'outDB'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:1070:55: style:inconclusive: Function 'estimateMemoryConsumption' argument 4 names different: declaration 'maxHitsPerQuery' definition 'maxResListLen'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.h:125:52: note: Function 'estimateMemoryConsumption' argument 4 names different: declaration 'maxHitsPerQuery' definition 'maxResListLen'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:1070:55: note: Function 'estimateMemoryConsumption' argument 4 names different: declaration 'maxHitsPerQuery' definition 'maxResListLen'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:1109:71: style:inconclusive: Function 'optimizeSplit' argument 4 names different: declaration 'kmerSize' definition 'externalKmerSize'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.h:120:124: note: Function 'optimizeSplit' argument 4 names different: declaration 'kmerSize' definition 'externalKmerSize'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:1109:71: note: Function 'optimizeSplit' argument 4 names different: declaration 'kmerSize' definition 'externalKmerSize'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcherTaxonomyHook.h:16:42: performance: Function parameter 'targetPath' should be passed by const reference. [passedByValue]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:712:13: performance: Passing the result of c_str() to a function that takes std::string as argument no. 1 is slow and redundant. [stlcstrParam]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:712:13: performance: Passing the result of c_str() to a function that takes std::string as argument no. 2 is slow and redundant. [stlcstrParam]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:1017:104: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:463:31: style: Unused private function: 'PrefilteringIndexReader::printMeta' [unusedPrivateFunction]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.h:92:17: note: Unused private function: 'PrefilteringIndexReader::printMeta'
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:463:31: note: Unused private function: 'PrefilteringIndexReader::printMeta'
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:70:22: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:82:25: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:245:25: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:252:25: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:260:37: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:267:26: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:278:31: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:285:30: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:374:29: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:377:30: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:381:63: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:391:68: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:404:28: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:406:30: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:423:71: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:423:103: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:435:63: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:435:95: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:480:17: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:62:43: style: Same value in both branches of ternary operator. [duplicateValueTernary]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:52:66: style:inconclusive: Function 'createIndexFile' argument 1 names different: declaration 'outDb' definition 'outDB'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.h:57:52: note: Function 'createIndexFile' argument 1 names different: declaration 'outDb' definition 'outDB'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:52:66: note: Function 'createIndexFile' argument 1 names different: declaration 'outDb' definition 'outDB'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:56:59: style:inconclusive: Function 'createIndexFile' argument 7 names different: declaration 'seedSubMat' definition 'subMat'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.h:61:45: note: Function 'createIndexFile' argument 7 names different: declaration 'seedSubMat' definition 'subMat'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:56:59: note: Function 'createIndexFile' argument 7 names different: declaration 'seedSubMat' definition 'subMat'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:57:52: style:inconclusive: Function 'createIndexFile' argument 9 names different: declaration 'spacedKmer' definition 'hasSpacedKmer'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.h:61:77: note: Function 'createIndexFile' argument 9 names different: declaration 'spacedKmer' definition 'hasSpacedKmer'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:57:52: note: Function 'createIndexFile' argument 9 names different: declaration 'spacedKmer' definition 'hasSpacedKmer'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:463:46: style:inconclusive: Function 'printMeta' argument 1 names different: declaration 'meta' definition 'metadata_tmp'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.h:92:32: note: Function 'printMeta' argument 1 names different: declaration 'meta' definition 'metadata_tmp'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:463:46: note: Function 'printMeta' argument 1 names different: declaration 'meta' definition 'metadata_tmp'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:140:16: style: Local variable 'offsetIndex' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:105:12: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:140:16: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:145:16: style: Local variable 'offsetData' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:110:12: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:145:16: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:201:13: style: Local variable 'alphabetSize' shadows outer argument [shadowArgument]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:58:76: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:201:13: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:590:71: style: Parameter 'dbname' can be declared as reference to const [constParameterReference]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:39:12: style: Variable 'version' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:46:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALIGN_INT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:92:74: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_AMINO_ACIDS [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/ReducedMatrix.cpp:10:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ERROR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/ReducedMatrix.cpp:216:16: style: The scope of the variable 'temp' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/ReducedMatrix.cpp:258:21: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/ReducedMatrix.cpp:243:16: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/ReducedMatrix.cpp:258:21: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/ReducedMatrix.cpp:216:21: style: Variable 'temp' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.cpp:13:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable nothrow [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.cpp:49:29: style:inconclusive: Technically the member function 'SequenceLookup::getData' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.h:27:17: note: Technically the member function 'SequenceLookup::getData' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.cpp:49:29: note: Technically the member function 'SequenceLookup::getData' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.cpp:53:25: style:inconclusive: Technically the member function 'SequenceLookup::getDataSize' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.h:29:13: note: Technically the member function 'SequenceLookup::getDataSize' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.cpp:53:25: note: Technically the member function 'SequenceLookup::getDataSize' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.cpp:61:24: style:inconclusive: Technically the member function 'SequenceLookup::getSequenceCount' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.h:31:12: note: Technically the member function 'SequenceLookup::getSequenceCount' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.cpp:61:24: note: Technically the member function 'SequenceLookup::getSequenceCount' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.cpp:13:5: warning: Class 'SequenceLookup' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.cpp:13:5: warning: Class 'SequenceLookup' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.cpp:11:39: style:inconclusive: Function 'SequenceLookup' argument 1 names different: declaration 'dbSize' definition 'sequenceCount'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.h:14:27: note: Function 'SequenceLookup' argument 1 names different: declaration 'dbSize' definition 'sequenceCount'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.cpp:11:39: note: Function 'SequenceLookup' argument 1 names different: declaration 'dbSize' definition 'sequenceCount'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.cpp:11:61: style:inconclusive: Function 'SequenceLookup' argument 2 names different: declaration 'entrySize' definition 'dataSize'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.h:14:42: note: Function 'SequenceLookup' argument 2 names different: declaration 'entrySize' definition 'dataSize'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.cpp:11:61: note: Function 'SequenceLookup' argument 2 names different: declaration 'entrySize' definition 'dataSize'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.cpp:21:39: style:inconclusive: Function 'SequenceLookup' argument 1 names different: declaration 'dbSize' definition 'sequenceCount'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.h:15:27: note: Function 'SequenceLookup' argument 1 names different: declaration 'dbSize' definition 'sequenceCount'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.cpp:21:39: note: Function 'SequenceLookup' argument 1 names different: declaration 'dbSize' definition 'sequenceCount'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.cpp:65:69: style:inconclusive: Function 'initLookupByExternalData' argument 2 names different: declaration 'dataSize' definition 'seqDataSize'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.h:35:57: note: Function 'initLookupByExternalData' argument 2 names different: declaration 'dataSize' definition 'seqDataSize'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.cpp:65:69: note: Function 'initLookupByExternalData' argument 2 names different: declaration 'dataSize' definition 'seqDataSize'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.cpp:32:49: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.cpp:72:57: style: Parameter 'seqData' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.cpp:72:74: style: Parameter 'seqOffsets' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/UngappedAlignment.cpp:11:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PROFILE_AA_SIZE [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/UngappedAlignment.cpp:36:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PROFILE_AA_SIZE [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/UngappedAlignment.cpp:260:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable compareDiagonalSeqByLen [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/UngappedAlignment.cpp:388:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_HMM_PROFILE [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/UngappedAlignment.cpp:422:91: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PROFILE_AA_SIZE [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:267:76: warning: The address of variable 'exactKmer' might be accessed at non-zero index. [objectIndex]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:252:21: note: Address of variable taken here.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:267:76: note: The address of variable 'exactKmer' might be accessed at non-zero index.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:361:41: style:inconclusive: Technically the member function 'QueryMatcher::getResult < UNGAPPED_DIAGONAL_SCORE >' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:223:32: note: Technically the member function 'QueryMatcher::getResult < UNGAPPED_DIAGONAL_SCORE >' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:361:41: note: Technically the member function 'QueryMatcher::getResult < UNGAPPED_DIAGONAL_SCORE >' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:361:41: style:inconclusive: Technically the member function 'QueryMatcher::getResult < KMER_SCORE >' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:223:32: note: Technically the member function 'QueryMatcher::getResult < KMER_SCORE >' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:361:41: note: Technically the member function 'QueryMatcher::getResult < KMER_SCORE >' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:361:41: style:inconclusive: Technically the member function 'QueryMatcher::getResult < 0 >' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:223:32: note: Technically the member function 'QueryMatcher::getResult < 0 >' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:361:41: note: Technically the member function 'QueryMatcher::getResult < 0 >' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:361:41: style:inconclusive: Technically the member function 'QueryMatcher::getResult < 1 >' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:223:32: note: Technically the member function 'QueryMatcher::getResult < 1 >' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:361:41: note: Technically the member function 'QueryMatcher::getResult < 1 >' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:345:22: style:inconclusive: Technically the member function 'QueryMatcher::getDoubleDiagonalMatches' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:230:12: note: Technically the member function 'QueryMatcher::getDoubleDiagonalMatches' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:345:22: note: Technically the member function 'QueryMatcher::getDoubleDiagonalMatches' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:495:22: style:inconclusive: Technically the member function 'QueryMatcher::radixSortByScoreSize' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:232:12: note: Technically the member function 'QueryMatcher::radixSortByScoreSize' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:495:22: note: Technically the member function 'QueryMatcher::radixSortByScoreSize' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:38:11: warning: Class 'QueryMatcher' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:38:11: warning: Class 'QueryMatcher' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:46:21: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:49:28: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/UngappedAlignment.cpp:6:20: warning: Member variable 'UngappedAlignment::queryLen' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/UngappedAlignment.cpp:30:24: performance:inconclusive: Technically the member function 'UngappedAlignment::scalarDiagonalScoring' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/UngappedAlignment.h:76:9: note: Technically the member function 'UngappedAlignment::scalarDiagonalScoring' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/UngappedAlignment.cpp:30:24: note: Technically the member function 'UngappedAlignment::scalarDiagonalScoring' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/UngappedAlignment.cpp:364:35: performance:inconclusive: Technically the member function 'UngappedAlignment::distanceFromDiagonal' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/UngappedAlignment.h:91:20: note: Technically the member function 'UngappedAlignment::distanceFromDiagonal' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/UngappedAlignment.cpp:364:35: note: Technically the member function 'UngappedAlignment::distanceFromDiagonal' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/UngappedAlignment.cpp:9:5: warning: Class 'UngappedAlignment' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/UngappedAlignment.cpp:9:5: warning: Class 'UngappedAlignment' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/UngappedAlignment.cpp:11:22: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/UngappedAlignment.cpp:13:25: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/UngappedAlignment.cpp:251:36: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/UngappedAlignment.cpp:255:36: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:26:33: style:inconclusive: Function 'QueryMatcher' argument 12 names different: declaration 'diagonalScoringMode' definition 'diagonalScoring'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:58:99: note: Function 'QueryMatcher' argument 12 names different: declaration 'diagonalScoringMode' definition 'diagonalScoring'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:26:33: note: Function 'QueryMatcher' argument 12 names different: declaration 'diagonalScoringMode' definition 'diagonalScoring'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:470:91: style:inconclusive: Function 'mergeElements' argument 3 names different: declaration 'keepHitsWithCounts' definition 'keepScoredHits'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:261:81: note: Function 'mergeElements' argument 3 names different: declaration 'keepHitsWithCounts' definition 'keepScoredHits'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:470:91: note: Function 'mergeElements' argument 3 names different: declaration 'keepHitsWithCounts' definition 'keepScoredHits'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:365:70: style:inconclusive: Function 'getResult < UNGAPPED_DIAGONAL_SCORE >' argument 5 names different: declaration 'ungappedAlignment' definition 'align'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:227:61: note: Function 'getResult < UNGAPPED_DIAGONAL_SCORE >' argument 5 names different: declaration 'ungappedAlignment' definition 'align'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:365:70: note: Function 'getResult < UNGAPPED_DIAGONAL_SCORE >' argument 5 names different: declaration 'ungappedAlignment' definition 'align'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:366:61: style:inconclusive: Function 'getResult < UNGAPPED_DIAGONAL_SCORE >' argument 6 names different: declaration 'rescale' definition 'rescaleScore'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:228:52: note: Function 'getResult < UNGAPPED_DIAGONAL_SCORE >' argument 6 names different: declaration 'rescale' definition 'rescaleScore'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:366:61: note: Function 'getResult < UNGAPPED_DIAGONAL_SCORE >' argument 6 names different: declaration 'rescale' definition 'rescaleScore'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:365:70: style:inconclusive: Function 'getResult < KMER_SCORE >' argument 5 names different: declaration 'ungappedAlignment' definition 'align'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:227:61: note: Function 'getResult < KMER_SCORE >' argument 5 names different: declaration 'ungappedAlignment' definition 'align'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:365:70: note: Function 'getResult < KMER_SCORE >' argument 5 names different: declaration 'ungappedAlignment' definition 'align'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:366:61: style:inconclusive: Function 'getResult < KMER_SCORE >' argument 6 names different: declaration 'rescale' definition 'rescaleScore'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:228:52: note: Function 'getResult < KMER_SCORE >' argument 6 names different: declaration 'rescale' definition 'rescaleScore'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:366:61: note: Function 'getResult < KMER_SCORE >' argument 6 names different: declaration 'rescale' definition 'rescaleScore'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:365:70: style:inconclusive: Function 'getResult < 0 >' argument 5 names different: declaration 'ungappedAlignment' definition 'align'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:227:61: note: Function 'getResult < 0 >' argument 5 names different: declaration 'ungappedAlignment' definition 'align'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:365:70: note: Function 'getResult < 0 >' argument 5 names different: declaration 'ungappedAlignment' definition 'align'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:366:61: style:inconclusive: Function 'getResult < 0 >' argument 6 names different: declaration 'rescale' definition 'rescaleScore'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:228:52: note: Function 'getResult < 0 >' argument 6 names different: declaration 'rescale' definition 'rescaleScore'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:366:61: note: Function 'getResult < 0 >' argument 6 names different: declaration 'rescale' definition 'rescaleScore'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:365:70: style:inconclusive: Function 'getResult < 1 >' argument 5 names different: declaration 'ungappedAlignment' definition 'align'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:227:61: note: Function 'getResult < 1 >' argument 5 names different: declaration 'ungappedAlignment' definition 'align'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:365:70: note: Function 'getResult < 1 >' argument 5 names different: declaration 'ungappedAlignment' definition 'align'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:366:61: style:inconclusive: Function 'getResult < 1 >' argument 6 names different: declaration 'rescale' definition 'rescaleScore'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:228:52: note: Function 'getResult < 1 >' argument 6 names different: declaration 'rescale' definition 'rescaleScore'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:366:61: note: Function 'getResult < 1 >' argument 6 names different: declaration 'rescale' definition 'rescaleScore'.
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:213:50: style: Parameter 'compositionBias' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:502:21: style: Variable 'ptr_prev' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/UngappedAlignment.cpp:417:106: style: Parameter 'dbSeq' can be declared as reference to const [constParameterReference]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/UngappedAlignment.cpp:433:74: style: Parameter 'result' can be declared as reference to const [constParameterReference]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/UngappedAlignment.cpp:386:47: style: Parameter 'biasCorrection' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/ungappedprefilter.cpp:26:97: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_PREFILTER_RES [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:101:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:111:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFO [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:157:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ERROR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:164:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFO [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:207:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFO [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:293:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WARNING [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:344:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ERROR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:394:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ERROR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:430:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFO [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:458:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFO [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:491:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ERROR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:560:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FLT_MAX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:596:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ERROR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.h:26:5: warning:inconclusive: Member variable 'TaxonNode::id' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.h:26:5: warning:inconclusive: Member variable 'TaxonNode::taxId' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.h:26:5: warning:inconclusive: Member variable 'TaxonNode::parentTaxId' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.h:26:5: warning:inconclusive: Member variable 'TaxonNode::rankIdx' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.h:26:5: warning:inconclusive: Member variable 'TaxonNode::nameIdx' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:367:27: style:inconclusive: Technically the member function 'NcbiTaxonomy::taxLineage' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.h:105:17: note: Technically the member function 'NcbiTaxonomy::taxLineage' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:367:27: note: Technically the member function 'NcbiTaxonomy::taxLineage' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:259:20: style:inconclusive: Technically the member function 'NcbiTaxonomy::IsAncestor' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.h:111:10: note: Technically the member function 'NcbiTaxonomy::IsAncestor' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:259:20: note: Technically the member function 'NcbiTaxonomy::IsAncestor' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:577:33: style:inconclusive: Technically the member function 'NcbiTaxonomy::weightedMajorityLCA' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.h:117:23: note: Technically the member function 'NcbiTaxonomy::weightedMajorityLCA' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:577:33: note: Technically the member function 'NcbiTaxonomy::weightedMajorityLCA' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:43:5: warning: Class 'NcbiTaxonomy' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:43:5: warning: Class 'NcbiTaxonomy' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:490:26: warning: If resource allocation fails, then there is a possible null pointer dereference: handle [nullPointerOutOfResources]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:488:29: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:488:29: note: Assignment 'handle=fopen(binFile.c_str(),"r")', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:490:26: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:722:12: warning: If memory allocation fails, then there is a possible null pointer dereference: p [nullPointerOutOfMemory]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:720:31: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:720:17: note: Assignment 'mem=(char*)malloc(memSize)', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:721:13: note: p is assigned 'mem' here.
