2025-05-05 01:00
ftp://ftp.de.debian.org/debian/pool/main/i/igor/igor_1.4.0+dfsg.orig.tar.xz
cppcheck-options: --library=posix --library=gnu --library=bsd --library=openmp  --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: 88ef81e (2025-05-02 08:42:38 +0200)
count: 867 818
elapsed-time: 5.0 5.0
head-timing-info:

old-timing-info:

head results:
IGoR-1.4.0/igor_src/CDR3SeqData.cpp:46:14: warning: Member variable 'CDR3SeqData::seq_index' is not initialized in the copy constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/CDR3SeqData.cpp:46:14: warning: Member variable 'CDR3SeqData::v_anchor' is not initialized in the copy constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/CDR3SeqData.cpp:46:14: warning: Member variable 'CDR3SeqData::j_anchor' is not initialized in the copy constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/CDR3SeqData.cpp:46:14: warning:inconclusive: Member variable 'CDR3SeqData::CDR3nt' is not assigned in the copy constructor. Should it be copied? [missingMemberCopy]
IGoR-1.4.0/igor_src/CDR3SeqData.cpp:46:14: warning:inconclusive: Member variable 'CDR3SeqData::CDR3aa' is not assigned in the copy constructor. Should it be copied? [missingMemberCopy]
IGoR-1.4.0/igor_src/CDR3SeqData.cpp:34:2: performance: Variable 'CDR3nt' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
IGoR-1.4.0/igor_src/CDR3SeqData.cpp:35:2: performance: Variable 'CDR3aa' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
IGoR-1.4.0/igor_src/Utils.h:179:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Utils.h:147:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Utils.h:155:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Utils.h:163:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Bestscenarioscounter.cpp:147:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Bestscenarioscounter.cpp:199:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Aligner.h:74:2: warning: Member variable 'Alignment_data::five_p_offset' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Aligner.h:74:2: warning: Member variable 'Alignment_data::three_p_offset' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Aligner.h:74:2: warning: Member variable 'Alignment_data::align_length' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Aligner.h:76:2: warning: Member variable 'Alignment_data::five_p_offset' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Aligner.h:76:2: warning: Member variable 'Alignment_data::three_p_offset' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Utils.h:134:13: error: No 'return' statement in non-void function causes undefined behavior. [operatorEqMissingReturnStatement]
IGoR-1.4.0/igor_src/Aligner.cpp:228:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Aligner.cpp:325:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Aligner.cpp:426:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Aligner.cpp:482:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Aligner.cpp:593:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Aligner.cpp:608:142: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Aligner.cpp:635:100: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Aligner.cpp:706:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Aligner.cpp:803:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Aligner.cpp:828:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Aligner.cpp:887:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Utils.h:134:13: warning: 'operator=' should check for assignment to self to avoid problems with dynamic memory. [operatorEqToSelf]
IGoR-1.4.0/igor_src/Utils.h:660:8: style:inconclusive: Technically the member function 'inverse_offset_comparator::operator()' can be const. [functionConst]
IGoR-1.4.0/igor_src/Rec_Event.h:229:8: style:inconclusive: Technically the member function 'Event_comparator::operator()' can be const. [functionConst]
IGoR-1.4.0/igor_src/Model_marginals.h:115:8: style:inconclusive: Technically the member function 'offset_comp::operator()' can be const. [functionConst]
IGoR-1.4.0/igor_src/Utils.h:506:7: style:inconclusive: Technically the member function 'Enum_fast_memory_dual_key_map < Seq_type , Seq_side , int >::get_current_memory_layer' can be const. [functionConst]
IGoR-1.4.0/igor_src/Utils.h:276:7: style:inconclusive: Technically the member function 'Enum_fast_memory_map < Seq_type , Int_Str * >::get_current_memory_layer' can be const. [functionConst]
IGoR-1.4.0/igor_src/Utils.h:280:8: style:inconclusive: Technically the member function 'Enum_fast_memory_map < Seq_type , Int_Str * >::get_all_current_memory_layer' can be const. [functionConst]
IGoR-1.4.0/igor_src/Utils.h:286:8: style:inconclusive: Technically the member function 'Enum_fast_memory_map < Seq_type , Int_Str * >::exist' can be const. [functionConst]
IGoR-1.4.0/igor_src/Utils.h:330:8: style:inconclusive: Technically the member function 'Enum_fast_memory_map < Seq_type , Int_Str * >::multiply_all' can be const. [functionConst]
IGoR-1.4.0/igor_src/Utils.h:276:7: style:inconclusive: Technically the member function 'Enum_fast_memory_map < Seq_type , std :: vector < int > * >::get_current_memory_layer' can be const. [functionConst]
IGoR-1.4.0/igor_src/Utils.h:280:8: style:inconclusive: Technically the member function 'Enum_fast_memory_map < Seq_type , std :: vector < int > * >::get_all_current_memory_layer' can be const. [functionConst]
IGoR-1.4.0/igor_src/Utils.h:286:8: style:inconclusive: Technically the member function 'Enum_fast_memory_map < Seq_type , std :: vector < int > * >::exist' can be const. [functionConst]
IGoR-1.4.0/igor_src/Utils.h:330:8: style:inconclusive: Technically the member function 'Enum_fast_memory_map < Seq_type , std :: vector < int > * >::multiply_all' can be const. [functionConst]
IGoR-1.4.0/igor_src/Utils.h:276:7: style:inconclusive: Technically the member function 'Enum_fast_memory_map < Seq_type , double >::get_current_memory_layer' can be const. [functionConst]
IGoR-1.4.0/igor_src/Utils.h:280:8: style:inconclusive: Technically the member function 'Enum_fast_memory_map < Seq_type , double >::get_all_current_memory_layer' can be const. [functionConst]
IGoR-1.4.0/igor_src/Utils.h:286:8: style:inconclusive: Technically the member function 'Enum_fast_memory_map < Seq_type , double >::exist' can be const. [functionConst]
IGoR-1.4.0/igor_src/Utils.h:330:8: style:inconclusive: Technically the member function 'Enum_fast_memory_map < Seq_type , double >::multiply_all' can be const. [functionConst]
IGoR-1.4.0/igor_src/Utils.h:276:7: style:inconclusive: Technically the member function 'Enum_fast_memory_map < int , unsigned long >::get_current_memory_layer' can be const. [functionConst]
IGoR-1.4.0/igor_src/Utils.h:280:8: style:inconclusive: Technically the member function 'Enum_fast_memory_map < int , unsigned long >::get_all_current_memory_layer' can be const. [functionConst]
IGoR-1.4.0/igor_src/Utils.h:286:8: style:inconclusive: Technically the member function 'Enum_fast_memory_map < int , unsigned long >::exist' can be const. [functionConst]
IGoR-1.4.0/igor_src/Utils.h:330:8: style:inconclusive: Technically the member function 'Enum_fast_memory_map < int , unsigned long >::multiply_all' can be const. [functionConst]
IGoR-1.4.0/igor_src/Utils.h:276:7: style:inconclusive: Technically the member function 'Enum_fast_memory_map < Event_safety , bool >::get_current_memory_layer' can be const. [functionConst]
IGoR-1.4.0/igor_src/Utils.h:280:8: style:inconclusive: Technically the member function 'Enum_fast_memory_map < Event_safety , bool >::get_all_current_memory_layer' can be const. [functionConst]
IGoR-1.4.0/igor_src/Utils.h:286:8: style:inconclusive: Technically the member function 'Enum_fast_memory_map < Event_safety , bool >::exist' can be const. [functionConst]
IGoR-1.4.0/igor_src/Utils.h:330:8: style:inconclusive: Technically the member function 'Enum_fast_memory_map < Event_safety , bool >::multiply_all' can be const. [functionConst]
IGoR-1.4.0/igor_src/Utils.h:96:7: style:inconclusive: Technically the member function 'null_delete < Error_rate >::operator()' can be const. [functionConst]
IGoR-1.4.0/igor_src/Utils.h:405:4: warning: Class 'Enum_fast_memory_dual_key_map < Seq_type , Seq_side , int >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
IGoR-1.4.0/igor_src/Utils.h:405:4: warning: Class 'Enum_fast_memory_dual_key_map < Seq_type , Seq_side , int >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
IGoR-1.4.0/igor_src/Utils.h:202:4: warning: Class 'Enum_fast_memory_map < Seq_type , Int_Str * >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
IGoR-1.4.0/igor_src/Utils.h:202:4: warning: Class 'Enum_fast_memory_map < Seq_type , Int_Str * >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
IGoR-1.4.0/igor_src/Utils.h:202:4: warning: Class 'Enum_fast_memory_map < Seq_type , std :: vector < int > * >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
IGoR-1.4.0/igor_src/Utils.h:202:4: warning: Class 'Enum_fast_memory_map < Seq_type , std :: vector < int > * >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
IGoR-1.4.0/igor_src/Utils.h:202:4: warning: Class 'Enum_fast_memory_map < Seq_type , double >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
IGoR-1.4.0/igor_src/Utils.h:202:4: warning: Class 'Enum_fast_memory_map < Seq_type , double >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
IGoR-1.4.0/igor_src/Utils.h:202:4: warning: Class 'Enum_fast_memory_map < int , unsigned long >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
IGoR-1.4.0/igor_src/Utils.h:202:4: warning: Class 'Enum_fast_memory_map < int , unsigned long >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
IGoR-1.4.0/igor_src/Utils.h:202:4: warning: Class 'Enum_fast_memory_map < Event_safety , bool >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
IGoR-1.4.0/igor_src/Utils.h:202:4: warning: Class 'Enum_fast_memory_map < Event_safety , bool >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:171:9: warning: The class 'Hypermutation_global_errorrate' defines member variable with name 'scenario_new_proba' also defined in its parent class 'Error_rate'. [duplInheritedMember]
IGoR-1.4.0/igor_src/Errorrate.h:92:14: note: Parent variable 'Error_rate::scenario_new_proba'
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:171:9: note: Derived variable 'Hypermutation_global_errorrate::scenario_new_proba'
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:152:9: warning: The class 'Hypermutation_full_Nmer_errorrate' defines member variable with name 'scenario_new_proba' also defined in its parent class 'Error_rate'. [duplInheritedMember]
IGoR-1.4.0/igor_src/Errorrate.h:92:14: note: Parent variable 'Error_rate::scenario_new_proba'
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:152:9: note: Derived variable 'Hypermutation_full_Nmer_errorrate::scenario_new_proba'
IGoR-1.4.0/igor_src/Insertion.h:57:2: style: Class 'Insertion' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
IGoR-1.4.0/igor_src/Deletion.h:61:2: style: Class 'Deletion' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
IGoR-1.4.0/igor_src/Genechoice.h:58:2: style: Class 'Gene_choice' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
IGoR-1.4.0/igor_src/Singleerrorrate.h:48:2: style: Class 'Single_error_rate' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
IGoR-1.4.0/igor_src/Dinuclmarkov.h:58:2: style: Class 'Dinucl_markov' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
IGoR-1.4.0/igor_src/Model_Parms.h:80:2: style: Class 'Model_Parms' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
IGoR-1.4.0/igor_src/Model_marginals.h:63:2: style: Class 'Model_marginals' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
IGoR-1.4.0/igor_src/Utils.h:201:3: style: Class 'Enum_fast_memory_map < Seq_type , Int_Str * >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
IGoR-1.4.0/igor_src/Utils.h:201:3: style: Class 'Enum_fast_memory_map < Seq_type , std :: vector < int > * >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