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:722:12: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:749:21: warning: If memory allocation fails, then there is a possible null pointer dereference: (int*)p [nullPointerOutOfMemory]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:494:33: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:494:22: note: Assignment 'data=(char*)mmap(NULL,sb.st_size,PROT_READ,MAP_PRIVATE,fileno(handle),0)', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:500:53: note: Calling function 'unserialize', 1st argument 'data' value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:748:21: note: Assignment 'p=mem', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:748:19: note: p is assigned 'mem' here.
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:748:19: note: p is assigned 'mem' here.
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:749:21: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:723:7: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:720:31: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:720:17: note: Assignment 'mem=(char*)malloc(memSize)', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:721:13: note: p is assigned 'mem' here.
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:723:7: note: Null pointer addition
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:750:7: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:494:33: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:494:22: note: Assignment 'data=(char*)mmap(NULL,sb.st_size,PROT_READ,MAP_PRIVATE,fileno(handle),0)', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:500:53: note: Calling function 'unserialize', 1st argument 'data' value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:748:21: note: Assignment 'p=mem', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:750:7: note: Null pointer addition
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:494:22: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:720:17: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:749:21: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:754:25: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:756:22: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:758:29: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:760:14: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:762:14: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:764:14: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:766:14: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:772:12: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:188:80: style:inconclusive: Function 'elh' argument 2 names different: declaration 'node' definition 'taxId'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.h:130:68: note: Function 'elh' argument 2 names different: declaration 'node' definition 'taxId'.
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:188:80: note: Function 'elh' argument 2 names different: declaration 'node' definition 'taxId'.
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:392:32: style:inconclusive: Function 'nodeId' argument 1 names different: declaration 'taxId' definition 'taxonId'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.h:132:22: note: Function 'nodeId' argument 1 names different: declaration 'taxId' definition 'taxonId'.
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:392:32: note: Function 'nodeId' argument 1 names different: declaration 'taxId' definition 'taxonId'.
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:400:37: style:inconclusive: Function 'nodeExists' argument 1 names different: declaration 'taxId' definition 'taxonId'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.h:113:27: note: Function 'nodeExists' argument 1 names different: declaration 'taxId' definition 'taxonId'.
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:400:37: note: Function 'nodeExists' argument 1 names different: declaration 'taxId' definition 'taxonId'.
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:704:70: style:inconclusive: Function 'serialize' argument 1 names different: declaration 'taxonomy' definition 't'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.h:121:67: note: Function 'serialize' argument 1 names different: declaration 'taxonomy' definition 't'.
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:704:70: note: Function 'serialize' argument 1 names different: declaration 'taxonomy' definition 't'.
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:747:47: style:inconclusive: Function 'unserialize' argument 1 names different: declaration 'data' definition 'mem'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.h:122:44: note: Function 'unserialize' argument 1 names different: declaration 'data' definition 'mem'.
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:747:47: note: Function 'unserialize' argument 1 names different: declaration 'data' definition 'mem'.
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:635:104: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/MappingReader.h:20:79: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SequentialScan [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/addtaxonomy.cpp:21:111: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_DATA [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/aggregatetax.cpp:23:119: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/MappingReader.h:20:9: warning: Class 'MappingReader' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/MappingReader.h:20:9: warning: Class 'MappingReader' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/MappingReader.h:18:5: style: Class 'MappingReader' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/MappingReader.h:13:16: warning: If memory allocation fails, then there is a possible null pointer dereference: data [nullPointerOutOfMemory]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/MappingReader.h:12:35: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/MappingReader.h:12:22: note: Assignment 'data=(char*)malloc(serialized_size)', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/MappingReader.h:13:16: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/MappingReader.h:27:31: warning: Possible null pointer dereference: file [nullPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/MappingReader.h:23:20: note: Assignment 'file=NULL', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/MappingReader.h:27:31: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/MappingReader.h:28:27: warning: Possible null pointer dereference: file [nullPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/MappingReader.h:23:20: note: Assignment 'file=NULL', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/MappingReader.h:28:27: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/MappingReader.h:29:13: warning: Possible null pointer dereference: file [nullPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/MappingReader.h:23:20: note: Assignment 'file=NULL', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/MappingReader.h:29:13: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/MappingReader.h:14:21: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/MappingReader.h:12:35: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/MappingReader.h:12:22: note: Assignment 'data=(char*)malloc(serialized_size)', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/MappingReader.h:14:21: note: Null pointer addition
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/MappingReader.h:12:22: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/MappingReader.h:27:22: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/MappingReader.h:46:30: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/addtaxonomy.cpp:86:23: style: Variable 'nextData' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/MappingReader.h:83:15: style: Variable 'found' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/createbintaxmapping.cpp:13:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ERROR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/createbintaxonomy.cpp:13:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ERROR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/createbintaxonomy.cpp:16:63: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: handle [nullPointerOutOfResources]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/createbintaxonomy.cpp:11:25: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/createbintaxonomy.cpp:11:25: note: Assignment 'handle=fopen(par.db4.c_str(),"w")', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/createbintaxonomy.cpp:16:63: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/createbintaxonomy.cpp:17:12: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: handle [nullPointerOutOfResources]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/createbintaxonomy.cpp:11:25: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/createbintaxonomy.cpp:11:25: note: Assignment 'handle=fopen(par.db4.c_str(),"w")', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/createbintaxonomy.cpp:17:12: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/createbintaxmapping.cpp:20:9: error: Resource leak: handle [resourceLeak]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/createtaxdb.cpp:16:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFO [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/TaxonomyExpression.h:67:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TE_CLOSURE1 [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/filtertaxdb.cpp:19:111: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_DATA [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/filtertaxseqdb.cpp:22:111: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_DATA [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/TaxonomyExpression.h:70:9: warning: Class 'TaxonomyExpression' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/TaxonomyExpression.h:70:9: warning: Class 'TaxonomyExpression' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/TaxonomyExpression.h:65:24: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/TaxonomyExpression.h:68:23: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/TaxonomyExpression.h:99:25: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/filtertaxdb.cpp:48:27: style: Variable 'nextData' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/lca.cpp:20:111: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_DATA [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/taxonomyreport.cpp:133:83: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_HMM_PROFILE [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/lca.cpp:164:35: style: Local variable 'result' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/lca.cpp:87:21: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/lca.cpp:164:35: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/taxonomyreport.cpp:43:13: warning: %i in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/taxonomyreport.cpp:43:13: warning: %i in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/taxonomyreport.cpp:53:9: warning: %i in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/taxonomyreport.cpp:53:9: warning: %i in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/taxonomyreport.cpp:102:13: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/taxonomyreport.cpp:111:9: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestAlignment.cpp:32:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestAlignmentPerformance.cpp:60:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestAlignmentPerformance.cpp:112:21: style: The comparison 'mode == 0' is always true. [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestAlignmentPerformance.cpp:85:16: note: 'mode' is assigned value '0' here.
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestAlignmentPerformance.cpp:112:21: note: The comparison 'mode == 0' is always true.
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestAlignmentTraceback.cpp:67:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestAlignmentTraceback.cpp:143:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestAlignment.cpp:151:15: style: Variable 'seqId' is reassigned a value before the old one has been used. [redundantAssignment]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestAlignment.cpp:147:11: note: seqId is assigned
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestAlignment.cpp:151:15: note: seqId is overwritten
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestAlignment.cpp:169:12: style: Redundant initialization for 'dbSize'. The initialized value is overwritten before it is read. [redundantInitialization]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestAlignment.cpp:168:19: note: dbSize is initialized
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestAlignment.cpp:169:12: note: dbSize is overwritten
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestAlignmentTraceback.cpp:188:45: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestAlignmentTraceback.cpp:37:75: style: Parameter 'subMat' can be declared as reference to const [constParameterReference]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestBacktraceTranslator.cpp:145:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFO [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestBestAlphabet.cpp:76:98: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_DATA [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestBestAlphabet.cpp:96:31: style: Array index 'pos' is used before limits check. [arrayIndexThenCheck]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestBestAlphabet.cpp:102:56: warning: %i in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestBestAlphabet.cpp:20:68: style: Parameter 'map2reduced' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestBestAlphabet.cpp:20:88: style: Parameter 'probsAA' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestAlp.cpp:134:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestCompositionBias.cpp:35:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestCompositionBias.cpp:57:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestCounting.cpp:30:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestDBReader.cpp:18:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestDBReaderIndexSerialization.cpp:7:97: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestDBReaderZstd.cpp:112:106: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_NUCLEOTIDES [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestDBReaderZstd.cpp:128:22: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestAlp.cpp:127:13: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestAlp.cpp:58:14: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestAlp.cpp:127:13: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestDiagonalScoring.cpp:28:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestDiagonalScoringPerformance.cpp:15:1: error: There is an unknown macro here somewhere. Configuration is required. If KSEQ_INIT is a macro then please configure it. [unknownMacro]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestExtendedSubstitutionMatrix.cpp:38:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestExtendedSubstitutionMatrix.cpp:32:24: style: Variable 'seq_ptr' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestExtendedSubstitutionMatrix.cpp:32:17: style: Variable 'seq_ptr' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGenerator.cpp:25:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorPerf.cpp:21:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorPerf.cpp:39:22: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorPerf.cpp:61:10: style: Variable 'testKmer' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorPerf.cpp:32:25: style: Variable 'testSeq' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorPerf.cpp:61:19: style: Variable 'testKmer' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorPerf.cpp:61:10: style: Variable 'testKmer' is allocated memory that is never used. [unusedAllocatedMemory]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGenerator.cpp:71:25: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGenerator.cpp:50:9: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGenerator.cpp:71:25: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGenerator.cpp:74:25: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGenerator.cpp:50:9: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGenerator.cpp:74:25: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorProfile.cpp:28:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerNucl.cpp:30:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorProfile.cpp:45:11: warning: If resource allocation fails, then there is a possible null pointer dereference: f [nullPointerOutOfResources]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorProfile.cpp:44:20: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorProfile.cpp:44:20: note: Assignment 'f=fopen(argv[1],"rb")', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorProfile.cpp:45:11: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorProfile.cpp:46:24: warning: If resource allocation fails, then there is a possible null pointer dereference: f [nullPointerOutOfResources]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorProfile.cpp:44:20: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorProfile.cpp:44:20: note: Assignment 'f=fopen(argv[1],"rb")', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorProfile.cpp:46:24: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorProfile.cpp:47:11: warning: If resource allocation fails, then there is a possible null pointer dereference: f [nullPointerOutOfResources]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorProfile.cpp:44:20: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorProfile.cpp:44:20: note: Assignment 'f=fopen(argv[1],"rb")', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorProfile.cpp:47:11: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorProfile.cpp:50:11: warning: If memory allocation fails, then there is a possible null pointer dereference: string [nullPointerOutOfMemory]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorProfile.cpp:49:35: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorProfile.cpp:49:20: note: Assignment 'string=(char*)malloc(fsize+1)', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorProfile.cpp:50:11: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorProfile.cpp:50:29: warning: If resource allocation fails, then there is a possible null pointer dereference: f [nullPointerOutOfResources]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorProfile.cpp:44:20: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorProfile.cpp:44:20: note: Assignment 'f=fopen(argv[1],"rb")', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorProfile.cpp:50:29: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorProfile.cpp:51:12: warning: If resource allocation fails, then there is a possible null pointer dereference: f [nullPointerOutOfResources]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorProfile.cpp:44:20: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorProfile.cpp:44:20: note: Assignment 'f=fopen(argv[1],"rb")', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorProfile.cpp:51:12: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorProfile.cpp:53:5: warning: If memory allocation fails, then there is a possible null pointer dereference: string [nullPointerOutOfMemory]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorProfile.cpp:49:35: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorProfile.cpp:49:20: note: Assignment 'string=(char*)malloc(fsize+1)', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorProfile.cpp:53:5: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorProfile.cpp:49:20: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorProfile.cpp:55:29: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorProfile.cpp:38:25: style: Variable 'testSeq' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerGeneratorProfile.cpp:42:10: style: Unused variable: buffer [unusedVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerNucl.cpp:13:10: style: Variable 'nuclCode' can be declared as const array [constVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKmerScore.cpp:19:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKwayMerge.cpp:138:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKwayMerge.cpp:16:5: warning:inconclusive: Member variable 'KmerEntry::seqId' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKwayMerge.cpp:16:5: warning:inconclusive: Member variable 'KmerEntry::diagonal' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKwayMerge.cpp:73:5: warning:inconclusive: Member variable 'KmerPosition::kmer' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKwayMerge.cpp:73:5: warning:inconclusive: Member variable 'KmerPosition::id' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKwayMerge.cpp:73:5: warning:inconclusive: Member variable 'KmerPosition::pos' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKwayMerge.cpp:73:5: warning:inconclusive: Member variable 'KmerPosition::file' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKwayMerge.cpp:81:10: style:inconclusive: Technically the member function 'CompareResultBySeqId::operator()' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKwayMerge.cpp:81:37: style: Parameter 'first' can be declared as reference to const [constParameterReference]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKwayMerge.cpp:81:59: style: Parameter 'second' can be declared as reference to const [constParameterReference]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKwayMerge.cpp:121:56: style: Parameter 'entrySizes' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKsw2.cpp:80:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAND_MAX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKsw2.cpp:118:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKsw2.cpp:201:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKsw2.cpp:392:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestMerge.cpp:14:12: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: outfile [nullPointerOutOfResources]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestMerge.cpp:12:26: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestMerge.cpp:12:26: note: Assignment 'outfile=fopen("/tmp/test_out","wb")', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestMerge.cpp:14:12: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKsw2.cpp:139:9: warning: Struct 'alignment_t' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKsw2.cpp:139:9: warning: Struct 'alignment_t' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKsw2.cpp:139:9: warning: Struct 'alignment_t' does not have a destructor which is recommended since it has dynamic memory/resource allocation(s). [noDestructor]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKsw2.cpp:137:5: style: Struct 'alignment_t' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKsw2.cpp:135:12: style: Class 'alignment_t' is unsafe, 'alignment_t::cigar' can leak by wrong usage. [unsafeClassCanLeak]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKsw2.cpp:50:11: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKsw2.cpp:77:19: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKsw2.cpp:335:37: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKsw2.cpp:347:56: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKsw2.cpp:259:13: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKsw2.cpp:159:12: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKsw2.cpp:259:13: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestMultipleAlignment.cpp:26:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKsw2.cpp:113:22: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKsw2.cpp:316:10: style: Variable 'p.pa' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKsw2.cpp:351:21: style: Unused variable: queryAln [unusedVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKsw2.cpp:352:21: style: Unused variable: targetAln [unusedVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestKsw2.cpp:353:21: style: Unused variable: middleAln [unusedVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestOrf.cpp:25:73: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FRAME_1 [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestOrf.cpp:44:73: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FRAME_2 [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestOrf.cpp:62:73: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FRAME_3 [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestOrf.cpp:78:82: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FRAME_1 [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestOrf.cpp:97:82: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FRAME_3 [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestOrf.cpp:113:82: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FRAME_2 [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestMultipleAlignment.cpp:88:43: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestOrf.cpp:26:103: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestOrf.cpp:45:103: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestOrf.cpp:63:103: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestOrf.cpp:79:103: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestOrf.cpp:98:103: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestOrf.cpp:114:103: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestPSSMPrune.cpp:24:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestPSSMPrune.cpp:62:30: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestProfileAlignment.cpp:30:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestProfileAlignment.cpp:778:97: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestProfileAlignment.cpp:859:15: error: Memory is allocated but not initialized: tinySubMat [uninitdata]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestProfileAlignment.cpp:42:25: style: Variable 'profile' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestProfileAlignment.cpp:42:17: style: Variable 'profile' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestReduceMatrix.cpp:26:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestScoreMatrixSerialization.cpp:16:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFO [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestSequenceIndex.cpp:22:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestSequenceIndex.cpp:48:19: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestTanTan.cpp:21:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestTanTan.cpp:47:17: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestTanTan.cpp:46:16: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestTanTan.cpp:47:17: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestTaxExpr.cpp:17:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestTaxonomy.cpp:15:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFO [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestTinyExpr.cpp:17:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestTranslate.cpp:9:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CANONICAL [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestTranslate.cpp:14:34: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:1919:32: style:inconclusive: Boolean expression 'isStartVar' is used in bitwise operation. [bitwiseOnBoolean]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:1921:30: style:inconclusive: Boolean expression 'isEndVar' is used in bitwise operation. [bitwiseOnBoolean]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:1923:33: style:inconclusive: Boolean expression 'isMiddleVar' is used in bitwise operation. [bitwiseOnBoolean]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:1927:32: style:inconclusive: Boolean expression 'isStartVar' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:1927:46: style:inconclusive: Boolean expression 'isEndVar' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestUtil.cpp:37:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/alignall.cpp:21:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALIGNMENT_MODE_UNGAPPED [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:34:13: warning: Member variable 'Parameters::globalAlignment' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:34:13: warning: Member variable 'Parameters::extendedDbtype' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:34:13: warning: Member variable 'Parameters::recoverDeleted' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2169:18: style:inconclusive: Technically the member function 'Parameters::printParameters' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.h:728:10: note: Technically the member function 'Parameters::printParameters' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2169:18: note: Technically the member function 'Parameters::printParameters' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2770:43: performance:inconclusive: Technically the member function 'Parameters::removeParameter' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.h:733:35: note: Technically the member function 'Parameters::removeParameter' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2770:43: note: Technically the member function 'Parameters::removeParameter' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2604:43: performance:inconclusive: Technically the member function 'Parameters::combineList' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.h:1182:35: note: Technically the member function 'Parameters::combineList' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2604:43: note: Technically the member function 'Parameters::combineList' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/util/alignall.cpp:90:40: style: Local variable 'key' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/alignall.cpp:84:36: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/alignall.cpp:90:40: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2681:25: style:inconclusive: Technically the member function 'Parameters::createParameterString' can be const. [functionConst]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.h:1187:17: note: Technically the member function 'Parameters::createParameterString' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2681:25: note: Technically the member function 'Parameters::createParameterString' can be const.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2780:18: performance:inconclusive: Technically the member function 'Parameters::overrideParameterDescription' can be static (but you may consider moving to unnamed namespace). [functionStatic]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.h:1189:10: note: Technically the member function 'Parameters::overrideParameterDescription' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2780:18: note: Technically the member function 'Parameters::overrideParameterDescription' can be static (but you may consider moving to unnamed namespace).