IGoR-1.4.0/igor_src/Utils.h:201:3: style: Class 'Enum_fast_memory_map < Seq_type , double >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
IGoR-1.4.0/igor_src/Utils.h:201:3: style: Class 'Enum_fast_memory_map < int , unsigned long >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
IGoR-1.4.0/igor_src/Utils.h:201:3: style: Class 'Enum_fast_memory_map < Event_safety , bool >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
IGoR-1.4.0/igor_src/Insertion.h:61:11: style: The destructor '~Insertion' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:104:11: note: Virtual destructor in base class
IGoR-1.4.0/igor_src/Insertion.h:61:11: note: Destructor in derived class
IGoR-1.4.0/igor_src/Insertion.h:64:29: style: The function 'copy' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:105:37: note: Virtual function in base class
IGoR-1.4.0/igor_src/Insertion.h:64:29: note: Function in derived class
IGoR-1.4.0/igor_src/Insertion.h:65:14: style: The function 'iterate' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:143:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Insertion.h:65:14: note: Function in derived class
IGoR-1.4.0/igor_src/Insertion.h:67:18: style: The function 'draw_random_realization' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:160:26: note: Virtual function in base class
IGoR-1.4.0/igor_src/Insertion.h:67:18: note: Function in derived class
IGoR-1.4.0/igor_src/Insertion.h:68:7: style: The function 'write2txt' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:161:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Insertion.h:68:7: note: Function in derived class
IGoR-1.4.0/igor_src/Insertion.h:70:7: style: The function 'initialize_event' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:163:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Insertion.h:70:7: note: Function in derived class
IGoR-1.4.0/igor_src/Insertion.h:71:7: style: The function 'add_to_marginals' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:165:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Insertion.h:71:7: note: Function in derived class
IGoR-1.4.0/igor_src/Insertion.h:72:7: style: The function 'set_crude_upper_bound_proba' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:166:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Insertion.h:72:7: note: Function in derived class
IGoR-1.4.0/igor_src/Insertion.h:73:7: style: The function 'initialize_crude_scenario_proba_bound' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:164:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Insertion.h:73:7: note: Function in derived class
IGoR-1.4.0/igor_src/Insertion.h:76:7: style: The function 'has_effect_on' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:183:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Insertion.h:76:7: note: Function in derived class
IGoR-1.4.0/igor_src/Insertion.h:77:7: style: The function 'iterate_initialize_Len_proba' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:185:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Insertion.h:77:7: note: Function in derived class
IGoR-1.4.0/igor_src/Insertion.h:78:7: style: The function 'initialize_Len_proba_bound' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:187:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Insertion.h:78:7: note: Function in derived class
IGoR-1.4.0/igor_src/Deletion.h:66:11: style: The destructor '~Deletion' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:104:11: note: Virtual destructor in base class
IGoR-1.4.0/igor_src/Deletion.h:66:11: note: Destructor in derived class
IGoR-1.4.0/igor_src/Deletion.h:69:29: style: The function 'copy' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:105:37: note: Virtual function in base class
IGoR-1.4.0/igor_src/Deletion.h:69:29: note: Function in derived class
IGoR-1.4.0/igor_src/Deletion.h:71:14: style: The function 'iterate' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:143:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Deletion.h:71:14: note: Function in derived class
IGoR-1.4.0/igor_src/Deletion.h:73:18: style: The function 'draw_random_realization' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:160:26: note: Virtual function in base class
IGoR-1.4.0/igor_src/Deletion.h:73:18: note: Function in derived class
IGoR-1.4.0/igor_src/Deletion.h:74:7: style: The function 'write2txt' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:161:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Deletion.h:74:7: note: Function in derived class
IGoR-1.4.0/igor_src/Deletion.h:75:7: style: The function 'initialize_event' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:163:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Deletion.h:75:7: note: Function in derived class
IGoR-1.4.0/igor_src/Deletion.h:76:7: style: The function 'add_to_marginals' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:165:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Deletion.h:76:7: note: Function in derived class
IGoR-1.4.0/igor_src/Deletion.h:82:7: style: The function 'has_effect_on' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:183:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Deletion.h:82:7: note: Function in derived class
IGoR-1.4.0/igor_src/Deletion.h:83:7: style: The function 'iterate_initialize_Len_proba' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:185:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Deletion.h:83:7: note: Function in derived class
IGoR-1.4.0/igor_src/Deletion.h:84:7: style: The function 'initialize_Len_proba_bound' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:187:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Deletion.h:84:7: note: Function in derived class
IGoR-1.4.0/igor_src/Genechoice.h:62:11: style: The destructor '~Gene_choice' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:104:11: note: Virtual destructor in base class
IGoR-1.4.0/igor_src/Genechoice.h:62:11: note: Destructor in derived class
IGoR-1.4.0/igor_src/Genechoice.h:64:29: style: The function 'copy' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:105:37: note: Virtual function in base class
IGoR-1.4.0/igor_src/Genechoice.h:64:29: note: Function in derived class
IGoR-1.4.0/igor_src/Genechoice.h:65:14: style: The function 'iterate' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:143:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Genechoice.h:65:14: note: Function in derived class
IGoR-1.4.0/igor_src/Genechoice.h:69:18: style: The function 'draw_random_realization' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:160:26: note: Virtual function in base class
IGoR-1.4.0/igor_src/Genechoice.h:69:18: note: Function in derived class
IGoR-1.4.0/igor_src/Genechoice.h:70:7: style: The function 'write2txt' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:161:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Genechoice.h:70:7: note: Function in derived class
IGoR-1.4.0/igor_src/Genechoice.h:71:7: style: The function 'initialize_event' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:163:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Genechoice.h:71:7: note: Function in derived class
IGoR-1.4.0/igor_src/Genechoice.h:72:7: style: The function 'add_to_marginals' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:165:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Genechoice.h:72:7: note: Function in derived class
IGoR-1.4.0/igor_src/Genechoice.h:76:7: style: The function 'has_effect_on' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:183:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Genechoice.h:76:7: note: Function in derived class
IGoR-1.4.0/igor_src/Genechoice.h:77:7: style: The function 'iterate_initialize_Len_proba' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:185:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Genechoice.h:77:7: note: Function in derived class
IGoR-1.4.0/igor_src/Genechoice.h:78:7: style: The function 'initialize_Len_proba_bound' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:187:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Genechoice.h:78:7: note: Function in derived class
IGoR-1.4.0/igor_src/Singleerrorrate.h:49:11: style: The destructor '~Single_error_rate' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:61:11: note: Virtual destructor in base class
IGoR-1.4.0/igor_src/Singleerrorrate.h:49:11: note: Destructor in derived class
IGoR-1.4.0/igor_src/Singleerrorrate.h:50:9: style: The function 'compare_sequences_error_prob' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:62:17: note: Virtual function in base class
IGoR-1.4.0/igor_src/Singleerrorrate.h:50:9: note: Function in derived class
IGoR-1.4.0/igor_src/Singleerrorrate.h:51:7: style: The function 'update' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:63:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Singleerrorrate.h:51:7: note: Function in derived class
IGoR-1.4.0/igor_src/Singleerrorrate.h:52:7: style: The function 'add_to_norm_counter' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:67:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Singleerrorrate.h:52:7: note: Function in derived class
IGoR-1.4.0/igor_src/Singleerrorrate.h:53:7: style: The function 'clean_seq_counters' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:68:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Singleerrorrate.h:53:7: note: Function in derived class
IGoR-1.4.0/igor_src/Singleerrorrate.h:56:7: style: The function 'write2txt' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:70:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Singleerrorrate.h:56:7: note: Function in derived class
IGoR-1.4.0/igor_src/Singleerrorrate.h:57:30: style: The function 'copy' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:71:38: note: Virtual function in base class
IGoR-1.4.0/igor_src/Singleerrorrate.h:57:30: note: Function in derived class
IGoR-1.4.0/igor_src/Singleerrorrate.h:58:14: style: The function 'type' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:72:22: note: Virtual function in base class
IGoR-1.4.0/igor_src/Singleerrorrate.h:58:14: note: Function in derived class
IGoR-1.4.0/igor_src/Singleerrorrate.h:59:14: style: The function 'add_checked' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:73:22: note: Virtual function in base class
IGoR-1.4.0/igor_src/Singleerrorrate.h:59:14: note: Function in derived class
IGoR-1.4.0/igor_src/Singleerrorrate.h:60:16: style: The function 'get_err_rate_upper_bound' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:78:24: note: Virtual function in base class
IGoR-1.4.0/igor_src/Singleerrorrate.h:60:16: note: Function in derived class
IGoR-1.4.0/igor_src/Singleerrorrate.h:61:7: style: The function 'build_upper_bound_matrix' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:79:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Singleerrorrate.h:61:7: note: Function in derived class
IGoR-1.4.0/igor_src/Singleerrorrate.h:62:6: style: The function 'get_number_non_zero_likelihood_seqs' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:80:14: note: Virtual function in base class
IGoR-1.4.0/igor_src/Singleerrorrate.h:62:6: note: Function in derived class
IGoR-1.4.0/igor_src/Singleerrorrate.h:63:19: style: The function 'generate_errors' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:81:27: note: Virtual function in base class
IGoR-1.4.0/igor_src/Singleerrorrate.h:63:19: note: Function in derived class
IGoR-1.4.0/igor_src/Dinuclmarkov.h:60:11: style: The destructor '~Dinucl_markov' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:104:11: note: Virtual destructor in base class
IGoR-1.4.0/igor_src/Dinuclmarkov.h:60:11: note: Destructor in derived class
IGoR-1.4.0/igor_src/Dinuclmarkov.h:63:29: style: The function 'copy' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:105:37: note: Virtual function in base class
IGoR-1.4.0/igor_src/Dinuclmarkov.h:63:29: note: Function in derived class