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:38:117: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:39:114: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:40:181: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:41:123: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:42:117: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:43:140: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:44:132: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:45:159: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:46:181: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:47:189: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:48:167: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:49:212: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:50:187: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:51:153: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:52:188: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:53:165: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:54:166: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:55:225: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:56:263: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:57:166: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:58:146: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:59:187: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:60:181: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:61:201: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:63:175: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:64:147: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:65:197: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:66:165: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:67:174: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:68:163: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:70:251: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:71:311: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:72:123: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:73:155: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:74:353: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:75:150: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:76:179: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:77:173: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:78:169: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:79:167: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:80:178: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:81:149: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:82:144: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:83:170: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:84:168: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:85:205: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:86:152: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:87:124: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:88:140: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:92:180: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:94:211: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:95:156: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:96:165: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:97:248: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:99:194: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:100:188: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:102:126: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:104:316: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:105:441: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:106:138: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:108:278: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:109:241: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:110:159: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:111:182: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:113:307: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:114:136: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:115:148: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:116:118: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:118:294: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:120:230: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:121:167: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:123:151: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:124:179: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:125:133: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:126:205: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:127:206: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:128:320: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:129:190: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:130:226: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:131:191: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:133:139: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:134:162: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:135:129: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:136:162: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:138:123: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:139:117: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:141:166: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:142:212: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:143:149: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:144:160: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:147:171: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:149:128: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:150:241: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:151:170: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:152:169: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:153:125: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:154:150: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:155:182: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:156:155: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:157:144: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:158:170: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:160:167: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:161:193: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:163:158: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:164:120: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:165:152: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:166:155: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:167:217: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:168:221: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:170:166: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:171:250: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:172:157: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:173:160: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:174:135: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:176:167: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:178:152: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:179:155: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:180:191: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:181:177: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:182:167: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:183:237: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:184:194: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:185:194: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:186:221: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:187:121: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:188:153: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:190:216: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:191:197: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:192:299: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:193:159: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:195:213: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:196:152: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:197:138: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:198:209: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:199:120: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:200:187: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:201:181: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:203:185: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:205:152: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:206:202: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:207:179: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:209:165: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:211:157: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:213:676: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:215:147: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:217:155: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:218:155: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:219:150: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:221:106: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:222:169: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:223:184: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:224:212: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:225:157: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:226:179: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:227:181: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:228:172: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:229:137: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:230:260: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:231:163: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:232:203: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:233:148: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:234:181: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:236:191: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:237:127: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:238:159: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:239:236: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:241:199: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:242:235: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:244:156: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:245:144: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:247:445: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:249:206: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:251:117: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:252:94: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:254:136: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:256:159: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:257:176: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:259:128: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:261:121: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:263:134: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:265:161: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:266:179: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:268:159: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:270:146: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:271:166: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:273:119: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:274:145: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:275:159: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:276:194: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:278:175: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:279:179: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:281:219: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:282:181: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:284:137: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:286:243: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:287:188: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:288:194: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:289:198: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:291:212: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:292:208: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:294:152: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:295:168: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:297:151: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:298:166: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:299:152: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:300:152: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:302:188: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:303:182: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:305:71: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:306:85: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:1500:45: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:1503:45: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:1506:45: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:1509:45: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:1512:60: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:1515:45: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:1518:41: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:1521:81: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:1524:73: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:1527:75: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:1530:74: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:1609:37: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:1682:31: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:1697:31: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:1719:35: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:1735:31: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:1746:31: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:1757:31: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:1763:27: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:1773:31: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:1788:31: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:1802:31: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:1811:48: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:1816:39: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2207:21: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2209:21: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2211:40: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2213:55: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2220:61: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2222:53: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2224:55: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2226:54: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2228:54: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2230:21: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2232:21: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2234:21: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2236:21: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2696:21: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2699:21: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2702:40: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2705:21: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2708:21: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2710:55: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2724:36: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2734:26: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2742:75: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2751:53: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2754:55: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2757:54: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2760:54: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/util/alignbykmer.cpp:22:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFO [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:1911:10: style: The scope of the variable 'isVar' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2681:84: style:inconclusive: Function 'createParameterString' argument 1 names different: declaration 'vector' definition 'par'. [funcArgNamesDifferent]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.h:1187:76: note: Function 'createParameterString' argument 1 names different: declaration 'vector' definition 'par'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2681:84: note: Function 'createParameterString' argument 1 names different: declaration 'vector' definition 'par'.
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2724:26: style: Variable 'value' can be declared as reference to const [constVariableReference]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/ByteParser.h:21:28: performance: Ineffective call of function 'substr' because it returns a copy of the object. Use operator= instead. [uselessCallsSubstr]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2192:18: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:1569:39: portability: Shifting signed 32-bit value by 31 bits is implementation-defined behaviour [shiftTooManyBitsSigned]
metaeuk-7-bba0d80/lib/mmseqs/src/util/alignbykmer.cpp:99:9: warning:inconclusive: Member variable 'KmerPos::ij' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/alignbykmer.cpp:99:9: warning:inconclusive: Member variable 'KmerPos::i' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/alignbykmer.cpp:99:9: warning:inconclusive: Member variable 'KmerPos::j' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/alignbykmer.cpp:130:9: warning:inconclusive: Member variable 'Stretche::i_start' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/alignbykmer.cpp:130:9: warning:inconclusive: Member variable 'Stretche::i_end' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/alignbykmer.cpp:130:9: warning:inconclusive: Member variable 'Stretche::j_start' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/alignbykmer.cpp:130:9: warning:inconclusive: Member variable 'Stretche::j_end' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/alignbykmer.cpp:130:9: warning:inconclusive: Member variable 'Stretche::kmerCnt' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/alignbykmer.cpp:147:9: warning:inconclusive: Member variable 'DpMatrixRow::prevPotentialId' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/alignbykmer.cpp:147:9: warning:inconclusive: Member variable 'DpMatrixRow::pathScore' is not initialized in the constructor. [uninitMemberVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/appenddbtoindex.cpp:9:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PARSE_VARIADIC [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/alignbykmer.cpp:245:36: style: The scope of the variable 'region_max_kmer_cnt' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/src/util/alignbykmer.cpp:301:33: style: Local variable 'id' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/alignbykmer.cpp:192:25: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/alignbykmer.cpp:301:33: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/util/alignbykmer.cpp:359:34: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/alignbykmer.cpp:161:17: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/alignbykmer.cpp:359:34: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/util/alignbykmer.cpp:373:34: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/alignbykmer.cpp:161:17: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/alignbykmer.cpp:373:34: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/util/alignbykmer.cpp:396:34: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/alignbykmer.cpp:161:17: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/alignbykmer.cpp:396:34: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/util/alignbykmer.cpp:407:34: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/alignbykmer.cpp:161:17: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/alignbykmer.cpp:407:34: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/util/alignbykmer.cpp:428:37: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/alignbykmer.cpp:161:17: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/alignbykmer.cpp:428:37: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/util/appenddbtoindex.cpp:115:19: style: Local variable 'data' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/appenddbtoindex.cpp:91:15: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/appenddbtoindex.cpp:115:19: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/util/appenddbtoindex.cpp:115:19: style: Variable 'data' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/util/clusthash.cpp:18:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CLUST_HASH_DEFAULT_ALPH_SIZE [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/apply.cpp:32:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_CLOEXEC [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/apply.cpp:57:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_CLOEXEC [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/apply.cpp:139:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PIPE_BUF [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/apply.cpp:243:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIG_IGN [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/apply.cpp:283:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PARSE_REST [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/apply.cpp:85:65: style: Condition 'attrs_allocated' is always false [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/src/util/apply.cpp:70:27: note: Assignment 'attrs_allocated=0', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/util/apply.cpp:85:65: note: Condition 'attrs_allocated' is always false
metaeuk-7-bba0d80/lib/mmseqs/src/util/apply.cpp:106:9: style: Condition 'attrs_allocated' is always false [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/src/util/apply.cpp:70:27: note: Assignment 'attrs_allocated=0', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/util/apply.cpp:77:9: note: Assuming condition is false
metaeuk-7-bba0d80/lib/mmseqs/src/util/apply.cpp:106:9: note: Condition 'attrs_allocated' is always false
metaeuk-7-bba0d80/lib/mmseqs/src/util/apply.cpp:206:35: style: Condition 'bytes_read==0' is always true [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/src/util/apply.cpp:200:35: note: Assuming that condition 'bytes_read<0' is not redundant
metaeuk-7-bba0d80/lib/mmseqs/src/util/apply.cpp:198:28: note: Assuming that condition 'bytes_read>0' is not redundant
metaeuk-7-bba0d80/lib/mmseqs/src/util/apply.cpp:206:35: note: Condition 'bytes_read==0' is always true
metaeuk-7-bba0d80/lib/mmseqs/src/util/apply.cpp:125:5: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
metaeuk-7-bba0d80/lib/mmseqs/src/util/apply.cpp:263:5: warning: If memory allocation fails, then there is a possible null pointer dereference: local_environ [nullPointerOutOfMemory]
metaeuk-7-bba0d80/lib/mmseqs/src/util/apply.cpp:261:42: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/util/apply.cpp:261:28: note: Assignment 'local_environ=(char**)malloc(sizeof(char*)*(env_size+2))', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/util/apply.cpp:263:5: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/util/apply.cpp:269:5: warning: If memory allocation fails, then there is a possible null pointer dereference: local_environ [nullPointerOutOfMemory]
metaeuk-7-bba0d80/lib/mmseqs/src/util/apply.cpp:261:42: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/util/apply.cpp:261:28: note: Assignment 'local_environ=(char**)malloc(sizeof(char*)*(env_size+2))', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/util/apply.cpp:269:5: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/util/apply.cpp:261:28: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/util/apply.cpp:263:26: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/util/compress.cpp:14:111: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/apply.cpp:121:26: style: Parameter 'data' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/util/compress.cpp:26:43: portability: Shifting signed 32-bit value by 31 bits is implementation-defined behaviour [shiftTooManyBitsSigned]
metaeuk-7-bba0d80/lib/mmseqs/src/util/compress.cpp:26:65: portability: Shifting signed 32-bit value by 31 bits is implementation-defined behaviour [shiftTooManyBitsSigned]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convert2fasta.cpp:22:97: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_DATA [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertca3m.cpp:18:144: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertkb.cpp:17:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertkb.cpp:31:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertkb.cpp:72:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PARSE_VARIADIC [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertalignments.cpp:103:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SequentialScan [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertalignments.cpp:127:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SequentialScan [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertalignments.cpp:152:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FORMAT_ALIGNMENT_BLAST_TAB_WITH_HEADERS [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertkb.cpp:135:64: style: Local variable 'it' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertkb.cpp:104:51: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertkb.cpp:135:64: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertkb.cpp:45:46: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertmsa.cpp:23:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ERROR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertprofiledb.cpp:93:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ERROR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertprofiledb.cpp:140:100: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertprofiledb.cpp:177:19: style: Local variable 'data' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertprofiledb.cpp:134:17: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertprofiledb.cpp:177:19: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertprofiledb.cpp:38:11: style: Variable 'seqStartPos' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/util/countkmer.cpp:23:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEQUENCES [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertalignments.cpp:390:29: warning: snprintf format string requires 1 parameter but 2 are given. [wrongPrintfScanfArgNum]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertalignments.cpp:461:41: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertalignments.cpp:461:41: warning: %d in format string (no. 5) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertalignments.cpp:461:41: warning: %d in format string (no. 6) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertalignments.cpp:702:37: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertalignments.cpp:702:37: warning: %d in format string (no. 5) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertalignments.cpp:702:37: warning: %d in format string (no. 6) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertalignments.cpp:725:37: warning: %d in format string (no. 5) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertalignments.cpp:760:33: warning: %d in format string (no. 2) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertalignments.cpp:770:37: warning: %d in format string (no. 3) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertalignments.cpp:770:37: warning: %d in format string (no. 4) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertalignments.cpp:770:37: warning: %d in format string (no. 5) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertalignments.cpp:104:18: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertalignments.cpp:128:18: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertalignments.cpp:308:21: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertalignments.cpp:371:36: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertalignments.cpp:385:27: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/util/countkmer.cpp:22:30: style: Variable 'ids' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertalignments.cpp:644:45: style: The scope of the variable 'matchCount' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertalignments.cpp:138:21: style: Local variable 'source' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertalignments.cpp:127:18: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertalignments.cpp:138:21: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertalignments.cpp:494:40: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertalignments.cpp:358:21: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertalignments.cpp:494:40: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertalignments.cpp:748:41: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertalignments.cpp:358:21: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertalignments.cpp:748:41: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertalignments.cpp:105:11: style: Variable 'end' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/util/convertalignments.cpp:129:11: style: Variable 'end' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/util/createclusterdb.cpp:14:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMMAND_ALIGN [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/createdb.cpp:17:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PARSE_VARIADIC [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/createseqfiledb.cpp:15:115: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/createsubdb.cpp:21:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ERROR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/createdb.cpp:122:57: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: source [nullPointerOutOfResources]
metaeuk-7-bba0d80/lib/mmseqs/src/util/createdb.cpp:87:25: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/util/createdb.cpp:87:25: note: Assignment 'source=fopen(sourceFile.c_str(),"w")', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/util/createdb.cpp:122:57: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/util/createdb.cpp:149:29: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