IGoR-1.4.0/igor_src/Dinuclmarkov.h:64:6: style: The function 'size' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:106:14: note: Virtual function in base class
IGoR-1.4.0/igor_src/Dinuclmarkov.h:64:6: note: Function in derived class
IGoR-1.4.0/igor_src/Dinuclmarkov.h:67:14: style: The function 'iterate' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:143:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Dinuclmarkov.h:67:14: note: Function in derived class
IGoR-1.4.0/igor_src/Dinuclmarkov.h:69:18: style: The function 'draw_random_realization' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:160:26: note: Virtual function in base class
IGoR-1.4.0/igor_src/Dinuclmarkov.h:69:18: note: Function in derived class
IGoR-1.4.0/igor_src/Dinuclmarkov.h:70:7: style: The function 'write2txt' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:161:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Dinuclmarkov.h:70:7: note: Function in derived class
IGoR-1.4.0/igor_src/Dinuclmarkov.h:71:7: style: The function 'ind_normalize' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:162:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Dinuclmarkov.h:71:7: note: Function in derived class
IGoR-1.4.0/igor_src/Dinuclmarkov.h:72:7: style: The function 'initialize_event' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:163:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Dinuclmarkov.h:72:7: note: Function in derived class
IGoR-1.4.0/igor_src/Dinuclmarkov.h:73:7: style: The function 'add_to_marginals' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:165:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Dinuclmarkov.h:73:7: note: Function in derived class
IGoR-1.4.0/igor_src/Dinuclmarkov.h:74:7: style: The function 'update_event_internal_probas' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:169:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Dinuclmarkov.h:74:7: note: Function in derived class
IGoR-1.4.0/igor_src/Dinuclmarkov.h:77:10: style: The function 'get_updated_ptr' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:178:18: note: Virtual function in base class
IGoR-1.4.0/igor_src/Dinuclmarkov.h:77:10: note: Function in derived class
IGoR-1.4.0/igor_src/Dinuclmarkov.h:78:7: style: The function 'initialize_crude_scenario_proba_bound' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:164:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Dinuclmarkov.h:78:7: note: Function in derived class
IGoR-1.4.0/igor_src/Dinuclmarkov.h:81:7: style: The function 'has_effect_on' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:183:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Dinuclmarkov.h:81:7: note: Function in derived class
IGoR-1.4.0/igor_src/Dinuclmarkov.h:82:7: style: The function 'iterate_initialize_Len_proba' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:185:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Dinuclmarkov.h:82:7: note: Function in derived class
IGoR-1.4.0/igor_src/Dinuclmarkov.h:83:7: style: The function 'initialize_Len_proba_bound' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Rec_Event.h:187:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Dinuclmarkov.h:83:7: note: Function in derived class
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:61:11: style: The destructor '~Hypermutation_global_errorrate' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:61:11: note: Virtual destructor in base class
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:61:11: note: Destructor in derived class
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:62:9: style: The function 'compare_sequences_error_prob' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:62:17: note: Virtual function in base class
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:62:9: note: Function in derived class
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:63:7: style: The function 'update' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:63:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:63:7: note: Function in derived class
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:64:7: style: The function 'initialize' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:64:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:64:7: note: Function in derived class
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:65:7: style: The function 'add_to_norm_counter' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:67:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:65:7: note: Function in derived class
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:66:7: style: The function 'clean_seq_counters' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:68:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:66:7: note: Function in derived class
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:68:7: style: The function 'write2txt' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:70:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:68:7: note: Function in derived class
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:70:30: style: The function 'copy' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:71:38: note: Virtual function in base class
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:70:30: note: Function in derived class
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:71:14: style: The function 'type' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:72:22: note: Virtual function in base class
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:71:14: note: Function in derived class
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:73:14: style: The function 'add_checked' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:73:22: note: Virtual function in base class
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:73:14: note: Function in derived class
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:74:16: style: The function 'get_err_rate_upper_bound' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:78:24: note: Virtual function in base class
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:74:16: note: Function in derived class
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:75:7: style: The function 'build_upper_bound_matrix' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:79:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:75:7: note: Function in derived class
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:76:6: style: The function 'get_number_non_zero_likelihood_seqs' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:80:14: note: Virtual function in base class
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:76:6: note: Function in derived class
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:77:19: style: The function 'generate_errors' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:81:27: note: Virtual function in base class
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:77:19: note: Function in derived class
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:57:11: style: The destructor '~Hypermutation_full_Nmer_errorrate' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:61:11: note: Virtual destructor in base class
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:57:11: note: Destructor in derived class
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:58:9: style: The function 'compare_sequences_error_prob' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:62:17: note: Virtual function in base class
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:58:9: note: Function in derived class
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:59:7: style: The function 'update' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:63:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:59:7: note: Function in derived class
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:60:7: style: The function 'initialize' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:64:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:60:7: note: Function in derived class
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:61:7: style: The function 'add_to_norm_counter' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:67:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:61:7: note: Function in derived class
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:62:7: style: The function 'clean_seq_counters' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:68:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:62:7: note: Function in derived class
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:64:7: style: The function 'write2txt' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:70:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:64:7: note: Function in derived class
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:66:30: style: The function 'copy' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:71:38: note: Virtual function in base class
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:66:30: note: Function in derived class
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:67:14: style: The function 'type' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:72:22: note: Virtual function in base class
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:67:14: note: Function in derived class
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:69:14: style: The function 'add_checked' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:73:22: note: Virtual function in base class
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:69:14: note: Function in derived class
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:70:16: style: The function 'get_err_rate_upper_bound' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:78:24: note: Virtual function in base class
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:70:16: note: Function in derived class
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:71:7: style: The function 'build_upper_bound_matrix' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:79:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:71:7: note: Function in derived class
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:72:6: style: The function 'get_number_non_zero_likelihood_seqs' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:80:14: note: Virtual function in base class
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:72:6: note: Function in derived class
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:73:19: style: The function 'generate_errors' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Errorrate.h:81:27: note: Virtual function in base class
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:73:19: note: Function in derived class
IGoR-1.4.0/igor_src/Rec_Event.h:149:61: performance: Function 'get_realizations_map()' should return member 'event_realizations' by const reference. [returnByReference]
IGoR-1.4.0/igor_src/Rec_Event.h:151:23: performance: Function 'get_name()' should return member 'name' by const reference. [returnByReference]
IGoR-1.4.0/igor_src/Rec_Event.h:152:20: performance: Function 'get_nickname()' should return member 'nickname' by const reference. [returnByReference]
IGoR-1.4.0/igor_src/Model_Parms.h:135:40: performance: Function 'get_event_list()' should return member 'events' by const reference. [returnByReference]
IGoR-1.4.0/igor_src/Model_Parms.h:137:52: performance: Function 'get_edges()' should return member 'edges' by const reference. [returnByReference]
IGoR-1.4.0/igor_src/Counter.h:66:14: performance: Function 'get_path_to_files()' should return member 'path_to_file' by const reference. [returnByReference]
IGoR-1.4.0/igor_src/Utils.h:147:4: style: Statements following 'throw' will never be executed. [unreachableCode]