metaeuk-7-bba0d80/lib/mmseqs/src/util/createdb.cpp:144:29: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/util/createdb.cpp:144:29: note: Assignment 'fp=fopen(filenames[fileIdx].c_str(),"rb")', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/util/createdb.cpp:149:29: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/util/createdb.cpp:154:34: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
metaeuk-7-bba0d80/lib/mmseqs/src/util/createdb.cpp:144:29: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/util/createdb.cpp:144:29: note: Assignment 'fp=fopen(filenames[fileIdx].c_str(),"rb")', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/util/createdb.cpp:154:34: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/util/createdb.cpp:159:24: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: fp [nullPointerOutOfResources]
metaeuk-7-bba0d80/lib/mmseqs/src/util/createdb.cpp:144:29: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/util/createdb.cpp:144:29: note: Assignment 'fp=fopen(filenames[fileIdx].c_str(),"rb")', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/util/createdb.cpp:159:24: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/util/db2tar.cpp:49:101: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/createtsv.cpp:20:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PARSE_VARIADIC [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/dbtype.cpp:10:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFO [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/diffseqdbs.cpp:41:116: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/diffseqdbs.cpp:116:47: style: Variable 'mappedKey' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/util/diskspaceavail.cpp:12:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFO [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/extractalignedregion.cpp:19:109: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/expandaln.cpp:33:87: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_HMM_PROFILE [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/expandaln.cpp:100:112: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/extractdomains.cpp:21:1: error: There is an unknown macro here somewhere. Configuration is required. If KSEQ_INIT is a macro then please configure it. [unknownMacro]
metaeuk-7-bba0d80/lib/mmseqs/src/util/extractframes.cpp:23:111: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/extractorfs.cpp:23:111: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/extractorfs.cpp:79:25: style: Variable 'headerAccession' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/expandaln.cpp:246:21: error: Common realloc mistake: 'compositionBias' nulled but not freed upon failure [memleakOnRealloc]
metaeuk-7-bba0d80/lib/mmseqs/src/util/expandaln.cpp:215:20: warning: If memory allocation fails, then there is a possible null pointer dereference: compositionBias [nullPointerOutOfMemory]
metaeuk-7-bba0d80/lib/mmseqs/src/util/expandaln.cpp:214:45: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/util/expandaln.cpp:214:31: note: Assignment 'compositionBias=(float*)malloc(compBufferSize)', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/util/expandaln.cpp:215:20: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/util/expandaln.cpp:214:31: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/util/expandaln.cpp:246:39: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/util/expandaln.cpp:394:58: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/util/expandaln.cpp:396:108: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/util/expandaln.cpp:27:110: style: Parameter 'subMat' can be declared as reference to const [constParameterReference]
metaeuk-7-bba0d80/lib/mmseqs/src/util/expandaln.cpp:27:125: style: Parameter 'compositionBias' can be declared as pointer to const [constParameterPointer]
metaeuk-7-bba0d80/lib/mmseqs/src/util/filtera3m.cpp:41:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable VECSIZE_INT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/filtera3m.cpp:106:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ERROR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/filtera3m.cpp:77:10: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/util/gff2db.cpp:15:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PARSE_VARIADIC [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/filterdb.cpp:97:111: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/gff2db.cpp:86:26: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/util/gff2db.cpp:118:24: style: Local variable 'end' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/gff2db.cpp:87:19: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/gff2db.cpp:118:24: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/util/gff2db.cpp:106:33: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/gff2db.cpp:79:21: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/gff2db.cpp:106:33: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/util/gff2db.cpp:157:33: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/gff2db.cpp:79:21: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/gff2db.cpp:157:33: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/util/gff2db.cpp:87:19: style: Variable 'end' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/util/gff2db.cpp:107:61: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
metaeuk-7-bba0d80/lib/mmseqs/src/util/indexdb.cpp:24:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_NUCLEOTIDES [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/indexdb.cpp:58:108: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/makepaddedseqdb.cpp:30:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/maskbygff.cpp:15:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_DATA [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/filterdb.cpp:141:31: warning: If resource allocation fails, then there is a possible null pointer dereference: orderFile [nullPointerOutOfResources]
metaeuk-7-bba0d80/lib/mmseqs/src/util/filterdb.cpp:135:37: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/util/filterdb.cpp:135:37: note: Assignment 'orderFile=fopen(filenames[i].c_str(),"r")', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/util/filterdb.cpp:141:31: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/util/masksequence.cpp:19:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_DATA [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/filterdb.cpp:360:35: style: Variable 'newValue' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/util/filterdb.cpp:417:27: style: Variable 'endLine' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/util/filterdb.cpp:343:40: error: Uninitialized variable: regex [legacyUninitvar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/mergedbs.cpp:10:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PARSE_VARIADIC [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/mergeclusters.cpp:23:108: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/mergeresultsbyset.cpp:15:114: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/mergeclusters.cpp:75:32: style: Local variable 'cluDb' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/mergeclusters.cpp:36:28: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/mergeclusters.cpp:75:32: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/util/mergeclusters.cpp:137:23: style: Variable 'tmpBuff' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/util/msa2result.cpp:15:1: error: There is an unknown macro here somewhere. Configuration is required. If KSEQ_INIT is a macro then please configure it. [unknownMacro]
metaeuk-7-bba0d80/lib/mmseqs/src/util/msa2profile.cpp:33:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMMAND_PROFILE [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/nrtotaxmapping.cpp:73:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ERROR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/nrtotaxmapping.cpp:32:5: style: Struct 'SortByName' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/util/nrtotaxmapping.cpp:235:18: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/util/nrtotaxmapping.cpp:154:19: style: Variable 'endName' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/util/offsetalignment.cpp:20:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable compareHitsByPosAndStrand [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/offsetalignment.cpp:107:84: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STRAND_MINUS [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/offsetalignment.cpp:178:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRELOAD_MODE_MMAP [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/msa2profile.cpp:356:55: style: Expression is always true because 'else if' condition is opposite to previous condition at line 354. [multiCondition]
metaeuk-7-bba0d80/lib/mmseqs/src/util/msa2profile.cpp:354:55: note: first condition
metaeuk-7-bba0d80/lib/mmseqs/src/util/msa2profile.cpp:356:55: note: else if condition is opposite to first condition
metaeuk-7-bba0d80/lib/mmseqs/src/util/msa2profile.cpp:99:29: style: The statement 'if (inHeader) inHeader=false' is logically equivalent to 'inHeader=false'. [duplicateConditionalAssign]
metaeuk-7-bba0d80/lib/mmseqs/src/util/msa2profile.cpp:100:38: note: Assignment 'inHeader=false'
metaeuk-7-bba0d80/lib/mmseqs/src/util/msa2profile.cpp:99:29: note: Condition 'inHeader' is redundant
metaeuk-7-bba0d80/lib/mmseqs/src/util/msa2profile.cpp:160:28: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/util/msa2profile.cpp:171:31: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/util/msa2profile.cpp:407:50: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/util/msa2profile.cpp:412:52: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/util/msa2profile.cpp:422:31: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/util/msa2profile.cpp:86:19: style: Variable 'entryData' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/util/orftocontig.cpp:18:118: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/pairaln.cpp:28:109: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_LOOKUP_REV [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/prefixid.cpp:14:99: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/offsetalignment.cpp:241:78: style: Condition 'targetNucl==true' is always true [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/src/util/offsetalignment.cpp:225:9: note: Assuming that condition 'targetNucl' is not redundant
metaeuk-7-bba0d80/lib/mmseqs/src/util/offsetalignment.cpp:241:78: note: Condition 'targetNucl==true' is always true
metaeuk-7-bba0d80/lib/mmseqs/src/util/offsetalignment.cpp:401:36: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/offsetalignment.cpp:367:21: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/offsetalignment.cpp:401:36: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/util/offsetalignment.cpp:432:32: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/offsetalignment.cpp:367:21: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/offsetalignment.cpp:432:32: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/util/offsetalignment.cpp:447:32: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/offsetalignment.cpp:367:21: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/offsetalignment.cpp:447:32: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/util/profile2neff.cpp:16:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMMAND_PROFILE [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/profile2pssm.cpp:16:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMMAND_PROFILE [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/profile2seq.cpp:15:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMMAND_PROFILE [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/recoverlongestorf.cpp:19:119: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/proteinaln2nucl.cpp:17:113: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/renamedbkeys.cpp:18:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ERROR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/renamedbkeys.cpp:48:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ERROR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/proteinaln2nucl.cpp:91:19: style: Variable 'nuclQuerySeq' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/util/proteinaln2nucl.cpp:95:19: style: Variable 'aaQuerySeq' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/util/proteinaln2nucl.cpp:116:23: style: Variable 'nuclTargetSeq' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/util/proteinaln2nucl.cpp:117:23: style: Variable 'aaTargetSeq' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2dnamsa.cpp:23:109: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2flat.cpp:13:111: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2flat.cpp:65:33: warning: Return value of function dbKeyBuffer.size() is not used. [ignoredReturnValue]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2flat.cpp:32:47: warning: If resource allocation fails, then there is a possible null pointer dereference: fastaFP [nullPointerOutOfResources]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2flat.cpp:24:26: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2flat.cpp:24:26: note: Assignment 'fastaFP=fopen(par.db4.c_str(),"w")', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2flat.cpp:32:47: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2flat.cpp:49:69: warning: If resource allocation fails, then there is a possible null pointer dereference: fastaFP [nullPointerOutOfResources]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2flat.cpp:24:26: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2flat.cpp:24:26: note: Assignment 'fastaFP=fopen(par.db4.c_str(),"w")', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2flat.cpp:49:69: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2flat.cpp:50:42: warning: If resource allocation fails, then there is a possible null pointer dereference: fastaFP [nullPointerOutOfResources]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2flat.cpp:24:26: note: Assuming allocation function fails
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2flat.cpp:24:26: note: Assignment 'fastaFP=fopen(par.db4.c_str(),"w")', assigned value is 0
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2flat.cpp:50:42: note: Null pointer dereference
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2flat.cpp:62:25: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2flat.cpp:29:17: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2flat.cpp:62:25: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2flat.cpp:26:10: style: Variable 'header_start' can be declared as const array [constVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2flat.cpp:27:10: style: Variable 'newline' can be declared as const array [constVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2flat.cpp:75:23: style: Variable 'endLenData' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2flat.cpp:81:23: style: Variable 'endLine' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2profile.cpp:25:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMMAND_EXPERT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2msa.cpp:32:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FORMAT_MSA_CA3M [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2profile.cpp:259:82: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2msa.cpp:455:40: style: Expression is always true because 'else if' condition is opposite to previous condition at line 453. [multiCondition]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2msa.cpp:453:34: note: first condition
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2msa.cpp:455:40: note: else if condition is opposite to first condition
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2msa.cpp:79:16: style: Condition 'isCA3M==true' is always false [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2msa.cpp:41:16: note: Assuming that condition 'isCA3M==true' is not redundant
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2msa.cpp:79:16: note: Condition 'isCA3M==true' is always false
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2msa.cpp:118:16: style: Condition 'isCA3M==true' is always false [knownConditionTrueFalse]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2msa.cpp:41:16: note: Assuming that condition 'isCA3M==true' is not redundant
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2msa.cpp:118:16: note: Condition 'isCA3M==true' is always false
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2msa.cpp:265:200: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2msa.cpp:335:200: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2msa.cpp:392:200: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2msa.cpp:487:61: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2rbh.cpp:14:117: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2msa.cpp:275:36: style: Local variable 'id' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2msa.cpp:195:21: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2msa.cpp:275:36: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2msa.cpp:307:32: style: Local variable 'id' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2msa.cpp:195:21: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2msa.cpp:307:32: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2msa.cpp:374:36: style: Local variable 'id' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2msa.cpp:195:21: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2msa.cpp:374:36: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2msa.cpp:421:32: style: Local variable 'id' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2msa.cpp:195:21: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2msa.cpp:421:32: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2msa.cpp:429:35: style: Local variable 'data' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2msa.cpp:226:19: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2msa.cpp:429:35: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2msa.cpp:48:85: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2msa.cpp:52:99: style: Clarify calculation precedence for '&' and '?'. [clarifyCalculation]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2rbh.cpp:39:29: style: Variable 'startRbhB' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2rbh.cpp:40:27: style: Variable 'endRbhB' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2repseq.cpp:15:114: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2rbh.cpp:41:32: style: Variable 'RbhBlength' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2stats.cpp:62:123: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2stats.cpp:116:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ERROR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2stats.cpp:184:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2stats.cpp:223:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2stats.cpp:260:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2stats.cpp:299:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2stats.cpp:360:125: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/reverseseq.cpp:16:114: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2stats.cpp:62:5: warning: Class 'StatsComputer' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2stats.cpp:62:5: warning: Class 'StatsComputer' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2stats.h:12:5: style: Class 'StatsComputer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
metaeuk-7-bba0d80/lib/mmseqs/src/util/sequence2profile.cpp:25:115: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2stats.cpp:381:19: style: Local variable 'stat' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2stats.h:17:9: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2stats.cpp:381:19: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2stats.cpp:399:23: style: Local variable 'stat' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2stats.h:17:9: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2stats.cpp:399:23: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2stats.cpp:149:19: style: Variable 'results' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2stats.cpp:310:39: style: Variable 'meanValString' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/result2stats.cpp:310:25: style: Variable 'meanValString' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/sequence2profile.cpp:42:23: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/util/setextendeddbtype.cpp:17:38: portability: Shifting signed 32-bit value by 31 bits is implementation-defined behaviour [shiftTooManyBitsSigned]
metaeuk-7-bba0d80/lib/mmseqs/src/util/sortresult.cpp:18:111: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/splitdb.cpp:9:127: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMMAND_COMMON [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/splitsequence.cpp:24:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/sortresult.cpp:66:29: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/sortresult.cpp:41:21: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/sortresult.cpp:66:29: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/util/sortresult.cpp:72:29: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/sortresult.cpp:41:21: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/sortresult.cpp:72:29: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/util/subtractdbs.cpp:21:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFO [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/summarizealis.cpp:18:111: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/subtractdbs.cpp:53:30: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/util/subtractdbs.cpp:90:30: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/util/subtractdbs.cpp:90:23: style: Local variable 'data' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/subtractdbs.cpp:71:19: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/subtractdbs.cpp:90:23: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/util/summarizeheaders.cpp:16:116: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/summarizeresult.cpp:17:111: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/summarizetabs.cpp:38:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WARNING [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/summarizetabs.cpp:72:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ERROR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/summarizetabs.cpp:103:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WARNING [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/summarizetabs.cpp:131:138: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_ALIGNMENT_RES [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/summarizetabs.cpp:183:111: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/summarizetabs.cpp:211:111: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/summarizeresult.cpp:29:12: style: The scope of the variable 'dbFrom' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/src/util/summarizeresult.cpp:82:29: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
metaeuk-7-bba0d80/lib/mmseqs/src/util/summarizetabs.cpp:21:17: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
metaeuk-7-bba0d80/lib/mmseqs/src/util/swapresults.cpp:48:113: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/tar2db.cpp:59:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PARSE_VARIADIC [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/tar2db.cpp:163:33: error: Common realloc mistake: 'dataBuffer' nulled but not freed upon failure [memleakOnRealloc]
metaeuk-7-bba0d80/lib/mmseqs/src/util/tar2db.cpp:190:37: error: Common realloc mistake: 'dataBuffer' nulled but not freed upon failure [memleakOnRealloc]
metaeuk-7-bba0d80/lib/mmseqs/src/util/tar2db.cpp:126:32: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/util/tar2db.cpp:128:35: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/util/tar2db.cpp:163:46: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/util/tar2db.cpp:190:50: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/util/tar2db.cpp:124:18: style: Local variable 'buffer' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/tar2db.cpp:90:14: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/tar2db.cpp:124:18: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/util/tar2db.cpp:266:28: style: Local variable 'len' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/tar2db.cpp:91:16: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/tar2db.cpp:266:28: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/util/tar2db.cpp:128:51: style: Variable 'inflateBuffer' is allocated memory that is never used. [unusedAllocatedMemory]
metaeuk-7-bba0d80/lib/mmseqs/src/util/touchdb.cpp:17:76: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SequentialScan [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/swapresults.cpp:44:12: style: The scope of the variable 'aaResSize' can be reduced. [variableScope]
metaeuk-7-bba0d80/lib/mmseqs/src/util/swapresults.cpp:169:16: style: Local variable 'bytesToWrite' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/swapresults.cpp:152:12: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/swapresults.cpp:169:16: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/util/transitivealign.cpp:24:116: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_DATA [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/translateaa.cpp:18:111: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/translateaa.cpp:71:19: style: Local variable 'data' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/translateaa.cpp:29:10: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/translateaa.cpp:71:19: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/util/translateaa.cpp:83:18: error: Memory is allocated but not initialized: aa [uninitdata]
metaeuk-7-bba0d80/lib/mmseqs/src/util/translateaa.cpp:63:15: style: Variable 'aa' is allocated memory that is never used. [unusedAllocatedMemory]
metaeuk-7-bba0d80/lib/mmseqs/src/util/transitivealign.cpp:130:45: style: Variable 'result.score' is reassigned a value before the old one has been used. [redundantAssignment]
metaeuk-7-bba0d80/lib/mmseqs/src/util/transitivealign.cpp:123:42: note: result.score is assigned
metaeuk-7-bba0d80/lib/mmseqs/src/util/transitivealign.cpp:130:45: note: result.score is overwritten
metaeuk-7-bba0d80/lib/mmseqs/src/util/transitivealign.cpp:233:16: style: Local variable 'bytesToWrite' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/transitivealign.cpp:215:12: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/transitivealign.cpp:233:16: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/util/transitivealign.cpp:285:18: style: Local variable 'resultWriter' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/transitivealign.cpp:47:14: note: Shadowed declaration
metaeuk-7-bba0d80/lib/mmseqs/src/util/transitivealign.cpp:285:18: note: Shadow variable
metaeuk-7-bba0d80/lib/mmseqs/src/util/translatenucs.cpp:18:111: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/transitivealign.cpp:297:44: style: Unused variable: curRes [unusedVariable]
metaeuk-7-bba0d80/lib/mmseqs/src/util/tsv2db.cpp:13:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFO [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/tsv2db.cpp:33:25: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/util/versionstring.cpp:8:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFO [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/unpackdb.cpp:20:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UNPACK_NAME_ACCESSION [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/view.cpp:10:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEQUENCES [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/util/view.cpp:50:15: style: Variable 'data' can be declared as pointer to const [constVariablePointer]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/ClusterUpdate.cpp:14:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALIGNMENT_MODE_SCORE_COV_SEQID [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/ClusterUpdate.cpp:22:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMMAND_EXPERT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/Cluster.cpp:18:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALIGNMENT_MODE_SCORE_COV_SEQID [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/Cluster.cpp:44:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALIGNMENT_MODE_UNGAPPED [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/Cluster.cpp:77:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFO [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/Cluster.cpp:109:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMMAND_EXPERT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/CreateIndex.cpp:26:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_HMM_PROFILE [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/CreateIndex.cpp:75:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMMAND_EXPERT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/CreateIndex.cpp:116:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMMAND_EXPERT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/CreateIndex.cpp:92:41: warning: Identical inner 'if' condition is always true. [identicalInnerCondition]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/CreateIndex.cpp:91:104: note: outer condition: par.PARAM_MAX_SEQ_LEN.wasSet==false
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/CreateIndex.cpp:92:41: note: identical inner condition: par.PARAM_MAX_SEQ_LEN.wasSet==false