IGoR-1.4.0/igor_src/Utils.h:155:4: style: Statements following 'throw' will never be executed. [unreachableCode]
IGoR-1.4.0/igor_src/Utils.h:163:4: style: Statements following 'throw' will never be executed. [unreachableCode]
IGoR-1.4.0/igor_src/Rec_Event.h:153:32: performance: Function parameter 'name' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Utils.h:116:40: performance: Function parameter 'vect' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/IntStr.h:111:15: style: Variable 'i' can be declared as reference to const [constVariableReference]
IGoR-1.4.0/igor_src/Utils.h:330:49: style: Parameter 'memory_adresses' can be declared as pointer to const [constParameterPointer]
IGoR-1.4.0/igor_src/IntStr.h:112:9: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
IGoR-1.4.0/igor_src/Bestscenarioscounter.h:51:2: style: Class 'Best_scenarios_counter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
IGoR-1.4.0/igor_src/Bestscenarioscounter.h:55:11: style: The destructor '~Best_scenarios_counter' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Counter.h:50:11: note: Virtual destructor in base class
IGoR-1.4.0/igor_src/Bestscenarioscounter.h:55:11: note: Destructor in derived class
IGoR-1.4.0/igor_src/Bestscenarioscounter.h:57:14: style: The function 'type' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Counter.h:52:22: note: Virtual function in base class
IGoR-1.4.0/igor_src/Bestscenarioscounter.h:57:14: note: Function in derived class
IGoR-1.4.0/igor_src/Bestscenarioscounter.h:59:7: style: The function 'initialize_counter' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Counter.h:54:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Bestscenarioscounter.h:59:7: note: Function in derived class
IGoR-1.4.0/igor_src/Bestscenarioscounter.h:61:7: style: The function 'count_scenario' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Counter.h:56:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Bestscenarioscounter.h:61:7: note: Function in derived class
IGoR-1.4.0/igor_src/Bestscenarioscounter.h:63:7: style: The function 'count_sequence' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Counter.h:57:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Bestscenarioscounter.h:63:7: note: Function in derived class
IGoR-1.4.0/igor_src/Bestscenarioscounter.h:65:7: style: The function 'add_checked' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Counter.h:60:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Bestscenarioscounter.h:65:7: note: Function in derived class
IGoR-1.4.0/igor_src/Bestscenarioscounter.h:67:7: style: The function 'dump_sequence_data' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Counter.h:62:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Bestscenarioscounter.h:67:7: note: Function in derived class
IGoR-1.4.0/igor_src/Bestscenarioscounter.h:69:27: style: The function 'copy' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Counter.h:69:35: note: Virtual function in base class
IGoR-1.4.0/igor_src/Bestscenarioscounter.h:69:27: note: Function in derived class
IGoR-1.4.0/igor_src/Bestscenarioscounter.cpp:37:76: performance: Function parameter 'path' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Bestscenarioscounter.cpp:40:76: performance: Function parameter 'path' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Bestscenarioscounter.cpp:190:14: style: Variable 'mismatches_list' can be declared as reference to const [constVariableReference]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:94:99: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:248:73: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:464:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:481:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:501:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:538:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Deletion.cpp:273:90: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Deletion.cpp:1224:93: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Deletion.cpp:1303:86: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:54:24: style:inconclusive: Boolean expression 'count_on==V_gene' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:54:70: style:inconclusive: Boolean expression 'count_on==VDJ_genes' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:59:25: style:inconclusive: Boolean expression 'count_on==D_gene' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:59:71: style:inconclusive: Boolean expression 'count_on==VDJ_genes' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:64:25: style:inconclusive: Boolean expression 'count_on==J_gene' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:64:71: style:inconclusive: Boolean expression 'count_on==VDJ_genes' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:31:23: warning: Member variable 'Coverage_err_counter::i' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:31:23: warning: Member variable 'Coverage_err_counter::tmp_cov_p' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:31:23: warning: Member variable 'Coverage_err_counter::tmp_err_p' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:31:23: warning: Member variable 'Coverage_err_counter::tmp_corr_len' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:31:23: warning: Member variable 'Coverage_err_counter::tmp_len_util' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:35:23: warning: Member variable 'Coverage_err_counter::i' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:35:23: warning: Member variable 'Coverage_err_counter::tmp_cov_p' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:35:23: warning: Member variable 'Coverage_err_counter::tmp_err_p' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:35:23: warning: Member variable 'Coverage_err_counter::tmp_corr_len' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:35:23: warning: Member variable 'Coverage_err_counter::tmp_len_util' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:40:23: warning: Member variable 'Coverage_err_counter::i' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:40:23: warning: Member variable 'Coverage_err_counter::tmp_cov_p' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:40:23: warning: Member variable 'Coverage_err_counter::tmp_err_p' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:40:23: warning: Member variable 'Coverage_err_counter::tmp_corr_len' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:40:23: warning: Member variable 'Coverage_err_counter::tmp_len_util' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:44:23: warning: Member variable 'Coverage_err_counter::i' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:44:23: warning: Member variable 'Coverage_err_counter::tmp_cov_p' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:44:23: warning: Member variable 'Coverage_err_counter::tmp_err_p' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:44:23: warning: Member variable 'Coverage_err_counter::tmp_corr_len' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:44:23: warning: Member variable 'Coverage_err_counter::tmp_len_util' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:474:28: performance:inconclusive: Technically the member function 'Coverage_err_counter::deallocate_coverage_and_errors_arrays' can be static (but you may consider moving to unnamed namespace). [functionStatic]
IGoR-1.4.0/igor_src/Coverageerrcounter.h:67:7: note: Technically the member function 'Coverage_err_counter::deallocate_coverage_and_errors_arrays' can be static (but you may consider moving to unnamed namespace).
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:474:28: note: Technically the member function 'Coverage_err_counter::deallocate_coverage_and_errors_arrays' can be static (but you may consider moving to unnamed namespace).
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:641:28: style:inconclusive: Technically the member function 'Coverage_err_counter::symmetrize_counter_array_recurs' can be const. [functionConst]
IGoR-1.4.0/igor_src/Coverageerrcounter.h:73:7: note: Technically the member function 'Coverage_err_counter::symmetrize_counter_array_recurs' can be const.
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:641:28: note: Technically the member function 'Coverage_err_counter::symmetrize_counter_array_recurs' can be const.
IGoR-1.4.0/igor_src/Coverageerrcounter.h:43:2: style: Class 'Coverage_err_counter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
IGoR-1.4.0/igor_src/Coverageerrcounter.h:47:11: style: The destructor '~Coverage_err_counter' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Counter.h:50:11: note: Virtual destructor in base class
IGoR-1.4.0/igor_src/Coverageerrcounter.h:47:11: note: Destructor in derived class
IGoR-1.4.0/igor_src/Coverageerrcounter.h:49:14: style: The function 'type' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Counter.h:52:22: note: Virtual function in base class
IGoR-1.4.0/igor_src/Coverageerrcounter.h:49:14: note: Function in derived class
IGoR-1.4.0/igor_src/Coverageerrcounter.h:51:7: style: The function 'initialize_counter' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Counter.h:54:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Coverageerrcounter.h:51:7: note: Function in derived class
IGoR-1.4.0/igor_src/Coverageerrcounter.h:53:7: style: The function 'count_scenario' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Counter.h:56:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Coverageerrcounter.h:53:7: note: Function in derived class
IGoR-1.4.0/igor_src/Coverageerrcounter.h:55:7: style: The function 'count_sequence' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Counter.h:57:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Coverageerrcounter.h:55:7: note: Function in derived class
IGoR-1.4.0/igor_src/Coverageerrcounter.h:57:7: style: The function 'add_checked' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Counter.h:60:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Coverageerrcounter.h:57:7: note: Function in derived class
IGoR-1.4.0/igor_src/Coverageerrcounter.h:59:7: style: The function 'dump_sequence_data' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Counter.h:62:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Coverageerrcounter.h:59:7: note: Function in derived class
IGoR-1.4.0/igor_src/Coverageerrcounter.h:60:7: style: The function 'dump_data_summary' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Counter.h:63:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Coverageerrcounter.h:60:7: note: Function in derived class
IGoR-1.4.0/igor_src/Coverageerrcounter.h:62:27: style: The function 'copy' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Counter.h:69:35: note: Virtual function in base class
IGoR-1.4.0/igor_src/Coverageerrcounter.h:62:27: note: Function in derived class
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:54:24: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:54:47: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:54:70: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:59:25: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:59:48: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:59:71: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:64:25: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:64:48: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:64:71: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:153:4: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:186:4: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:226:4: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:605:95: style:inconclusive: Function 'recurs_errors_count' argument 2 names different: declaration 'v_mismatch_list' definition 'mismatch_list'. [funcArgNamesDifferent]
IGoR-1.4.0/igor_src/Coverageerrcounter.h:71:79: note: Function 'recurs_errors_count' argument 2 names different: declaration 'v_mismatch_list' definition 'mismatch_list'.