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/Databases.cpp:184:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/Databases.cpp:241:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable name [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/Databases.cpp:255:65: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PARSE_ALLOW_EMPTY [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/EasyCluster.cpp:17:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEQUENCE_SPLIT_MODE_SOFT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/EasyCluster.cpp:33:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMMAND_EXPERT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/EasyLinclust.cpp:18:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEQUENCE_SPLIT_MODE_SOFT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/EasyLinclust.cpp:40:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMMAND_EXPERT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/EasyRbh.cpp:13:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMMAND_EXPERT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/EasySearch.cpp:18:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALIGNMENT_MODE_SCORE_COV_SEQID [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/EasySearch.cpp:32:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMMAND_EXPERT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/EasyTaxonomy.cpp:10:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEQUENCE_SPLIT_MODE_SOFT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/EasyTaxonomy.cpp:23:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMMAND_EXPERT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/Enrich.cpp:64:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RESCORE_MODE_ALIGNMENT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/Linclust.cpp:18:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALIGNMENT_MODE_SCORE_COV [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/Linclust.cpp:24:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMMAND_EXPERT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/Linsearch.cpp:20:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALIGNMENT_MODE_SCORE_COV [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/Linsearch.cpp:37:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMMAND_EXPERT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/Map.cpp:18:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RESCORE_MODE_ALIGNMENT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/Map.cpp:30:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMMAND_EXPERT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/Rbh.cpp:12:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALIGNMENT_MODE_SCORE_COV_SEQID [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/Rbh.cpp:24:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMMAND_EXPERT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/Taxonomy.cpp:19:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALIGNMENT_MODE_SCORE_ONLY [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/Taxonomy.cpp:41:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMMAND_EXPERT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/Search.cpp:23:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALIGNMENT_MODE_SCORE_COV [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/Search.cpp:42:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_NUCLEOTIDES [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/Search.cpp:182:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALIGNMENT_MODE_UNGAPPED [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/Search.cpp:205:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable COMMAND_EXPERT [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/workflow/Taxonomy.cpp:63:18: style: Variable 'indexStr' is assigned a value that is never used. [unreadVariable]
metaeuk-7-bba0d80/src/exonpredictor/collectoptimalset.cpp:118:101: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable comparePotentialExons [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/src/exonpredictor/collectoptimalset.cpp:229:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ERROR [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/src/exonpredictor/collectoptimalset.cpp:123:56: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
metaeuk-7-bba0d80/src/exonpredictor/groupstoacc.cpp:21:121: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/src/exonpredictor/reduceredundancy.cpp:26:86: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable comparePredictionsByContigStart [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/src/exonpredictor/reduceredundancy.cpp:113:92: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable comparePredictionsByEvalue [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/src/exonpredictor/reduceredundancy.cpp:153:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable noOverlapClusterId [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/src/exonpredictor/reduceredundancy.cpp:174:119: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/src/exonpredictor/resultspercontig.cpp:39:118: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/src/exonpredictor/resultspercontig.cpp:184:25: style: Local variable 'i' shadows outer variable [shadowVariable]
metaeuk-7-bba0d80/src/exonpredictor/resultspercontig.cpp:148:21: note: Shadowed declaration
metaeuk-7-bba0d80/src/exonpredictor/resultspercontig.cpp:184:25: note: Shadow variable
metaeuk-7-bba0d80/src/exonpredictor/unitesetstofasta.cpp:39:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PLUS [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/src/exonpredictor/unitesetstofasta.cpp:131:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PLUS [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/src/exonpredictor/unitesetstofasta.cpp:253:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PLUS [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/src/exonpredictor/unitesetstofasta.cpp:276:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PLUS [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/src/exonpredictor/unitesetstofasta.cpp:346:116: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable USE_INDEX [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/src/workflow/EasyPredict.cpp:12:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALIGNMENT_MODE_SCORE_COV [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/src/workflow/PredictExons.cpp:12:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALIGNMENT_MODE_SCORE_COV [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/src/workflow/PredictExons.cpp:23:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBTYPE_HMM_PROFILE [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/src/exonpredictor/unitesetstofasta.cpp:508:29: error: Common realloc mistake: 'translatedSeqBuff' nulled but not freed upon failure [memleakOnRealloc]
metaeuk-7-bba0d80/src/exonpredictor/unitesetstofasta.cpp:540:29: error: Common realloc mistake: 'translatedSeqBuff' nulled but not freed upon failure [memleakOnRealloc]
metaeuk-7-bba0d80/src/exonpredictor/unitesetstofasta.cpp:602:21: error: Common realloc mistake: 'translatedSeqBuff' nulled but not freed upon failure [memleakOnRealloc]
metaeuk-7-bba0d80/src/exonpredictor/unitesetstofasta.cpp:634:21: error: Common realloc mistake: 'translatedSeqBuff' nulled but not freed upon failure [memleakOnRealloc]
metaeuk-7-bba0d80/src/exonpredictor/unitesetstofasta.cpp:417:35: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/src/exonpredictor/unitesetstofasta.cpp:508:49: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/src/exonpredictor/unitesetstofasta.cpp:540:49: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/src/exonpredictor/unitesetstofasta.cpp:602:41: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/src/exonpredictor/unitesetstofasta.cpp:634:41: style: C-style pointer casting [cstyleCast]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestPSSM.cpp:23:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
metaeuk-7-bba0d80/lib/mmseqs/src/test/TestPSSM.cpp:1615:65: style: C-style pointer casting [cstyleCast]
diff:
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/lib/alp/njn_uniform.hpp:51:32: error: syntax error [syntaxError]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alignment_evaluer.cpp:101:14: performance: Function parameter 'function_name_' should be passed by const reference. [passedByValue]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alignment_evaluer.cpp:1082:9: style: Local variable 'area' shadows outer function [shadowFunction]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alignment_evaluer.hpp:150:9: note: Shadowed declaration
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alignment_evaluer.cpp:1082:9: note: Shadow variable
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alignment_evaluer.hpp:60:3: warning: Member variable 'gapped_computation_parameters_struct::d_total_realizations_number_with_ALP' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alignment_evaluer.hpp:60:3: warning: Member variable 'gapped_computation_parameters_struct::d_total_realizations_number_with_killing' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1203:12: style: Local variable 'i' shadows outer variable [shadowVariable]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1143:11: note: Shadowed declaration
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1203:12: note: Shadow variable
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1203:12: style: The scope of the variable 'i' can be reduced. [variableScope]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:127:3: warning: Class 'alp' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:127:3: warning: Class 'alp' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1389:12: style: Local variable 'i' shadows outer variable [shadowVariable]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1322:11: note: Shadowed declaration
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1389:12: note: Shadow variable
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1389:12: style: The scope of the variable 'i' can be reduced. [variableScope]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1648:12: style: Local variable 'i' shadows outer variable [shadowVariable]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1580:11: note: Shadowed declaration
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1648:12: note: Shadow variable
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1673:12: style: Local variable 'i' shadows outer variable [shadowVariable]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1580:11: note: Shadowed declaration
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1673:12: note: Shadow variable
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1673:12: style: The scope of the variable 'i' can be reduced. [variableScope]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1881:12: style: Local variable 'i' shadows outer variable [shadowVariable]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1813:11: note: Shadowed declaration
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1881:12: note: Shadow variable
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1906:12: style: Local variable 'i' shadows outer variable [shadowVariable]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1813:11: note: Shadowed declaration
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1906:12: note: Shadow variable
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1906:12: style: The scope of the variable 'i' can be reduced. [variableScope]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1998:8: warning: Member variable 'state::d_HD_ij_next' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1998:8: warning: Member variable 'state::d_HI_ij_next' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1998:8: warning: Member variable 'state::d_HS_ij_next' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1998:8: warning: Member variable 'state::d_H_ij_next' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1998:8: warning: Member variable 'state::d_H_matr_len' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1998:8: warning: Member variable 'state::d_M' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1998:8: warning: Member variable 'state::d_sentinel_i_next' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:1998:8: warning: Member variable 'state::d_sentinel_j_next' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:2025:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable state [valueFlowBailoutIncompleteVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:2108:11: style: Parameter 'M_upper_level_' can be declared as pointer to const [constParameterPointer]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:2208:24: style: Variable 'd_is_tmp' can be declared as pointer to const [constVariableReference]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:2252:4: style: Variable 'UI' is assigned a value that is never used. [unreadVariable]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:2255:4: style: Variable 'VD' is assigned a value that is never used. [unreadVariable]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:269:11: style: The scope of the variable 'i' can be reduced. [variableScope]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:386:11: style: The scope of the variable 'i' can be reduced. [variableScope]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:44:6: warning: Member variable 'alp::d_IS_state' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:44:6: warning: Member variable 'alp::d_diff_opt' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:44:6: warning: Member variable 'alp::d_nalp_killing' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.cpp:44:6: warning: Member variable 'alp::d_sentinels_flag' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.hpp:153:14: performance:inconclusive: Technically the member function 'Sls::alp::swap' can be static (but you may consider moving to unnamed namespace). [functionStatic]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.hpp:195:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.hpp:212:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp.hpp:94:2: style: Class 'alp' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:1011:8: performance: Function parameter 'RR_file_name_' should be passed by const reference. [passedByValue]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:1023:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:108:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:1179:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MIN [valueFlowBailoutIncompleteVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:1234:49: style: C-style pointer casting [cstyleCast]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:1253:14: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:1262:4: style: C-style pointer casting [cstyleCast]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:1289:3: warning: Class 'importance_sampling' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:1289:3: warning: Class 'importance_sampling' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:1347:27: style: Redundant assignment of 'd_elements_values[ind]' to itself. [selfAssignment]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:1400:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable q_elem [valueFlowBailoutIncompleteVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:1514:8: performance: Function parameter 'str_' should be passed by const reference. [passedByValue]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:1523:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:209:8: performance: Function parameter 'randout_' should be passed by const reference. [passedByValue]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:306:24: warning:inconclusive: Division of result of sizeof() on pointer type. [divideSizeof]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:372:11: warning: Member variable 'alp_data::d_realizations_number2' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:372:11: warning: Member variable 'alp_data::d_time_before1' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:374:8: performance: Function parameter 'randout_' should be passed by const reference. [passedByValue]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:384:8: performance: Function parameter 'smatr_file_name_' should be passed by const reference. [passedByValue]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:385:8: performance: Function parameter 'RR1_file_name_' should be passed by const reference. [passedByValue]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:386:8: performance: Function parameter 'RR2_file_name_' should be passed by const reference. [passedByValue]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:418:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable struct_for_randomization [valueFlowBailoutIncompleteVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:42:8: performance: Function parameter 'randout_' should be passed by const reference. [passedByValue]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:43:8: performance: Function parameter 'smatr_file_name_' should be passed by const reference. [passedByValue]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:44:8: performance: Function parameter 'RR1_file_name_' should be passed by const reference. [passedByValue]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:45:8: performance: Function parameter 'RR2_file_name_' should be passed by const reference. [passedByValue]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:478:11: warning: Member variable 'alp_data::d_realizations_number2' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:478:11: warning: Member variable 'alp_data::d_time_before1' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:480:27: style: Parameter 'randomization_parameters_' can be declared as pointer to const [constParameterPointer]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:532:3: warning: Class 'alp_data' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:532:3: warning: Class 'alp_data' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:53:10: style: Parameter 'letterFreqs1_' can be declared as pointer to const [constParameterReference]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:54:10: style: Parameter 'letterFreqs2_' can be declared as pointer to const [constParameterReference]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:575:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable struct_for_randomization [valueFlowBailoutIncompleteVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:686:23: warning:inconclusive: Division of result of sizeof() on pointer type. [divideSizeof]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:693:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable struct_for_randomization [valueFlowBailoutIncompleteVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:702:16: style:inconclusive: Technically the member function 'Sls::alp_data::check_out_file' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:396:8: note: Technically the member function 'Sls::alp_data::check_out_file' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:702:16: note: Technically the member function 'Sls::alp_data::check_out_file' can be const.
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:703:9: performance: Function parameter 'out_file_name_' should be passed by const reference. [passedByValue]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:710:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:731:8: style: Variable 'str_for_test0' can be declared as const array [constVariable]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:732:9: style: Variable 'test_flag0' can be declared as pointer to const [constVariablePointer]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:739:8: style: Variable 'str_for_test' can be declared as const array [constVariable]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:741:8: style: Variable 'test_flag' can be declared as pointer to const [constVariablePointer]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:789:33: style: C-style pointer casting [cstyleCast]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:792:10: style: Variable 'd_RR1' can be declared as pointer to const [constVariablePointer]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:793:10: style: Variable 'd_RR2' can be declared as pointer to const [constVariablePointer]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:810:8: performance: Function parameter 'smatr_file_name_' should be passed by const reference. [passedByValue]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:820:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:860:8: performance: Function parameter 'RR_file_name_' should be passed by const reference. [passedByValue]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:882:8: performance: Function parameter 'RR_file_name_' should be passed by const reference. [passedByValue]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:894:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_EPSILON [valueFlowBailoutIncompleteVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:990:13: style: Local variable 'i' shadows outer variable [shadowVariable]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:950:12: note: Shadowed declaration
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.cpp:990:13: note: Shadow variable
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:103:3: style: Class 'array_positive < alp * >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:103:3: style: Class 'array_positive < double >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:103:3: style: Class 'array_positive < long >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:103:3: style: Class 'array_positive < state * >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:103:3: style: Class 'array_positive' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:169:3: style: Class 'array < long >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:169:3: style: Class 'array' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:386:17: performance:inconclusive: Technically the member function 'Sls::alp_data::ran2' can be static (but you may consider moving to unnamed namespace). [functionStatic]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:473:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:501:13: style: The scope of the variable 'i' can be reduced. [variableScope]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:513:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:541:7: style: Variable 'v1' is assigned a value that is never used. [unreadVariable]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:596:15: style: Condition 'v2_minus<0' is always true [knownConditionTrueFalse]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:581:15: note: Assuming that condition 'v2_minus>=0' is not redundant
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:589:21: note: Assuming condition is false
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:596:15: note: Condition 'v2_minus<0' is always true
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:720:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:757:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:778:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:807:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:854:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:863:3: style: Exception should be caught by reference. [catchExceptionByValue]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_data.hpp:916:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:1077:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MAX [valueFlowBailoutIncompleteVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:1104:15: style:inconclusive: Technically the member function 'Sls::alp_sim::memory_release_for_calculate_main_parameters2m' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.hpp:354:8: note: Technically the member function 'Sls::alp_sim::memory_release_for_calculate_main_parameters2m' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:1104:15: note: Technically the member function 'Sls::alp_sim::memory_release_for_calculate_main_parameters2m' can be const.
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:1469:13: style: Local variable 'j' shadows outer variable [shadowVariable]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:1336:12: note: Shadowed declaration
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:1469:13: note: Shadow variable
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:1487:11: style: Local variable 'test_difference' shadows outer argument [shadowArgument]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:1250:9: note: Shadowed declaration
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:1487:11: note: Shadow variable
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:1488:11: style: Local variable 'test_difference_error' shadows outer argument [shadowArgument]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:1251:9: note: Shadowed declaration
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:1488:11: note: Shadow variable
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2006:11: style: The scope of the variable 'i' can be reduced. [variableScope]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2017:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable alp [valueFlowBailoutIncompleteVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2062:12: style: Local variable 'i' shadows outer variable [shadowVariable]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2049:11: note: Shadowed declaration
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2062:12: note: Shadow variable
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2066:9: style: Local variable 'flag' shadows outer variable [shadowVariable]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2043:7: note: Shadowed declaration
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2066:9: note: Shadow variable
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2090:11: style: Local variable 'flag' shadows outer variable [shadowVariable]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2066:9: note: Shadowed declaration
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2090:11: note: Shadow variable
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2148:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable alp [valueFlowBailoutIncompleteVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2241:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable alp [valueFlowBailoutIncompleteVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2302:12: style: The scope of the variable 'alp_number' can be reduced. [variableScope]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2337:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable alp [valueFlowBailoutIncompleteVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2363:13: style: Local variable 'i' shadows outer variable [shadowVariable]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2326:12: note: Shadowed declaration
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2363:13: note: Shadow variable
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2477:14: style: Local variable 'i' shadows outer variable [shadowVariable]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2363:13: note: Shadowed declaration
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2477:14: note: Shadow variable
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2593:15: performance:inconclusive: Technically the member function 'Sls::alp_sim::memory_release_for_get_minimal_simulation' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.hpp:102:8: note: Technically the member function 'Sls::alp_sim::memory_release_for_get_minimal_simulation' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2593:15: note: Technically the member function 'Sls::alp_sim::memory_release_for_get_minimal_simulation' can be static (but you may consider moving to unnamed namespace).
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2762:11: style: Parameter 'i_' can be declared as reference to const [constParameterReference]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2763:10: style: Parameter 'exp_array_' can be declared as pointer to const [constParameterReference]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2773:15: performance:inconclusive: Technically the member function 'Sls::alp_sim::memory_release_for_calculate_FSC' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.hpp:148:8: note: Technically the member function 'Sls::alp_sim::memory_release_for_calculate_FSC' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2773:15: note: Technically the member function 'Sls::alp_sim::memory_release_for_calculate_FSC' can be static (but you may consider moving to unnamed namespace).
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:277:12: style: The scope of the variable 'number_of_realizations_with_ALP_pred' can be reduced. [variableScope]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2908:32: style: C-style pointer casting [cstyleCast]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2918:11: style: Local variable 'tmp' shadows outer variable [shadowVariable]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2908:27: note: Shadowed declaration
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2918:11: note: Shadow variable
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3028:13: style: Local variable 'j' shadows outer variable [shadowVariable]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:2988:12: note: Shadowed declaration
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3028:13: note: Shadow variable
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3493:15: performance:inconclusive: Technically the member function 'Sls::alp_sim::sigma_calculation' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.hpp:206:8: note: Technically the member function 'Sls::alp_sim::sigma_calculation' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3493:15: note: Technically the member function 'Sls::alp_sim::sigma_calculation' can be static (but you may consider moving to unnamed namespace).
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3534:15: performance:inconclusive: Technically the member function 'Sls::alp_sim::calculate_C' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.hpp:136:8: note: Technically the member function 'Sls::alp_sim::calculate_C' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3534:15: note: Technically the member function 'Sls::alp_sim::calculate_C' can be static (but you may consider moving to unnamed namespace).
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3585:33: style: C-style pointer casting [cstyleCast]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3586:40: style: C-style pointer casting [cstyleCast]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3686:33: style: C-style pointer casting [cstyleCast]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3687:40: style: C-style pointer casting [cstyleCast]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:372:9: style: Condition '!loop_break_flag' is always true [knownConditionTrueFalse]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:329:7: note: Assuming that condition 'loop_break_flag' is not redundant
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:372:9: note: Condition '!loop_break_flag' is always true
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3731:13: style: Local variable 'number_of_elements' shadows outer variable [shadowVariable]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3620:12: note: Shadowed declaration
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3731:13: note: Shadow variable
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3733:9: style: Local variable 'cut_left_tail' shadows outer variable [shadowVariable]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3622:8: note: Shadowed declaration
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3733:9: note: Shadow variable
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3734:9: style: Local variable 'cut_right_tail' shadows outer variable [shadowVariable]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3623:8: note: Shadowed declaration
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3734:9: note: Shadow variable
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3738:11: style: Local variable 'beta1' shadows outer variable [shadowVariable]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3617:10: note: Shadowed declaration
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3738:11: note: Shadow variable
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3740:11: style: Local variable 'beta1_error' shadows outer variable [shadowVariable]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3618:10: note: Shadowed declaration
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3740:11: note: Shadow variable
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3742:9: style: Local variable 'res_was_calculated' shadows outer variable [shadowVariable]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3634:8: note: Shadowed declaration
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3742:9: note: Shadow variable
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:383:12: style: The scope of the variable 'number_of_realizations_with_killing_pred' can be reduced. [variableScope]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3947:14: style: Variable 'alp_tmp' can be declared as reference to const [constVariableReference]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3948:12: style: Variable 'weight_tmp' can be declared as reference to const [constVariableReference]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3951:5: style: C-style pointer casting [cstyleCast]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3952:5: style: C-style pointer casting [cstyleCast]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3957:32: style: C-style pointer casting [cstyleCast]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:3958:39: style: C-style pointer casting [cstyleCast]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:4042:14: style: Variable 'alp_tmp' can be declared as reference to const [constVariableReference]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:4043:12: style: Variable 'weight_tmp' can be declared as reference to const [constVariableReference]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:4146:14: style: Variable 'alp_tmp' can be declared as reference to const [constVariableReference]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:4147:12: style: Variable 'weight_tmp' can be declared as reference to const [constVariableReference]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:4314:35: style: Variable 'tmp_struct.d_calculate_alp_number' is reassigned a value before the old one has been used. [redundantAssignment]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:4311:35: note: tmp_struct.d_calculate_alp_number is assigned
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:4314:35: note: tmp_struct.d_calculate_alp_number is overwritten
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:4354:9: style: The scope of the variable 'sum2_error' can be reduced. [variableScope]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:4410:45: style: C-style pointer casting [cstyleCast]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:4430:33: style: C-style pointer casting [cstyleCast]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:4431:40: style: C-style pointer casting [cstyleCast]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:4460:13: style: Local variable 'k' shadows outer variable [shadowVariable]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:4427:12: note: Shadowed declaration
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:4460:13: note: Shadow variable
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:45:10: warning: Member variable 'alp_sim::m_G' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:45:10: warning: Member variable 'alp_sim::m_G1' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:45:10: warning: Member variable 'alp_sim::m_G2' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:45:10: warning: Member variable 'alp_sim::m_GaplessA' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:45:10: warning: Member variable 'alp_sim::m_GaplessAError' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:45:10: warning: Member variable 'alp_sim::m_GaplessAlpha' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:45:10: warning: Member variable 'alp_sim::m_GaplessAlphaError' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:475:9: style: Condition '!loop_break_flag' is always true [knownConditionTrueFalse]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:432:7: note: Assuming that condition 'loop_break_flag' is not redundant
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:475:9: note: Condition '!loop_break_flag' is always true
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:570:6: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:575:6: note: Found duplicate branches for 'if' and 'else'.
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:570:6: note: Found duplicate branches for 'if' and 'else'.
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:590:10: style: The scope of the variable 'sucess_flag' can be reduced. [variableScope]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:660:5: style: Exception should be caught by reference. [catchExceptionByValue]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:72:3: warning: Class 'alp_sim' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:72:3: warning: Class 'alp_sim' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.cpp:751:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_alp_sim.hpp:78:3: style: Class 'alp_sim' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.cpp:1040:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.cpp:113:5: style: Condition 'blast_' is always false [knownConditionTrueFalse]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.cpp:67:9: note: Assignment 'blast_=false', assigned value is 0
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.cpp:113:5: note: Condition 'blast_' is always false
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.cpp:153:21: style: Condition 'blast_' is always false [knownConditionTrueFalse]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.cpp:67:9: note: Assignment 'blast_=false', assigned value is 0
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.cpp:153:21: note: Condition 'blast_' is always false
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.cpp:411:5: style: Condition 'blast_' is always false [knownConditionTrueFalse]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.cpp:383:9: note: Assignment 'blast_=false', assigned value is 0
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.cpp:411:5: note: Condition 'blast_' is always false
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.cpp:438:21: style: Condition 'blast_' is always false [knownConditionTrueFalse]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.cpp:383:9: note: Assignment 'blast_=false', assigned value is 0
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.cpp:438:21: note: Condition 'blast_' is always false
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.cpp:819:15: style:inconclusive: Technically the member function 'Sls::pvalues::calculate_P_values' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:244:8: note: Technically the member function 'Sls::pvalues::calculate_P_values' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.cpp:819:15: note: Technically the member function 'Sls::pvalues::calculate_P_values' can be const.
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.cpp:864:10: style: The scope of the variable 'P_tmp' can be reduced. [variableScope]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.cpp:864:16: style: The scope of the variable 'E_tmp' can be reduced. [variableScope]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.cpp:901:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MAX [valueFlowBailoutIncompleteVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:257:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAND_MAX [valueFlowBailoutIncompleteVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::C' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::C_error' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::G' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::G1' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::G2' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::K' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::K_error' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::a' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::a_I' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::a_I_error' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::a_J' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::a_J_error' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::a_error' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::alpha' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::alpha_I' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::alpha_I_error' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::alpha_J' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::alpha_J_error' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::alpha_error' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::c_y_thr' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::gapless_a' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::gapless_a_error' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::gapless_alpha' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::gapless_alpha_error' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::lambda' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::lambda_error' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::m_CalcTime' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::sigma' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::sigma_error' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::vi_y_thr' is not initialized in the constructor. [uninitMemberVar]
head metaeuk-7-bba0d80/lib/mmseqs/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::vj_y_thr' is not initialized in the constructor. [uninitMemberVar]
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:106:8: error: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:104:18: note: Assuming allocation function fails
     metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:104:8: note: Assignment 'mem=(uint8_t*)calloc(tlen_*6+qlen_+1,16)', assigned value is 0
     metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:105:4: note: u is assigned '(__m128i*)(((unsigned long)mem+15)>>4<<4)' here.
     metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:106:8: note: Null pointer addition
head metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:106:8: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:104:18: note: Assuming allocation function fails
     metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:104:8: note: Assignment 'mem=(uint8_t*)calloc(tlen_*6+qlen_+1,16)', assigned value is 0
     metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:105:4: note: u is assigned '(__m128i*)(((unsigned long)mem+15)>>4<<4)' here.
     metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:106:8: note: Null pointer addition
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:115:17: error: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:114:15: note: Assuming allocation function fails
     metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:114:9: note: Assignment 'off=(int*)malloc((qlen+tlen-1)*sizeof(int)*2)', assigned value is 0
     metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:115:17: note: Null pointer addition
head metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:115:17: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:114:15: note: Assuming allocation function fails
     metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:114:9: note: Assignment 'off=(int*)malloc((qlen+tlen-1)*sizeof(int)*2)', assigned value is 0
     metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:115:17: note: Null pointer addition
head metaeuk-7-bba0d80/lib/mmseqs/lib/ksw2/ksw2_extz2_sse.cpp:124:64: style: C-style pointer casting [cstyleCast]
head metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Alignment.cpp:544:19: style: Unused private function: 'Alignment::estimateHDDMemoryConsumption' [unusedPrivateFunction]
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Alignment.h:123:19: note: Unused private function: 'Alignment::estimateHDDMemoryConsumption'
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Alignment.cpp:544:19: note: Unused private function: 'Alignment::estimateHDDMemoryConsumption'
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/alignment/Alignment.h:123:19: style: Unused private function: 'Alignment::estimateHDDMemoryConsumption' [unusedPrivateFunction]
head metaeuk-7-bba0d80/lib/mmseqs/src/alignment/BandedNucleotideAligner.cpp:195:17: style: Variable 'letterCode' is assigned a value that is never used. [unreadVariable]
head metaeuk-7-bba0d80/lib/mmseqs/src/alignment/BandedNucleotideAligner.cpp:61:55: style: C-style pointer casting [cstyleCast]
head metaeuk-7-bba0d80/lib/mmseqs/src/alignment/BandedNucleotideAligner.cpp:68:62: style: C-style pointer casting [cstyleCast]
head metaeuk-7-bba0d80/lib/mmseqs/src/alignment/BandedNucleotideAligner.cpp:93:56: style: C-style pointer casting [cstyleCast]
head metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:570:17: style:inconclusive: Technically the member function 'MsaFilter::getKept' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.h:42:10: note: Technically the member function 'MsaFilter::getKept' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:570:17: note: Technically the member function 'MsaFilter::getKept' can be const.
head metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:627:16: style:inconclusive: Technically the member function 'MsaFilter::prune' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.h:55:9: note: Technically the member function 'MsaFilter::prune' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:627:16: note: Technically the member function 'MsaFilter::prune' can be const.
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.h:42:10: style:inconclusive: Technically the member function 'MsaFilter::getKept' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:570:17: note: Technically the member function 'MsaFilter::getKept' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.h:42:10: note: Technically the member function 'MsaFilter::getKept' can be const.
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.h:55:9: style:inconclusive: Technically the member function 'MsaFilter::prune' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.cpp:627:16: note: Technically the member function 'MsaFilter::prune' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MsaFilter.h:55:9: note: Technically the member function 'MsaFilter::prune' can be const.
head metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.cpp:221:49: style:inconclusive: Technically the member function 'MultipleAlignment::singleSequenceMSA' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.h:59:15: note: Technically the member function 'MultipleAlignment::singleSequenceMSA' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.cpp:221:49: note: Technically the member function 'MultipleAlignment::singleSequenceMSA' can be const.
head metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.cpp:76:27: style:inconclusive: Technically the member function 'MultipleAlignment::updateGapsInCenterSequence' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.h:53:12: note: Technically the member function 'MultipleAlignment::updateGapsInCenterSequence' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.cpp:76:27: note: Technically the member function 'MultipleAlignment::updateGapsInCenterSequence' can be const.
head metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.cpp:95:25: style:inconclusive: Technically the member function 'MultipleAlignment::updateGapsInSequenceSet' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.h:55:10: note: Technically the member function 'MultipleAlignment::updateGapsInSequenceSet' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.cpp:95:25: note: Technically the member function 'MultipleAlignment::updateGapsInSequenceSet' can be const.
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.h:53:12: style:inconclusive: Technically the member function 'MultipleAlignment::updateGapsInCenterSequence' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.cpp:76:27: note: Technically the member function 'MultipleAlignment::updateGapsInCenterSequence' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.h:53:12: note: Technically the member function 'MultipleAlignment::updateGapsInCenterSequence' can be const.
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.h:55:10: style:inconclusive: Technically the member function 'MultipleAlignment::updateGapsInSequenceSet' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.cpp:95:25: note: Technically the member function 'MultipleAlignment::updateGapsInSequenceSet' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.h:55:10: note: Technically the member function 'MultipleAlignment::updateGapsInSequenceSet' can be const.
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.h:59:15: style:inconclusive: Technically the member function 'MultipleAlignment::singleSequenceMSA' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.cpp:221:49: note: Technically the member function 'MultipleAlignment::singleSequenceMSA' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/MultipleAlignment.h:59:15: note: Technically the member function 'MultipleAlignment::singleSequenceMSA' can be const.
head metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:634:22: performance:inconclusive: Technically the member function 'PSSMCalculator::computeConsensusSequence' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.h:158:10: note: Technically the member function 'PSSMCalculator::computeConsensusSequence' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:634:22: note: Technically the member function 'PSSMCalculator::computeConsensusSequence' can be static (but you may consider moving to unnamed namespace).
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.h:158:10: performance:inconclusive: Technically the member function 'PSSMCalculator::computeConsensusSequence' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.cpp:634:22: note: Technically the member function 'PSSMCalculator::computeConsensusSequence' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/PSSMCalculator.h:158:10: note: Technically the member function 'PSSMCalculator::computeConsensusSequence' can be static (but you may consider moving to unnamed namespace).
head metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1618:25: performance:inconclusive: Technically the member function 'SmithWaterman::to_cigar_int' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:383:21: note: Technically the member function 'SmithWaterman::to_cigar_int' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1618:25: note: Technically the member function 'SmithWaterman::to_cigar_int' can be static (but you may consider moving to unnamed namespace).
head metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1691:24: style:inconclusive: Technically the member function 'SmithWaterman::scoreIdentical' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:248:13: note: Technically the member function 'SmithWaterman::scoreIdentical' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1691:24: note: Technically the member function 'SmithWaterman::scoreIdentical' can be const.
head metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:238:24: performance:inconclusive: Technically the member function 'SmithWaterman::computeBias' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:409:13: note: Technically the member function 'SmithWaterman::computeBias' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:238:24: note: Technically the member function 'SmithWaterman::computeBias' can be static (but you may consider moving to unnamed namespace).
head metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:249:21: performance:inconclusive: Technically the member function 'SmithWaterman::reverseMat' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:411:10: note: Technically the member function 'SmithWaterman::reverseMat' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:249:21: note: Technically the member function 'SmithWaterman::reverseMat' can be static (but you may consider moving to unnamed namespace).
head metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:249:21: style: Unused private function: 'SmithWaterman::reverseMat' [unusedPrivateFunction]
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:411:10: note: Unused private function: 'SmithWaterman::reverseMat'
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:249:21: note: Unused private function: 'SmithWaterman::reverseMat'
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:248:13: style:inconclusive: Technically the member function 'SmithWaterman::scoreIdentical' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1691:24: note: Technically the member function 'SmithWaterman::scoreIdentical' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:248:13: note: Technically the member function 'SmithWaterman::scoreIdentical' can be const.
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:383:21: performance:inconclusive: Technically the member function 'SmithWaterman::to_cigar_int' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:1618:25: note: Technically the member function 'SmithWaterman::to_cigar_int' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:383:21: note: Technically the member function 'SmithWaterman::to_cigar_int' can be static (but you may consider moving to unnamed namespace).
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:409:13: performance:inconclusive: Technically the member function 'SmithWaterman::computeBias' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:238:24: note: Technically the member function 'SmithWaterman::computeBias' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:409:13: note: Technically the member function 'SmithWaterman::computeBias' can be static (but you may consider moving to unnamed namespace).
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:411:10: performance:inconclusive: Technically the member function 'SmithWaterman::reverseMat' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.cpp:249:21: note: Technically the member function 'SmithWaterman::reverseMat' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:411:10: note: Technically the member function 'SmithWaterman::reverseMat' can be static (but you may consider moving to unnamed namespace).
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/alignment/StripedSmithWaterman.h:411:10: style: Unused private function: 'SmithWaterman::reverseMat' [unusedPrivateFunction]
head metaeuk-7-bba0d80/lib/mmseqs/src/clustering/Clustering.cpp:103:18: performance:inconclusive: Technically the member function 'Clustering::writeData' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/clustering/Clustering.h:24:10: note: Technically the member function 'Clustering::writeData' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/clustering/Clustering.cpp:103:18: note: Technically the member function 'Clustering::writeData' can be static (but you may consider moving to unnamed namespace).
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/clustering/Clustering.h:24:10: performance:inconclusive: Technically the member function 'Clustering::writeData' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/clustering/Clustering.cpp:103:18: note: Technically the member function 'Clustering::writeData' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/clustering/Clustering.h:24:10: note: Technically the member function 'Clustering::writeData' can be static (but you may consider moving to unnamed namespace).
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.cpp:161:25: style:inconclusive: Technically the member function 'BaseMatrix::getMatrixName' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.h:66:17: note: Technically the member function 'BaseMatrix::getMatrixName' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.cpp:161:25: note: Technically the member function 'BaseMatrix::getMatrixName' can be const.
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.h:66:17: style:inconclusive: Technically the member function 'BaseMatrix::getMatrixName' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.cpp:161:25: note: Technically the member function 'BaseMatrix::getMatrixName' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/BaseMatrix.h:66:17: note: Technically the member function 'BaseMatrix::getMatrixName' can be const.
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.cpp:158:25: performance:inconclusive: Technically the member function 'CSProfile::computeProfileContextScore' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.h:83:11: note: Technically the member function 'CSProfile::computeProfileContextScore' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.cpp:158:25: note: Technically the member function 'CSProfile::computeProfileContextScore' can be static (but you may consider moving to unnamed namespace).
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.cpp:202:25: performance:inconclusive: Technically the member function 'CSProfile::computeSeqContextScore' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.h:79:11: note: Technically the member function 'CSProfile::computeSeqContextScore' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.cpp:202:25: note: Technically the member function 'CSProfile::computeSeqContextScore' can be static (but you may consider moving to unnamed namespace).
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.h:79:11: performance:inconclusive: Technically the member function 'CSProfile::computeSeqContextScore' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.cpp:202:25: note: Technically the member function 'CSProfile::computeSeqContextScore' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.h:79:11: note: Technically the member function 'CSProfile::computeSeqContextScore' can be static (but you may consider moving to unnamed namespace).
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.h:83:11: performance:inconclusive: Technically the member function 'CSProfile::computeProfileContextScore' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.cpp:158:25: note: Technically the member function 'CSProfile::computeProfileContextScore' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/CSProfile.h:83:11: note: Technically the member function 'CSProfile::computeProfileContextScore' can be static (but you may consider moving to unnamed namespace).