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:605:95: note: Function 'recurs_errors_count' argument 2 names different: declaration 'v_mismatch_list' definition 'mismatch_list'.
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:40:51: performance: Function parameter 'path' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:44:51: performance: Function parameter 'path' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:443:127: performance: Function parameter 'realizations' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:474:129: performance: Function parameter 'realizations' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:149:20: style: Variable 'except' can be declared as reference to const [constVariableReference]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:182:20: style: Variable 'except' can be declared as reference to const [constVariableReference]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:222:20: style: Variable 'except' can be declared as reference to const [constVariableReference]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:536:66: style: Parameter 'normalizing_cst' can be declared as reference to const [constParameterReference]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:266:64: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:323:54: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:451:123: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:478:124: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
IGoR-1.4.0/igor_src/Aligner.cpp:752:21: style:inconclusive: Boolean expression '!allow_in_dels' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Aligner.cpp:752:44: style:inconclusive: Boolean expression '!insertions.empty()' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Aligner.cpp:900:16: style:inconclusive: Boolean expression 'nt_1<4' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Aligner.cpp:1097:37: style:inconclusive: Boolean expression 'subs_score>=data_gap_score' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Aligner.cpp:1097:90: style:inconclusive: Boolean expression 'subs_score>0' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Aligner.cpp:1112:48: style:inconclusive: Boolean expression 'data_gap_score>=genomic_gap_score' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Aligner.cpp:1112:71: style:inconclusive: Boolean expression 'data_gap_score>0' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Aligner.cpp:1120:34: style:inconclusive: Boolean expression 'genomic_gap_score>0' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Aligner.cpp:1260:35: style:inconclusive: Boolean expression 'i!=explored_row_coord' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Aligner.cpp:1271:36: style:inconclusive: Boolean expression 'explored_row_coord==n_rows' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Aligner.cpp:1370:30: style:inconclusive: Boolean expression 'offset>=min_offset' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Aligner.cpp:1451:15: style:inconclusive: Boolean expression 'best_only' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Aligner.cpp:1494:6: warning: Return value of function std::stoi() is not used. [ignoredReturnValue]
IGoR-1.4.0/igor_src/Aligner.cpp:1531:5: warning: Return value of function std::stoi() is not used. [ignoredReturnValue]
IGoR-1.4.0/igor_src/Aligner.cpp:1538:5: warning: Return value of function std::stoi() is not used. [ignoredReturnValue]
IGoR-1.4.0/igor_src/Aligner.cpp:31:10: warning:inconclusive: Member variable 'Aligner::gap_penalty' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Aligner.cpp:31:10: warning:inconclusive: Member variable 'Aligner::gene' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Aligner.cpp:31:10: warning:inconclusive: Member variable 'Aligner::local_align' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Aligner.cpp:31:10: warning:inconclusive: Member variable 'Aligner::flip_seqs' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Utils.h:96:7: style:inconclusive: Technically the member function 'null_delete::operator()' can be const. [functionConst]
IGoR-1.4.0/igor_src/Utils.h:276:7: style:inconclusive: Technically the member function 'Enum_fast_memory_map::get_current_memory_layer' can be const. [functionConst]
IGoR-1.4.0/igor_src/Utils.h:280:8: style:inconclusive: Technically the member function 'Enum_fast_memory_map::get_all_current_memory_layer' can be const. [functionConst]
IGoR-1.4.0/igor_src/Utils.h:286:8: style:inconclusive: Technically the member function 'Enum_fast_memory_map::exist' can be const. [functionConst]
IGoR-1.4.0/igor_src/Utils.h:330:8: style:inconclusive: Technically the member function 'Enum_fast_memory_map::multiply_all' can be const. [functionConst]
IGoR-1.4.0/igor_src/Utils.h:506:7: style:inconclusive: Technically the member function 'Enum_fast_memory_dual_key_map::get_current_memory_layer' can be const. [functionConst]
IGoR-1.4.0/igor_src/Aligner.cpp:606:15: performance:inconclusive: Technically the member function 'Aligner::write_alignments_seq_csv' can be static (but you may consider moving to unnamed namespace). [functionStatic]
IGoR-1.4.0/igor_src/Aligner.h:128:7: note: Technically the member function 'Aligner::write_alignments_seq_csv' can be static (but you may consider moving to unnamed namespace).
IGoR-1.4.0/igor_src/Aligner.cpp:606:15: note: Technically the member function 'Aligner::write_alignments_seq_csv' can be static (but you may consider moving to unnamed namespace).
IGoR-1.4.0/igor_src/Aligner.cpp:859:14: performance:inconclusive: Technically the member function 'Aligner::incorporate_in_dels' can be static (but you may consider moving to unnamed namespace). [functionStatic]
IGoR-1.4.0/igor_src/Aligner.h:132:6: note: Technically the member function 'Aligner::incorporate_in_dels' can be static (but you may consider moving to unnamed namespace).
IGoR-1.4.0/igor_src/Aligner.cpp:859:14: note: Technically the member function 'Aligner::incorporate_in_dels' can be static (but you may consider moving to unnamed namespace).
IGoR-1.4.0/igor_src/Utils.h:202:4: warning: Class 'Enum_fast_memory_map' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
IGoR-1.4.0/igor_src/Utils.h:202:4: warning: Class 'Enum_fast_memory_map' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
IGoR-1.4.0/igor_src/Utils.h:405:4: warning: Class 'Enum_fast_memory_dual_key_map' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
IGoR-1.4.0/igor_src/Utils.h:405:4: warning: Class 'Enum_fast_memory_dual_key_map' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
IGoR-1.4.0/igor_src/Utils.h:201:3: style: Class 'Enum_fast_memory_map' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
IGoR-1.4.0/igor_src/Aligner.cpp:752:21: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Aligner.cpp:752:44: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Aligner.cpp:1254:7: style: The statement 'if (!last_column_explored) last_column_explored=true' is logically equivalent to 'last_column_explored=true'. [duplicateConditionalAssign]
IGoR-1.4.0/igor_src/Aligner.cpp:1254:51: note: Assignment 'last_column_explored=true'
IGoR-1.4.0/igor_src/Aligner.cpp:1254:7: note: Condition '!last_column_explored' is redundant
IGoR-1.4.0/igor_src/Aligner.cpp:340:5: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
IGoR-1.4.0/igor_src/Aligner.cpp:746:9: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
IGoR-1.4.0/igor_src/Deletion.h:134:6: style:inconclusive: Member variable 'Deletion::d_3_max_del' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/Deletion.cpp:51:101: note: Member variable 'Deletion::d_3_max_del' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:134:6: note: Member variable 'Deletion::d_3_max_del' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:96:13: style:inconclusive: Member variable 'Deletion::v_3_new_offset' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/Deletion.cpp:51:126: note: Member variable 'Deletion::v_3_new_offset' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:96:13: note: Member variable 'Deletion::v_3_new_offset' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:133:6: style:inconclusive: Member variable 'Deletion::v_3_min_del' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/Deletion.cpp:52:3: note: Member variable 'Deletion::v_3_min_del' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:133:6: note: Member variable 'Deletion::v_3_min_del' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:97:13: style:inconclusive: Member variable 'Deletion::d_5_min_offset' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/Deletion.cpp:52:60: note: Member variable 'Deletion::d_5_min_offset' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:97:13: note: Member variable 'Deletion::d_5_min_offset' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:100:13: style:inconclusive: Member variable 'Deletion::j_5_max_offset' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/Deletion.cpp:52:104: note: Member variable 'Deletion::j_5_max_offset' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:100:13: note: Member variable 'Deletion::j_5_max_offset' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:111:7: style:inconclusive: Member variable 'Deletion::dj_check' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/Deletion.cpp:52:160: note: Member variable 'Deletion::dj_check' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:111:7: note: Member variable 'Deletion::dj_check' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:139:7: style:inconclusive: Member variable 'Deletion::d_chosen' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/Deletion.cpp:52:220: note: Member variable 'Deletion::d_chosen' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:139:7: note: Member variable 'Deletion::d_chosen' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:149:9: style:inconclusive: Member variable 'Deletion::new_tmp_err_w_proba' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/Deletion.cpp:53:3: note: Member variable 'Deletion::new_tmp_err_w_proba' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:149:9: note: Member variable 'Deletion::new_tmp_err_w_proba' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:128:6: style:inconclusive: Member variable 'Deletion::d_5_max_del' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/Deletion.cpp:53:29: note: Member variable 'Deletion::d_5_max_del' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:128:6: note: Member variable 'Deletion::d_5_max_del' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:107:13: style:inconclusive: Member variable 'Deletion::v_3_min_offset' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/Deletion.cpp:53:54: note: Member variable 'Deletion::v_3_min_offset' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:107:13: note: Member variable 'Deletion::v_3_min_offset' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:147:9: style:inconclusive: Member variable 'Deletion::err_rate_upper_bound' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/Deletion.cpp:53:127: note: Member variable 'Deletion::err_rate_upper_bound' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:147:9: note: Member variable 'Deletion::err_rate_upper_bound' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:138:7: style:inconclusive: Member variable 'Deletion::v_chosen' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/Deletion.cpp:53:154: note: Member variable 'Deletion::v_chosen' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:138:7: note: Member variable 'Deletion::v_chosen' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:93:7: style:inconclusive: Member variable 