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/CommandCaller.cpp:48:21: performance:inconclusive: Technically the member function 'CommandCaller::addVariable' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/CommandCaller.h:12:10: note: Technically the member function 'CommandCaller::addVariable' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/CommandCaller.cpp:48:21: note: Technically the member function 'CommandCaller::addVariable' can be static (but you may consider moving to unnamed namespace).
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/CommandCaller.cpp:56:20: performance:inconclusive: Technically the member function 'CommandCaller::callProgram' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/CommandCaller.h:14:9: note: Technically the member function 'CommandCaller::callProgram' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/CommandCaller.cpp:56:20: note: Technically the member function 'CommandCaller::callProgram' can be static (but you may consider moving to unnamed namespace).
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/CommandCaller.cpp:70:21: performance:inconclusive: Technically the member function 'CommandCaller::execProgram' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/CommandCaller.h:19:10: note: Technically the member function 'CommandCaller::execProgram' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/CommandCaller.cpp:70:21: note: Technically the member function 'CommandCaller::execProgram' can be static (but you may consider moving to unnamed namespace).
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/CommandCaller.h:12:10: performance:inconclusive: Technically the member function 'CommandCaller::addVariable' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/CommandCaller.cpp:48:21: note: Technically the member function 'CommandCaller::addVariable' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/CommandCaller.h:12:10: note: Technically the member function 'CommandCaller::addVariable' can be static (but you may consider moving to unnamed namespace).
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/CommandCaller.h:14:9: performance:inconclusive: Technically the member function 'CommandCaller::callProgram' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/CommandCaller.cpp:56:20: note: Technically the member function 'CommandCaller::callProgram' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/CommandCaller.h:14:9: note: Technically the member function 'CommandCaller::callProgram' can be static (but you may consider moving to unnamed namespace).
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/CommandCaller.h:19:10: performance:inconclusive: Technically the member function 'CommandCaller::execProgram' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/CommandCaller.cpp:70:21: note: Technically the member function 'CommandCaller::execProgram' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/CommandCaller.h:19:10: note: Technically the member function 'CommandCaller::execProgram' can be static (but you may consider moving to unnamed namespace).
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:1020:19: performance:inconclusive: Technically the member function 'DBReader < std :: string >::setSequentialAdvice' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:446:10: note: Technically the member function 'DBReader < std :: string >::setSequentialAdvice' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:1020:19: note: Technically the member function 'DBReader < std :: string >::setSequentialAdvice' can be static (but you may consider moving to unnamed namespace).
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:214:19: performance:inconclusive: Technically the member function 'DBReader < std :: string >::sortIndex' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:320:10: note: Technically the member function 'DBReader < std :: string >::sortIndex' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:214:19: note: Technically the member function 'DBReader < std :: string >::sortIndex' can be static (but you may consider moving to unnamed namespace).
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:217:19: performance:inconclusive: Technically the member function 'DBReader < std :: string >::sortIndex' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:321:10: note: Technically the member function 'DBReader < std :: string >::sortIndex' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:217:19: note: Technically the member function 'DBReader < std :: string >::sortIndex' can be static (but you may consider moving to unnamed namespace).
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:221:19: style:inconclusive: Technically the member function 'DBReader < std :: string >::isSortedByOffset' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:322:10: note: Technically the member function 'DBReader < std :: string >::isSortedByOffset' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:221:19: note: Technically the member function 'DBReader < std :: string >::isSortedByOffset' can be const.
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:562:43: style:inconclusive: Technically the member function 'DBReader < std :: string >::getAminoAcidDBSize' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:168:12: note: Technically the member function 'DBReader < std :: string >::getAminoAcidDBSize' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:562:43: note: Technically the member function 'DBReader < std :: string >::getAminoAcidDBSize' can be const.
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:646:38: style:inconclusive: Technically the member function 'DBReader < std :: string >::getDbKey' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:193:7: note: Technically the member function 'DBReader < std :: string >::getDbKey' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:646:38: note: Technically the member function 'DBReader < std :: string >::getDbKey' can be const.
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:683:38: style:inconclusive: Technically the member function 'DBReader < std :: string >::getLookupKey' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:245:7: note: Technically the member function 'DBReader < std :: string >::getLookupKey' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:683:38: note: Technically the member function 'DBReader < std :: string >::getLookupKey' can be const.
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:692:48: style:inconclusive: Technically the member function 'DBReader < std :: string >::getLookupEntryName' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:246:17: note: Technically the member function 'DBReader < std :: string >::getLookupEntryName' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:692:48: note: Technically the member function 'DBReader < std :: string >::getLookupEntryName' can be const.
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:701:49: style:inconclusive: Technically the member function 'DBReader < std :: string >::getLookupFileNumber' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:247:18: note: Technically the member function 'DBReader < std :: string >::getLookupFileNumber' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:701:49: note: Technically the member function 'DBReader < std :: string >::getLookupFileNumber' can be const.
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:79:19: style:inconclusive: Technically the member function 'DBReader < std :: string >::printMagicNumber' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:341:10: note: Technically the member function 'DBReader < std :: string >::printMagicNumber' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:79:19: note: Technically the member function 'DBReader < std :: string >::printMagicNumber' can be const.
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:858:37: style:inconclusive: Technically the member function 'DBReader < std :: string >::getLastKey' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:343:7: note: Technically the member function 'DBReader < std :: string >::getLastKey' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:858:37: note: Technically the member function 'DBReader < std :: string >::getLastKey' can be const.
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:931:7: error: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:928:32: note: Assuming allocation function fails
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:928:18: note: Assignment 'data=(char*)malloc(indexMemorySize(idx))', assigned value is 0
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:929:13: note: p is assigned 'data' here.
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:931:7: note: Null pointer addition
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:931:7: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:928:32: note: Assuming allocation function fails
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:928:18: note: Assignment 'data=(char*)malloc(indexMemorySize(idx))', assigned value is 0
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:929:13: note: p is assigned 'data' here.
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:931:7: note: Null pointer addition
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:986:21: style:inconclusive: Technically the member function 'DBReader < std :: string >::getOffset' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:436:12: note: Technically the member function 'DBReader < std :: string >::getOffset' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:986:21: note: Technically the member function 'DBReader < std :: string >::getOffset' can be const.
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:168:12: style:inconclusive: Technically the member function 'DBReader < std :: string >::getAminoAcidDBSize' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:562:43: note: Technically the member function 'DBReader < std :: string >::getAminoAcidDBSize' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:168:12: note: Technically the member function 'DBReader < std :: string >::getAminoAcidDBSize' can be const.
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:193:7: style:inconclusive: Technically the member function 'DBReader < std :: string >::getDbKey' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:646:38: note: Technically the member function 'DBReader < std :: string >::getDbKey' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:193:7: note: Technically the member function 'DBReader < std :: string >::getDbKey' can be const.
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:245:7: style:inconclusive: Technically the member function 'DBReader < std :: string >::getLookupKey' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:683:38: note: Technically the member function 'DBReader < std :: string >::getLookupKey' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:245:7: note: Technically the member function 'DBReader < std :: string >::getLookupKey' can be const.
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:246:17: style:inconclusive: Technically the member function 'DBReader < std :: string >::getLookupEntryName' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:692:48: note: Technically the member function 'DBReader < std :: string >::getLookupEntryName' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:246:17: note: Technically the member function 'DBReader < std :: string >::getLookupEntryName' can be const.
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:247:18: style:inconclusive: Technically the member function 'DBReader < std :: string >::getLookupFileNumber' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:701:49: note: Technically the member function 'DBReader < std :: string >::getLookupFileNumber' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:247:18: note: Technically the member function 'DBReader < std :: string >::getLookupFileNumber' can be const.
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:320:10: performance:inconclusive: Technically the member function 'DBReader < std :: string >::sortIndex' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:214:19: note: Technically the member function 'DBReader < std :: string >::sortIndex' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:320:10: note: Technically the member function 'DBReader < std :: string >::sortIndex' can be static (but you may consider moving to unnamed namespace).
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:321:10: performance:inconclusive: Technically the member function 'DBReader < std :: string >::sortIndex' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:217:19: note: Technically the member function 'DBReader < std :: string >::sortIndex' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:321:10: note: Technically the member function 'DBReader < std :: string >::sortIndex' can be static (but you may consider moving to unnamed namespace).
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:322:10: style:inconclusive: Technically the member function 'DBReader < std :: string >::isSortedByOffset' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:221:19: note: Technically the member function 'DBReader < std :: string >::isSortedByOffset' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:322:10: note: Technically the member function 'DBReader < std :: string >::isSortedByOffset' can be const.
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:341:10: style:inconclusive: Technically the member function 'DBReader < std :: string >::printMagicNumber' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:79:19: note: Technically the member function 'DBReader < std :: string >::printMagicNumber' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:341:10: note: Technically the member function 'DBReader < std :: string >::printMagicNumber' can be const.
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:343:7: style:inconclusive: Technically the member function 'DBReader < std :: string >::getLastKey' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:858:37: note: Technically the member function 'DBReader < std :: string >::getLastKey' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:343:7: note: Technically the member function 'DBReader < std :: string >::getLastKey' can be const.
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:436:12: style:inconclusive: Technically the member function 'DBReader < std :: string >::getOffset' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:986:21: note: Technically the member function 'DBReader < std :: string >::getOffset' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:436:12: note: Technically the member function 'DBReader < std :: string >::getOffset' can be const.
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:446:10: performance:inconclusive: Technically the member function 'DBReader < std :: string >::setSequentialAdvice' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.cpp:1020:19: note: Technically the member function 'DBReader < std :: string >::setSequentialAdvice' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBReader.h:446:10: note: Technically the member function 'DBReader < std :: string >::setSequentialAdvice' can be static (but you may consider moving to unnamed namespace).
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:200:63: portability: Shifting signed 32-bit value by 31 bits is implementation-defined behaviour [shiftTooManyBitsSigned]
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:240:79: style: C-style pointer casting [cstyleCast]
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:437:16: style:inconclusive: Technically the member function 'DBWriter::checkClosed' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.h:73:10: note: Technically the member function 'DBWriter::checkClosed' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:437:16: note: Technically the member function 'DBWriter::checkClosed' can be const.
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:491:36: style: C-style pointer casting [cstyleCast]
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:491:50: style: C-style pointer casting [cstyleCast]
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.h:73:10: style:inconclusive: Technically the member function 'DBWriter::checkClosed' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.cpp:437:16: note: Technically the member function 'DBWriter::checkClosed' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/DBWriter.h:73:10: note: Technically the member function 'DBWriter::checkClosed' can be const.
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/ExpressionParser.cpp:42:24: performance:inconclusive: Technically the member function 'ExpressionParser::findBound' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/ExpressionParser.h:36:10: note: Technically the member function 'ExpressionParser::findBound' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/ExpressionParser.cpp:42:24: note: Technically the member function 'ExpressionParser::findBound' can be static (but you may consider moving to unnamed namespace).
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/ExpressionParser.h:36:10: performance:inconclusive: Technically the member function 'ExpressionParser::findBound' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/ExpressionParser.cpp:42:24: note: Technically the member function 'ExpressionParser::findBound' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/ExpressionParser.h:36:10: note: Technically the member function 'ExpressionParser::findBound' can be static (but you may consider moving to unnamed namespace).
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.cpp:10:28: performance:inconclusive: Technically the member function 'LibraryReader::strscn' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.h:19:17: note: Technically the member function 'LibraryReader::strscn' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.cpp:10:28: note: Technically the member function 'LibraryReader::strscn' can be static (but you may consider moving to unnamed namespace).
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.cpp:18:21: performance:inconclusive: Technically the member function 'LibraryReader::StreamStartsWith' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.h:14:10: note: Technically the member function 'LibraryReader::StreamStartsWith' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.cpp:18:21: note: Technically the member function 'LibraryReader::StreamStartsWith' can be static (but you may consider moving to unnamed namespace).
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.cpp:31:20: performance:inconclusive: Technically the member function 'LibraryReader::ReadInt' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.h:15:9: note: Technically the member function 'LibraryReader::ReadInt' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.cpp:31:20: note: Technically the member function 'LibraryReader::ReadInt' can be static (but you may consider moving to unnamed namespace).
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.cpp:46:23: performance:inconclusive: Technically the member function 'LibraryReader::ReadDouble' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.h:16:12: note: Technically the member function 'LibraryReader::ReadDouble' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.cpp:46:23: note: Technically the member function 'LibraryReader::ReadDouble' can be static (but you may consider moving to unnamed namespace).
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.cpp:74:28: performance:inconclusive: Technically the member function 'LibraryReader::getline' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.h:21:17: note: Technically the member function 'LibraryReader::getline' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.cpp:74:28: note: Technically the member function 'LibraryReader::getline' can be static (but you may consider moving to unnamed namespace).
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.cpp:86:21: performance:inconclusive: Technically the member function 'LibraryReader::ReadBool' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.h:18:10: note: Technically the member function 'LibraryReader::ReadBool' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.cpp:86:21: note: Technically the member function 'LibraryReader::ReadBool' can be static (but you may consider moving to unnamed namespace).
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.h:14:10: performance:inconclusive: Technically the member function 'LibraryReader::StreamStartsWith' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.cpp:18:21: note: Technically the member function 'LibraryReader::StreamStartsWith' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.h:14:10: note: Technically the member function 'LibraryReader::StreamStartsWith' can be static (but you may consider moving to unnamed namespace).
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.h:15:9: performance:inconclusive: Technically the member function 'LibraryReader::ReadInt' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.cpp:31:20: note: Technically the member function 'LibraryReader::ReadInt' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.h:15:9: note: Technically the member function 'LibraryReader::ReadInt' can be static (but you may consider moving to unnamed namespace).
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.h:16:12: performance:inconclusive: Technically the member function 'LibraryReader::ReadDouble' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.cpp:46:23: note: Technically the member function 'LibraryReader::ReadDouble' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.h:16:12: note: Technically the member function 'LibraryReader::ReadDouble' can be static (but you may consider moving to unnamed namespace).
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.h:18:10: performance:inconclusive: Technically the member function 'LibraryReader::ReadBool' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.cpp:86:21: note: Technically the member function 'LibraryReader::ReadBool' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.h:18:10: note: Technically the member function 'LibraryReader::ReadBool' can be static (but you may consider moving to unnamed namespace).
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.h:19:17: performance:inconclusive: Technically the member function 'LibraryReader::strscn' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.cpp:10:28: note: Technically the member function 'LibraryReader::strscn' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.h:19:17: note: Technically the member function 'LibraryReader::strscn' can be static (but you may consider moving to unnamed namespace).
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.h:21:17: performance:inconclusive: Technically the member function 'LibraryReader::getline' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.cpp:74:28: note: Technically the member function 'LibraryReader::getline' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/LibraryReader.h:21:17: note: Technically the member function 'LibraryReader::getline' can be static (but you may consider moving to unnamed namespace).
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.cpp:161:38: style:inconclusive: Technically the member function 'Orf::getSequence' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.h:91:37: note: Technically the member function 'Orf::getSequence' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.cpp:161:38: note: Technically the member function 'Orf::getSequence' can be const.
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.h:91:37: style:inconclusive: Technically the member function 'Orf::getSequence' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.cpp:161:38: note: Technically the member function 'Orf::getSequence' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/Orf.h:91:37: note: Technically the member function 'Orf::getSequence' can be const.
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2169:18: style:inconclusive: Technically the member function 'Parameters::printParameters' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.h:728:10: note: Technically the member function 'Parameters::printParameters' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2169:18: note: Technically the member function 'Parameters::printParameters' can be const.
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2192:18: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2604:43: performance:inconclusive: Technically the member function 'Parameters::combineList' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.h:1182:35: note: Technically the member function 'Parameters::combineList' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2604:43: note: Technically the member function 'Parameters::combineList' can be static (but you may consider moving to unnamed namespace).
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2681:25: style:inconclusive: Technically the member function 'Parameters::createParameterString' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.h:1187:17: note: Technically the member function 'Parameters::createParameterString' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2681:25: note: Technically the member function 'Parameters::createParameterString' can be const.
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2770:43: performance:inconclusive: Technically the member function 'Parameters::removeParameter' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.h:733:35: note: Technically the member function 'Parameters::removeParameter' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2770:43: note: Technically the member function 'Parameters::removeParameter' can be static (but you may consider moving to unnamed namespace).
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2780:18: performance:inconclusive: Technically the member function 'Parameters::overrideParameterDescription' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.h:1189:10: note: Technically the member function 'Parameters::overrideParameterDescription' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2780:18: note: Technically the member function 'Parameters::overrideParameterDescription' can be static (but you may consider moving to unnamed namespace).
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.h:1182:35: performance:inconclusive: Technically the member function 'Parameters::combineList' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2604:43: note: Technically the member function 'Parameters::combineList' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.h:1182:35: note: Technically the member function 'Parameters::combineList' can be static (but you may consider moving to unnamed namespace).
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.h:1187:17: style:inconclusive: Technically the member function 'Parameters::createParameterString' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2681:25: note: Technically the member function 'Parameters::createParameterString' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.h:1187:17: note: Technically the member function 'Parameters::createParameterString' can be const.
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.h:1189:10: performance:inconclusive: Technically the member function 'Parameters::overrideParameterDescription' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2780:18: note: Technically the member function 'Parameters::overrideParameterDescription' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.h:1189:10: note: Technically the member function 'Parameters::overrideParameterDescription' can be static (but you may consider moving to unnamed namespace).