'Deletion::vd_check' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/Deletion.cpp:53:170: note: Member variable 'Deletion::vd_check' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:93:7: note: Member variable 'Deletion::vd_check' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:122:13: style:inconclusive: Member variable 'Deletion::d_3_min_offset' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/Deletion.cpp:54:3: note: Member variable 'Deletion::d_3_min_offset' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:122:13: note: Member variable 'Deletion::d_3_min_offset' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:98:13: style:inconclusive: Member variable 'Deletion::d_5_max_offset' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/Deletion.cpp:54:31: note: Member variable 'Deletion::d_5_max_offset' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:98:13: note: Member variable 'Deletion::d_5_max_offset' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:106:13: style:inconclusive: Member variable 'Deletion::d_5_new_offset' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/Deletion.cpp:54:84: note: Member variable 'Deletion::d_5_new_offset' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:106:13: note: Member variable 'Deletion::d_5_new_offset' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:94:7: style:inconclusive: Member variable 'Deletion::vj_check' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/Deletion.cpp:54:112: note: Member variable 'Deletion::vj_check' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:94:7: note: Member variable 'Deletion::vj_check' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:105:13: style:inconclusive: Member variable 'Deletion::d_5_offset' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/Deletion.cpp:54:211: note: Member variable 'Deletion::d_5_offset' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:105:13: note: Member variable 'Deletion::d_5_offset' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:95:13: style:inconclusive: Member variable 'Deletion::v_3_offset' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/Deletion.cpp:55:3: note: Member variable 'Deletion::v_3_offset' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:95:13: note: Member variable 'Deletion::v_3_offset' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:162:6: style:inconclusive: Member variable 'Deletion::deletion_value' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/Deletion.cpp:55:89: note: Member variable 'Deletion::deletion_value' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:162:6: note: Member variable 'Deletion::deletion_value' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:130:6: style:inconclusive: Member variable 'Deletion::j_5_max_del' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/Deletion.cpp:55:117: note: Member variable 'Deletion::j_5_max_del' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:130:6: note: Member variable 'Deletion::j_5_max_del' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:112:13: style:inconclusive: Member variable 'Deletion::d_3_offset' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/Deletion.cpp:55:142: note: Member variable 'Deletion::d_3_offset' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:112:13: note: Member variable 'Deletion::d_3_offset' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:113:13: style:inconclusive: Member variable 'Deletion::d_3_new_offset' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/Deletion.cpp:55:191: note: Member variable 'Deletion::d_3_new_offset' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:113:13: note: Member variable 'Deletion::d_3_new_offset' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:121:13: style:inconclusive: Member variable 'Deletion::j_5_new_offset' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/Deletion.cpp:55:241: note: Member variable 'Deletion::j_5_new_offset' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.h:121:13: note: Member variable 'Deletion::j_5_new_offset' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Deletion.cpp:337:73: style: Checking if unsigned expression 'vd_length_best_proba_map.count(d_5_offset-v_3_new_offset-1)' is less than zero. [unsignedLessThanZero]
IGoR-1.4.0/igor_src/Deletion.cpp:343:73: style: Checking if unsigned expression 'vj_length_best_proba_map.count(j_5_offset-v_3_new_offset-1)' is less than zero. [unsignedLessThanZero]
IGoR-1.4.0/igor_src/Deletion.cpp:567:74: style: Checking if unsigned expression 'vd_length_best_proba_map.count(d_5_new_offset-v_3_offset-1)' is less than zero. [unsignedLessThanZero]
IGoR-1.4.0/igor_src/Deletion.cpp:829:74: style: Checking if unsigned expression 'dj_length_best_proba_map.count(j_5_offset-d_3_new_offset-1)' is less than zero. [unsignedLessThanZero]
IGoR-1.4.0/igor_src/Deletion.cpp:1119:75: style: Checking if unsigned expression 'dj_length_best_proba_map.count(j_5_new_offset-d_3_offset-1)' is less than zero. [unsignedLessThanZero]
IGoR-1.4.0/igor_src/Deletion.cpp:1125:73: style: Checking if unsigned expression 'vj_length_best_proba_map.count(j_5_new_offset-v_3_offset-1)' is less than zero. [unsignedLessThanZero]
IGoR-1.4.0/igor_src/Deletion.cpp:64:95: style: Parameter 'realizations' can be declared as reference to const [constParameterReference]
IGoR-1.4.0/igor_src/Deletion.cpp:1183:81: style: Parameter 'iter' can be declared as reference to const [constParameterReference]
IGoR-1.4.0/igor_src/Aligner.cpp:1484:18: style: The scope of the variable 'separated_strings' can be reduced. [variableScope]
IGoR-1.4.0/igor_src/Aligner.cpp:1521:17: style: The scope of the variable 'separated_strings' can be reduced. [variableScope]
IGoR-1.4.0/igor_src/Aligner.cpp:1473:77: style:inconclusive: Function 'read_gene_anchors_csv' argument 2 names different: declaration 'separator' definition 'sep'. [funcArgNamesDifferent]
IGoR-1.4.0/igor_src/Aligner.h:160:86: note: Function 'read_gene_anchors_csv' argument 2 names different: declaration 'separator' definition 'sep'.
IGoR-1.4.0/igor_src/Aligner.cpp:1473:77: note: Function 'read_gene_anchors_csv' argument 2 names different: declaration 'separator' definition 'sep'.
IGoR-1.4.0/igor_src/Aligner.cpp:1511:94: style:inconclusive: Function 'read_template_specific_offset_csv' argument 2 names different: declaration 'separator' definition 'sep'. [funcArgNamesDifferent]
IGoR-1.4.0/igor_src/Aligner.h:161:110: note: Function 'read_template_specific_offset_csv' argument 2 names different: declaration 'separator' definition 'sep'.
IGoR-1.4.0/igor_src/Aligner.cpp:1511:94: note: Function 'read_template_specific_offset_csv' argument 2 names different: declaration 'separator' definition 'sep'.
IGoR-1.4.0/igor_src/Aligner.cpp:238:56: performance: Function parameter 'nt_seq' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:246:56: performance: Function parameter 'nt_seq' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:246:158: performance: Function parameter 'restricted_genomic_list' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:254:56: performance: Function parameter 'nt_seq' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:262:56: performance: Function parameter 'nt_seq' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:262:180: performance: Function parameter 'restricted_genomic_list' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:270:56: performance: Function parameter 'nt_seq' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:270:149: performance: Function parameter 'genomic_offset_bounds' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:277:56: performance: Function parameter 'nt_seq' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:277:149: performance: Function parameter 'genomic_offset_bounds' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:277:184: performance: Function parameter 'restricted_genomic_list' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:282:56: performance: Function parameter 'nt_seq' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:282:170: performance: Function parameter 'genomic_offset_bounds' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:309:56: performance: Function parameter 'nt_seq' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:309:170: performance: Function parameter 'genomic_offset_bounds' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:364:108: performance: Function parameter 'sequence_list' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:372:108: performance: Function parameter 'sequence_list' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:380:108: performance: Function parameter 'sequence_list' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:385:108: performance: Function parameter 'sequence_list' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:390:108: performance: Function parameter 'sequence_list' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:390:208: performance: Function parameter 'genomic_offset_bounds' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:436:34: performance: Function parameter 'filename' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:436:84: performance: Function parameter 'sequence_list' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:443:34: performance: Function parameter 'filename' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:443:84: performance: Function parameter 'sequence_list' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:450:34: performance: Function parameter 'filename' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:450:84: performance: Function parameter 'sequence_list' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:450:184: performance: Function parameter 'genomic_offset_bounds' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:563:33: performance: Function parameter 'filename' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:563:83: performance: Function parameter 'sequence_list' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:569:33: performance: Function parameter 'filename' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:569:83: performance: Function parameter 'sequence_list' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:591:83: performance: Function parameter 'indexed_seq_list' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:606:106: performance: Function parameter 'indexed_alignments' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:618:98: performance: Function parameter 'seq_alignments' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:794:113: performance: Function parameter 'filename' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:794:235: performance: Function parameter 'indexed_sequences' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:800:113: performance: Function parameter 'filename' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:800:235: performance: Function parameter 'indexed_sequences' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:810:125: performance: Function parameter 'filename' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:810:243: performance: Function parameter 'indexed_sequences' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:868:23: performance: Function parameter 'nt_sequence' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:1066:98: performance: Function parameter 'indexed_seqs' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:1466:35: performance: Function parameter 'align1' should be passed by const reference. However it seems that 'align_compare' is a callback function. [passedByValueCallback]
IGoR-1.4.0/igor_src/Aligner.cpp:827:57: note: Function pointer used here.