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.h:728:10: style:inconclusive: Technically the member function 'Parameters::printParameters' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2169:18: note: Technically the member function 'Parameters::printParameters' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.h:728:10: note: Technically the member function 'Parameters::printParameters' can be const.
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.h:733:35: performance:inconclusive: Technically the member function 'Parameters::removeParameter' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.cpp:2770:43: note: Technically the member function 'Parameters::removeParameter' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/Parameters.h:733:35: note: Technically the member function 'Parameters::removeParameter' can be static (but you may consider moving to unnamed namespace).
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.cpp:269:22: performance:inconclusive: Technically the member function 'ProfileStates::entropy' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.h:117:11: note: Technically the member function 'ProfileStates::entropy' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.cpp:269:22: note: Technically the member function 'ProfileStates::entropy' can be static (but you may consider moving to unnamed namespace).
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.h:117:11: performance:inconclusive: Technically the member function 'ProfileStates::entropy' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.cpp:269:22: note: Technically the member function 'ProfileStates::entropy' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/ProfileStates.h:117:11: note: Technically the member function 'ProfileStates::entropy' can be static (but you may consider moving to unnamed namespace).
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/ScoreMatrix.h:49:44: style: C-style pointer casting [cstyleCast]
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.cpp:261:26: style:inconclusive: Technically the member function 'SubstitutionMatrix::mappingHasAminoAcidLetters' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.h:41:10: note: Technically the member function 'SubstitutionMatrix::mappingHasAminoAcidLetters' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.cpp:261:26: note: Technically the member function 'SubstitutionMatrix::mappingHasAminoAcidLetters' can be const.
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.cpp:265:13: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.cpp:313:25: style: Unused private function: 'SubstitutionMatrix::parseAlphabet' [unusedPrivateFunction]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.h:75:9: note: Unused private function: 'SubstitutionMatrix::parseAlphabet'
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.cpp:313:25: note: Unused private function: 'SubstitutionMatrix::parseAlphabet'
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.h:41:10: style:inconclusive: Technically the member function 'SubstitutionMatrix::mappingHasAminoAcidLetters' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.cpp:261:26: note: Technically the member function 'SubstitutionMatrix::mappingHasAminoAcidLetters' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.h:41:10: note: Technically the member function 'SubstitutionMatrix::mappingHasAminoAcidLetters' can be const.
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/SubstitutionMatrix.h:75:9: style: Unused private function: 'SubstitutionMatrix::parseAlphabet' [unusedPrivateFunction]
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/commons/Util.h:27:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head metaeuk-7-bba0d80/lib/mmseqs/src/commons/Util.h:27:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value [valueFlowBailoutIncompleteVar]
head metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Indexer.cpp:41:15: performance:inconclusive: Technically the member function 'Indexer::printKmer' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Indexer.h:119:10: note: Technically the member function 'Indexer::printKmer' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Indexer.cpp:41:15: note: Technically the member function 'Indexer::printKmer' can be static (but you may consider moving to unnamed namespace).
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Indexer.h:119:10: performance:inconclusive: Technically the member function 'Indexer::printKmer' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Indexer.cpp:41:15: note: Technically the member function 'Indexer::printKmer' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Indexer.h:119:10: note: Technically the member function 'Indexer::printKmer' can be static (but you may consider moving to unnamed namespace).
head metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:1017:104: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
head metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:955:20: performance:inconclusive: Technically the member function 'Prefiltering::printStatistics' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.h:137:10: note: Technically the member function 'Prefiltering::printStatistics' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:955:20: note: Technically the member function 'Prefiltering::printStatistics' can be static (but you may consider moving to unnamed namespace).
head metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:998:20: style:inconclusive: Technically the member function 'Prefiltering::mergePrefilterSplits' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.h:49:10: note: Technically the member function 'Prefiltering::mergePrefilterSplits' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:998:20: note: Technically the member function 'Prefiltering::mergePrefilterSplits' can be const.
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.h:137:10: performance:inconclusive: Technically the member function 'Prefiltering::printStatistics' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:955:20: note: Technically the member function 'Prefiltering::printStatistics' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.h:137:10: note: Technically the member function 'Prefiltering::printStatistics' can be static (but you may consider moving to unnamed namespace).
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.h:49:10: style:inconclusive: Technically the member function 'Prefiltering::mergePrefilterSplits' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.cpp:998:20: note: Technically the member function 'Prefiltering::mergePrefilterSplits' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/Prefiltering.h:49:10: note: Technically the member function 'Prefiltering::mergePrefilterSplits' can be const.
head metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:423:103: style: C-style pointer casting [cstyleCast]
head metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:435:95: style: C-style pointer casting [cstyleCast]
head metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:463:31: style: Unused private function: 'PrefilteringIndexReader::printMeta' [unusedPrivateFunction]
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.h:92:17: note: Unused private function: 'PrefilteringIndexReader::printMeta'
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.cpp:463:31: note: Unused private function: 'PrefilteringIndexReader::printMeta'
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/PrefilteringIndexReader.h:92:17: style: Unused private function: 'PrefilteringIndexReader::printMeta' [unusedPrivateFunction]
head metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:345:22: style:inconclusive: Technically the member function 'QueryMatcher::getDoubleDiagonalMatches' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:230:12: note: Technically the member function 'QueryMatcher::getDoubleDiagonalMatches' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:345:22: note: Technically the member function 'QueryMatcher::getDoubleDiagonalMatches' can be const.
head metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:361:41: style:inconclusive: Technically the member function 'QueryMatcher::getResult < 0 >' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:223:32: note: Technically the member function 'QueryMatcher::getResult < 0 >' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:361:41: note: Technically the member function 'QueryMatcher::getResult < 0 >' can be const.
head metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:361:41: style:inconclusive: Technically the member function 'QueryMatcher::getResult < 1 >' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:223:32: note: Technically the member function 'QueryMatcher::getResult < 1 >' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:361:41: note: Technically the member function 'QueryMatcher::getResult < 1 >' can be const.
head metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:361:41: style:inconclusive: Technically the member function 'QueryMatcher::getResult < KMER_SCORE >' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:223:32: note: Technically the member function 'QueryMatcher::getResult < KMER_SCORE >' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:361:41: note: Technically the member function 'QueryMatcher::getResult < KMER_SCORE >' can be const.
head metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:361:41: style:inconclusive: Technically the member function 'QueryMatcher::getResult < UNGAPPED_DIAGONAL_SCORE >' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:223:32: note: Technically the member function 'QueryMatcher::getResult < UNGAPPED_DIAGONAL_SCORE >' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:361:41: note: Technically the member function 'QueryMatcher::getResult < UNGAPPED_DIAGONAL_SCORE >' can be const.
head metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:495:22: style:inconclusive: Technically the member function 'QueryMatcher::radixSortByScoreSize' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:232:12: note: Technically the member function 'QueryMatcher::radixSortByScoreSize' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:495:22: note: Technically the member function 'QueryMatcher::radixSortByScoreSize' can be const.
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:223:32: style:inconclusive: Technically the member function 'QueryMatcher::getResult < 0 >' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:361:41: note: Technically the member function 'QueryMatcher::getResult < 0 >' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:223:32: note: Technically the member function 'QueryMatcher::getResult < 0 >' can be const.
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:223:32: style:inconclusive: Technically the member function 'QueryMatcher::getResult < 1 >' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:361:41: note: Technically the member function 'QueryMatcher::getResult < 1 >' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:223:32: note: Technically the member function 'QueryMatcher::getResult < 1 >' can be const.
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:223:32: style:inconclusive: Technically the member function 'QueryMatcher::getResult < KMER_SCORE >' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:361:41: note: Technically the member function 'QueryMatcher::getResult < KMER_SCORE >' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:223:32: note: Technically the member function 'QueryMatcher::getResult < KMER_SCORE >' can be const.
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:223:32: style:inconclusive: Technically the member function 'QueryMatcher::getResult < UNGAPPED_DIAGONAL_SCORE >' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:361:41: note: Technically the member function 'QueryMatcher::getResult < UNGAPPED_DIAGONAL_SCORE >' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:223:32: note: Technically the member function 'QueryMatcher::getResult < UNGAPPED_DIAGONAL_SCORE >' can be const.
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:230:12: style:inconclusive: Technically the member function 'QueryMatcher::getDoubleDiagonalMatches' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:345:22: note: Technically the member function 'QueryMatcher::getDoubleDiagonalMatches' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:230:12: note: Technically the member function 'QueryMatcher::getDoubleDiagonalMatches' can be const.
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:232:12: style:inconclusive: Technically the member function 'QueryMatcher::radixSortByScoreSize' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.cpp:495:22: note: Technically the member function 'QueryMatcher::radixSortByScoreSize' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/QueryMatcher.h:232:12: note: Technically the member function 'QueryMatcher::radixSortByScoreSize' can be const.
head metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.cpp:49:29: style:inconclusive: Technically the member function 'SequenceLookup::getData' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.h:27:17: note: Technically the member function 'SequenceLookup::getData' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.cpp:49:29: note: Technically the member function 'SequenceLookup::getData' can be const.
head metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.cpp:53:25: style:inconclusive: Technically the member function 'SequenceLookup::getDataSize' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.h:29:13: note: Technically the member function 'SequenceLookup::getDataSize' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.cpp:53:25: note: Technically the member function 'SequenceLookup::getDataSize' can be const.
head metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.cpp:61:24: style:inconclusive: Technically the member function 'SequenceLookup::getSequenceCount' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.h:31:12: note: Technically the member function 'SequenceLookup::getSequenceCount' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.cpp:61:24: note: Technically the member function 'SequenceLookup::getSequenceCount' can be const.
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.h:27:17: style:inconclusive: Technically the member function 'SequenceLookup::getData' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.cpp:49:29: note: Technically the member function 'SequenceLookup::getData' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.h:27:17: note: Technically the member function 'SequenceLookup::getData' can be const.
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.h:29:13: style:inconclusive: Technically the member function 'SequenceLookup::getDataSize' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.cpp:53:25: note: Technically the member function 'SequenceLookup::getDataSize' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.h:29:13: note: Technically the member function 'SequenceLookup::getDataSize' can be const.
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.h:31:12: style:inconclusive: Technically the member function 'SequenceLookup::getSequenceCount' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.cpp:61:24: note: Technically the member function 'SequenceLookup::getSequenceCount' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/SequenceLookup.h:31:12: note: Technically the member function 'SequenceLookup::getSequenceCount' can be const.
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/UngappedAlignment.cpp:0:0: debug: ValueFlow maximum iterations exceeded [valueFlowMaxIterations]
head metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/UngappedAlignment.cpp:30:24: performance:inconclusive: Technically the member function 'UngappedAlignment::scalarDiagonalScoring' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/UngappedAlignment.h:76:9: note: Technically the member function 'UngappedAlignment::scalarDiagonalScoring' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/UngappedAlignment.cpp:30:24: note: Technically the member function 'UngappedAlignment::scalarDiagonalScoring' can be static (but you may consider moving to unnamed namespace).
head metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/UngappedAlignment.cpp:364:35: performance:inconclusive: Technically the member function 'UngappedAlignment::distanceFromDiagonal' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/UngappedAlignment.h:91:20: note: Technically the member function 'UngappedAlignment::distanceFromDiagonal' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/UngappedAlignment.cpp:364:35: note: Technically the member function 'UngappedAlignment::distanceFromDiagonal' can be static (but you may consider moving to unnamed namespace).
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/UngappedAlignment.h:76:9: performance:inconclusive: Technically the member function 'UngappedAlignment::scalarDiagonalScoring' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/UngappedAlignment.cpp:30:24: note: Technically the member function 'UngappedAlignment::scalarDiagonalScoring' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/UngappedAlignment.h:76:9: note: Technically the member function 'UngappedAlignment::scalarDiagonalScoring' can be static (but you may consider moving to unnamed namespace).
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/UngappedAlignment.h:91:20: performance:inconclusive: Technically the member function 'UngappedAlignment::distanceFromDiagonal' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/UngappedAlignment.cpp:364:35: note: Technically the member function 'UngappedAlignment::distanceFromDiagonal' can be static (but you may consider moving to unnamed namespace).
     metaeuk-7-bba0d80/lib/mmseqs/src/prefiltering/UngappedAlignment.h:91:20: note: Technically the member function 'UngappedAlignment::distanceFromDiagonal' can be static (but you may consider moving to unnamed namespace).
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/MappingReader.h:14:21: error: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/MappingReader.h:12:35: note: Assuming allocation function fails
     metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/MappingReader.h:12:22: note: Assignment 'data=(char*)malloc(serialized_size)', assigned value is 0
     metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/MappingReader.h:14:21: note: Null pointer addition
head metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/MappingReader.h:14:21: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/MappingReader.h:12:35: note: Assuming allocation function fails
     metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/MappingReader.h:12:22: note: Assignment 'data=(char*)malloc(serialized_size)', assigned value is 0
     metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/MappingReader.h:14:21: note: Null pointer addition
head metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:259:20: style:inconclusive: Technically the member function 'NcbiTaxonomy::IsAncestor' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.h:111:10: note: Technically the member function 'NcbiTaxonomy::IsAncestor' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:259:20: note: Technically the member function 'NcbiTaxonomy::IsAncestor' can be const.
head metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:367:27: style:inconclusive: Technically the member function 'NcbiTaxonomy::taxLineage' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.h:105:17: note: Technically the member function 'NcbiTaxonomy::taxLineage' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:367:27: note: Technically the member function 'NcbiTaxonomy::taxLineage' can be const.
head metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:577:33: style:inconclusive: Technically the member function 'NcbiTaxonomy::weightedMajorityLCA' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.h:117:23: note: Technically the member function 'NcbiTaxonomy::weightedMajorityLCA' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:577:33: note: Technically the member function 'NcbiTaxonomy::weightedMajorityLCA' can be const.
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:723:7: error: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:720:31: note: Assuming allocation function fails
     metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:720:17: note: Assignment 'mem=(char*)malloc(memSize)', assigned value is 0
     metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:721:13: note: p is assigned 'mem' here.
     metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:723:7: note: Null pointer addition
head metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:723:7: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:720:31: note: Assuming allocation function fails
     metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:720:17: note: Assignment 'mem=(char*)malloc(memSize)', assigned value is 0
     metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:721:13: note: p is assigned 'mem' here.
     metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:723:7: note: Null pointer addition
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:750:7: error: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:494:33: note: Assuming allocation function fails
     metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:494:22: note: Assignment 'data=(char*)mmap(NULL,sb.st_size,PROT_READ,MAP_PRIVATE,fileno(handle),0)', assigned value is 0
     metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:500:53: note: Calling function 'unserialize', 1st argument 'data' value is 0
     metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:748:21: note: Assignment 'p=mem', assigned value is 0
     metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:750:7: note: Null pointer addition
head metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:750:7: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:494:33: note: Assuming allocation function fails
     metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:494:22: note: Assignment 'data=(char*)mmap(NULL,sb.st_size,PROT_READ,MAP_PRIVATE,fileno(handle),0)', assigned value is 0
     metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:500:53: note: Calling function 'unserialize', 1st argument 'data' value is 0
     metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:748:21: note: Assignment 'p=mem', assigned value is 0
     metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:750:7: note: Null pointer addition
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.h:105:17: style:inconclusive: Technically the member function 'NcbiTaxonomy::taxLineage' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:367:27: note: Technically the member function 'NcbiTaxonomy::taxLineage' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.h:105:17: note: Technically the member function 'NcbiTaxonomy::taxLineage' can be const.
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.h:111:10: style:inconclusive: Technically the member function 'NcbiTaxonomy::IsAncestor' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:259:20: note: Technically the member function 'NcbiTaxonomy::IsAncestor' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.h:111:10: note: Technically the member function 'NcbiTaxonomy::IsAncestor' can be const.
2.17.0 metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.h:117:23: style:inconclusive: Technically the member function 'NcbiTaxonomy::weightedMajorityLCA' can be const. [functionConst]
     metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.cpp:577:33: note: Technically the member function 'NcbiTaxonomy::weightedMajorityLCA' can be const.
     metaeuk-7-bba0d80/lib/mmseqs/src/taxonomy/NcbiTaxonomy.h:117:23: note: Technically the member function 'NcbiTaxonomy::weightedMajorityLCA' can be const.
head metaeuk-7-bba0d80/lib/mmseqs/src/test/TestExtendedSubstitutionMatrix.cpp:32:17: style: Variable 'seq_ptr' is assigned a value that is never used. [unreadVariable]
head metaeuk-7-bba0d80/lib/mmseqs/src/test/TestProfileAlignment.cpp:42:17: style: Variable 'profile' is assigned a value that is never used. [unreadVariable]
head metaeuk-7-bba0d80/lib/mmseqs/src/util/compress.cpp:26:65: portability: Shifting signed 32-bit value by 31 bits is implementation-defined behaviour [shiftTooManyBitsSigned]
head metaeuk-7-bba0d80/lib/mmseqs/src/util/convertkb.cpp:45:46: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
head metaeuk-7-bba0d80/lib/mmseqs/src/util/gff2db.cpp:107:61: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
head metaeuk-7-bba0d80/lib/mmseqs/src/util/result2stats.cpp:310:25: style: Variable 'meanValString' is assigned a value that is never used. [unreadVariable]
head metaeuk-7-bba0d80/lib/mmseqs/src/util/summarizeresult.cpp:82:29: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
head metaeuk-7-bba0d80/lib/mmseqs/src/util/summarizetabs.cpp:21:17: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
head metaeuk-7-bba0d80/src/exonpredictor/collectoptimalset.cpp:123:56: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]


DONE