IGoR-1.4.0/igor_src/Aligner.cpp:1466:35: note: Function parameter 'align1' should be passed by const reference. However it seems that 'align_compare' is a callback function.
IGoR-1.4.0/igor_src/Aligner.cpp:1466:59: performance: Function parameter 'align2' should be passed by const reference. However it seems that 'align_compare' is a callback function. [passedByValueCallback]
IGoR-1.4.0/igor_src/Aligner.cpp:827:57: note: Function pointer used here.
IGoR-1.4.0/igor_src/Aligner.cpp:1466:59: note: Function parameter 'align2' should be passed by const reference. However it seems that 'align_compare' is a callback function.
IGoR-1.4.0/igor_src/Aligner.cpp:1473:77: performance: Function parameter 'sep' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:1511:94: performance: Function parameter 'sep' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:1558:73: performance: Function parameter 'sep' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:1580:20: performance: Range variable 'field' should be declared as const reference. [iterateByValue]
IGoR-1.4.0/igor_src/Aligner.cpp:337:21: style: Variable 'e' can be declared as reference to const [constVariableReference]
IGoR-1.4.0/igor_src/Aligner.cpp:742:25: style: Variable 'except' can be declared as reference to const [constVariableReference]
IGoR-1.4.0/igor_src/Aligner.cpp:859:42: style: Parameter 'data_seq' can be declared as reference to const [constParameterReference]
IGoR-1.4.0/igor_src/Aligner.cpp:859:61: style: Parameter 'genomic_seq' can be declared as reference to const [constParameterReference]
IGoR-1.4.0/igor_src/Aligner.cpp:1092:145: style: Parameter 'score_matrix' can be declared as reference to const [constParameterReference]
IGoR-1.4.0/igor_src/Aligner.cpp:1092:173: style: Parameter 'row_memory_matrix' can be declared as reference to const [constParameterReference]
IGoR-1.4.0/igor_src/Aligner.cpp:1092:206: style: Parameter 'col_memory_matrix' can be declared as reference to const [constParameterReference]
IGoR-1.4.0/igor_src/Aligner.cpp:1139:9: style: Variable 'tmp' can be declared as reference to const [constVariableReference]
IGoR-1.4.0/igor_src/Aligner.cpp:143:21: error: Iterator 'letter' used after element has been erased. [eraseDereference]
IGoR-1.4.0/igor_src/Aligner.cpp:141:6: note: Iterator 'letter' used after element has been erased.
IGoR-1.4.0/igor_src/Aligner.cpp:143:21: note: Iterator 'letter' used after element has been erased.
IGoR-1.4.0/igor_src/Aligner.cpp:172:19: error: Iterator 'letter' used after element has been erased. [eraseDereference]
IGoR-1.4.0/igor_src/Aligner.cpp:169:4: note: Iterator 'letter' used after element has been erased.
IGoR-1.4.0/igor_src/Aligner.cpp:172:19: note: Iterator 'letter' used after element has been erased.
IGoR-1.4.0/igor_src/Aligner.cpp:1646:39: performance: Searching before insertion is not necessary. [stlFindInsert]
IGoR-1.4.0/igor_src/Deletion.cpp:241:8: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
IGoR-1.4.0/igor_src/Deletion.cpp:736:9: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
IGoR-1.4.0/igor_src/Deletion.cpp:744:11: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
IGoR-1.4.0/igor_src/Aligner.cpp:1581:13: style: Consider using std::transform algorithm instead of a raw loop. [useStlAlgorithm]
IGoR-1.4.0/igor_src/Aligner.cpp:141:12: error:inconclusive: Using iterator to local container 'seq_str' that may be invalid. [invalidContainer]
IGoR-1.4.0/igor_src/Aligner.cpp:140:45: note: Iterator to container is created here.
IGoR-1.4.0/igor_src/Aligner.cpp:141:19: note: Assuming condition is true.
IGoR-1.4.0/igor_src/Aligner.cpp:142:21: note: Assuming condition is true.
IGoR-1.4.0/igor_src/Aligner.cpp:142:21: note: Assuming condition is true.
IGoR-1.4.0/igor_src/Aligner.cpp:141:19: note: Assuming condition is true.
IGoR-1.4.0/igor_src/Aligner.cpp:143:16: note: After calling 'erase', iterators or references to the container's data may be invalid .
IGoR-1.4.0/igor_src/Aligner.cpp:124:10: note: Variable created here.
IGoR-1.4.0/igor_src/Aligner.cpp:141:12: note: Using iterator to local container 'seq_str' that may be invalid.
IGoR-1.4.0/igor_src/Aligner.cpp:169:10: error:inconclusive: Using iterator to local container 'seq_str' that may be invalid. [invalidContainer]
IGoR-1.4.0/igor_src/Aligner.cpp:168:43: note: Iterator to container is created here.
IGoR-1.4.0/igor_src/Aligner.cpp:169:17: note: Assuming condition is true.
IGoR-1.4.0/igor_src/Aligner.cpp:171:19: note: Assuming condition is true.
IGoR-1.4.0/igor_src/Aligner.cpp:171:19: note: Assuming condition is true.
IGoR-1.4.0/igor_src/Aligner.cpp:169:17: note: Assuming condition is true.
IGoR-1.4.0/igor_src/Aligner.cpp:172:14: note: After calling 'erase', iterators or references to the container's data may be invalid .
IGoR-1.4.0/igor_src/Aligner.cpp:124:10: note: Variable created here.
IGoR-1.4.0/igor_src/Aligner.cpp:169:10: note: Using iterator to local container 'seq_str' that may be invalid.
IGoR-1.4.0/igor_src/Aligner.cpp:824:115: error: Dereference of an invalid iterator: seq_alignments.begin()-1 [derefInvalidIterator]
IGoR-1.4.0/igor_src/Aligner.cpp:1584:21: warning: Uninitialized variable: line_size [uninitvar]
IGoR-1.4.0/igor_src/Aligner.cpp:1567:15: note: Assuming condition is false
IGoR-1.4.0/igor_src/Aligner.cpp:1584:21: note: Uninitialized variable: line_size
IGoR-1.4.0/igor_src/Aligner.cpp:479:50: style: Unused variable: alignment_map [unusedVariable]
IGoR-1.4.0/igor_src/Aligner.cpp:1077:20: style: Variable 'dur' is assigned a value that is never used. [unreadVariable]
IGoR-1.4.0/igor_src/Aligner.cpp:150:12: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
IGoR-1.4.0/igor_src/Aligner.cpp:179:10: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
IGoR-1.4.0/igor_src/Aligner.cpp:316:134: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
IGoR-1.4.0/igor_src/Aligner.cpp:345:106: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
IGoR-1.4.0/igor_src/Aligner.cpp:413:125: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
IGoR-1.4.0/igor_src/Aligner.cpp:522:125: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
IGoR-1.4.0/igor_src/Aligner.cpp:594:124: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
IGoR-1.4.0/igor_src/Dinuclmarkov.cpp:282:88: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Errorrate.cpp:30:13: warning: Member variable 'Error_rate::scenario_new_proba' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Errorrate.cpp:30:13: warning: Member variable 'Error_rate::viterbi_run' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Errorrate.h:87:7: style:inconclusive: Member variable 'Error_rate::updated' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/Errorrate.cpp:30:166: note: Member variable 'Error_rate::updated' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Errorrate.h:87:7: note: Member variable 'Error_rate::updated' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/ExtractFeatures.cpp:88:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/ExtractFeatures.cpp:218:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Errorscounter.cpp:145:129: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Errorscounter.cpp:170:137: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/ExtractFeatures.cpp:28:18: warning: Member variable 'ExtractFeatures::p_sorted_alignments' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/ExtractFeatures.cpp:31:18: warning:inconclusive: Member variable 'ExtractFeatures::UMap_v_genomic' is not assigned in the copy constructor. Should it be copied? [missingMemberCopy]
IGoR-1.4.0/igor_src/ExtractFeatures.cpp:31:18: warning:inconclusive: Member variable 'ExtractFeatures::UMap_j_genomic' is not assigned in the copy constructor. Should it be copied? [missingMemberCopy]
IGoR-1.4.0/igor_src/ExtractFeatures.cpp:31:18: warning:inconclusive: Member variable 'ExtractFeatures::UMap_v_CDR3_anchors' is not assigned in the copy constructor. Should it be copied? [missingMemberCopy]
IGoR-1.4.0/igor_src/ExtractFeatures.cpp:31:18: warning:inconclusive: Member variable 'ExtractFeatures::UMap_j_CDR3_anchors' is not assigned in the copy constructor. Should it be copied? [missingMemberCopy]
IGoR-1.4.0/igor_src/ExtractFeatures.cpp:31:18: warning: Member variable 'ExtractFeatures::p_sorted_alignments' is not initialized in the copy constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/ExtractFeatures.cpp:215:25: style:inconclusive: Technically the member function 'ExtractFeatures::generateCDR3_csv_line' can be const. [functionConst]
IGoR-1.4.0/igor_src/ExtractFeatures.h:70:12: note: Technically the member function 'ExtractFeatures::generateCDR3_csv_line' can be const.
IGoR-1.4.0/igor_src/ExtractFeatures.cpp:215:25: note: Technically the member function 'ExtractFeatures::generateCDR3_csv_line' can be const.
IGoR-1.4.0/igor_src/ExtractFeatures.cpp:67:69: style:inconclusive: Function 'load_VJanchors' argument 1 names different: declaration 'flnV_CDR3_anchors' definition 'v_CDR3_anchors'. [funcArgNamesDifferent]
IGoR-1.4.0/igor_src/ExtractFeatures.h:57:56: note: Function 'load_VJanchors' argument 1 names different: declaration 'flnV_CDR3_anchors' definition 'v_CDR3_anchors'.
IGoR-1.4.0/igor_src/ExtractFeatures.cpp:67:69: note: Function 'load_VJanchors' argument 1 names different: declaration 'flnV_CDR3_anchors' definition 'v_CDR3_anchors'.
IGoR-1.4.0/igor_src/ExtractFeatures.cpp:67:116: style:inconclusive: Function 'load_VJanchors' argument 2 names different: declaration 'flnJ_CDR3_anchors' definition 'j_CDR3_anchors'. [funcArgNamesDifferent]
IGoR-1.4.0/igor_src/ExtractFeatures.h:57:106: note: Function 'load_VJanchors' argument 2 names different: declaration 'flnJ_CDR3_anchors' definition 'j_CDR3_anchors'.
IGoR-1.4.0/igor_src/ExtractFeatures.cpp:67:116: note: Function 'load_VJanchors' argument 2 names different: declaration 'flnJ_CDR3_anchors' definition 'j_CDR3_anchors'.
IGoR-1.4.0/igor_src/ExtractFeatures.cpp:42:75: performance: Function parameter 'v_genomic' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/ExtractFeatures.cpp:42:114: performance: Function parameter 'j_genomic' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/ExtractFeatures.cpp:57:45: performance: Function parameter 'flnV_CDR3_anchors' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/ExtractFeatures.cpp:57:71: performance: Function parameter 'flnJ_CDR3_anchors' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/ExtractFeatures.cpp:67:69: performance: Function parameter 'v_CDR3_anchors' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/ExtractFeatures.cpp:67:116: performance: Function parameter 'j_CDR3_anchors' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/ExtractFeatures.cpp:124:44: performance: Function parameter 'seq_str' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/ExtractFeatures.cpp:169:44: performance: Function parameter 'seq_str' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/ExtractFeatures.cpp:215:59: performance: Function parameter 'cdr3InputSeq' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Dinuclmarkov.cpp:304:26: style:inconclusive: Boolean expression 'first_nt_index<4' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Dinuclmarkov.cpp:333:27: style:inconclusive: Boolean expression 'first_nt_index<4' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Dinuclmarkov.cpp:30:16: warning: Member variable 'Dinucl_markov::max_vd_ins' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Dinuclmarkov.cpp:30:16: warning: Member variable 'Dinucl_markov::vd_realizations_indices' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Dinuclmarkov.cpp:30:16: warning: Member variable 'Dinucl_markov::vd_seq_size' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Dinuclmarkov.cpp:30:16: warning: Member variable 'Dinucl_markov::max_vj_ins' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Dinuclmarkov.cpp:30:16: warning: Member variable 'Dinucl_markov::vj_realizations_indices' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Dinuclmarkov.cpp:30:16: warning: Member variable 'Dinucl_markov::vj_seq_size' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Dinuclmarkov.cpp:30:16: warning: Member variable 'Dinucl_markov::max_dj_ins' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Dinuclmarkov.cpp:30:16: warning: Member variable 'Dinucl_markov::dj_realizations_indices' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Dinuclmarkov.cpp:30:16: warning: Member variable 'Dinucl_markov::dj_seq_size' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Dinuclmarkov.cpp:30:16: warning: Member variable 'Dinucl_markov::previous_seq_size' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Dinuclmarkov.cpp:30:16: warning: Member variable 'Dinucl_markov::previous_nt_str' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Dinuclmarkov.cpp:30:16: warning: Member variable 'Dinucl_markov::base_index' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Dinuclmarkov.cpp:30:16: warning: Member variable 'Dinucl_markov::unmutable_base_index' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Dinuclmarkov.cpp:30:16: warning: Member variable 'Dinucl_markov::new_scenario_proba' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Dinuclmarkov.cpp:30:16: warning: Member variable 'Dinucl_markov::proba_contribution' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Dinuclmarkov.cpp:30:16: warning: Member variable 'Dinucl_markov::correct_class' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Dinuclmarkov.cpp:30:16: warning: Member variable 'Dinucl_markov::memory_layer_proba_map_junction_1' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Dinuclmarkov.cpp:30:16: warning: Member variable 'Dinucl_markov::memory_layer_proba_map_junction_2' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Dinuclmarkov.cpp:30:16: warning: Member variable 'Dinucl_markov::first_nt_index' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Dinuclmarkov.cpp:30:16: warning: Member variable 'Dinucl_markov::sec_nt_index' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Dinuclmarkov.cpp:30:16: warning: Member variable 'Dinucl_markov::offset' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Dinuclmarkov.cpp:30:16: warning: Member variable 'Dinucl_markov::realization_final_index' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Dinuclmarkov.cpp:41:2: warning: Class 'Dinucl_markov' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
IGoR-1.4.0/igor_src/Dinuclmarkov.cpp:41:2: warning: Class 'Dinucl_markov' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
IGoR-1.4.0/igor_src/Dinuclmarkov.cpp:219:9: style: The scope of the variable 'prob_count' can be reduced. [variableScope]
IGoR-1.4.0/igor_src/Dinuclmarkov.cpp:289:63: style: Parameter 'previous_assigned_nt' can be declared as reference to const [constParameterReference]
IGoR-1.4.0/igor_src/Errorscounter.h:43:2: style: Class 'Errors_counter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
IGoR-1.4.0/igor_src/Errorscounter.h:47:11: style: The destructor '~Errors_counter' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Counter.h:50:11: note: Virtual destructor in base class
IGoR-1.4.0/igor_src/Errorscounter.h:47:11: note: Destructor in derived class
IGoR-1.4.0/igor_src/Errorscounter.h:49:14: style: The function 'type' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Counter.h:52:22: note: Virtual function in base class
IGoR-1.4.0/igor_src/Errorscounter.h:49:14: note: Function in derived class
IGoR-1.4.0/igor_src/Errorscounter.h:51:7: style: The function 'initialize_counter' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Counter.h:54:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Errorscounter.h:51:7: note: Function in derived class
IGoR-1.4.0/igor_src/Errorscounter.h:53:7: style: The function 'count_scenario' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Counter.h:56:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Errorscounter.h:53:7: note: Function in derived class
IGoR-1.4.0/igor_src/Errorscounter.h:55:7: style: The function 'count_sequence' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Counter.h:57:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Errorscounter.h:55:7: note: Function in derived class
IGoR-1.4.0/igor_src/Errorscounter.h:57:7: style: The function 'add_checked' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Counter.h:60:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Errorscounter.h:57:7: note: Function in derived class
IGoR-1.4.0/igor_src/Errorscounter.h:59:7: style: The function 'dump_sequence_data' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Counter.h:62:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Errorscounter.h:59:7: note: Function in derived class
IGoR-1.4.0/igor_src/Errorscounter.h:61:27: style: The function 'copy' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Counter.h:69:35: note: Virtual function in base class
IGoR-1.4.0/igor_src/Errorscounter.h:61:27: note: Function in derived class
IGoR-1.4.0/igor_src/Errorscounter.cpp:40:60: performance: Function parameter 'path' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Errorscounter.cpp:47:61: performance: Function parameter 'path' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/GenModel.h:114:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/GenModel.cpp:49:127: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INFINITY [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/GenModel.cpp:56:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/GenModel.cpp:486:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/GenModel.cpp:505:78: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/GenModel.cpp:626:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/GenModel.cpp:635:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/GenModel.cpp:757:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Genechoice.cpp:984:87: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:172:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:945:80: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:1047:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:1184:115: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/GenModel.cpp:623:16: performance:inconclusive: Technically the member function 'GenModel::write_seq2txt' can be static (but you may consider moving to unnamed namespace). [functionStatic]
IGoR-1.4.0/igor_src/GenModel.h:168:7: note: Technically the member function 'GenModel::write_seq2txt' can be static (but you may consider moving to unnamed namespace).
IGoR-1.4.0/igor_src/GenModel.cpp:623:16: note: Technically the member function 'GenModel::write_seq2txt' can be static (but you may consider moving to unnamed namespace).
IGoR-1.4.0/igor_src/Utils.h:96:7: style:inconclusive: Technically the member function 'null_delete < std :: ostream >::operator()' can be const. [functionConst]
IGoR-1.4.0/igor_src/GenModel.h:153:2: style: Class 'GenModel' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
IGoR-1.4.0/igor_src/GenModel.cpp:161:10: style: The scope of the variable 'sequences_processed' can be reduced. [variableScope]
IGoR-1.4.0/igor_src/GenModel.cpp:343:12: style: The scope of the variable 'init_proba' can be reduced. [variableScope]
IGoR-1.4.0/igor_src/GenModel.h:159:180: performance: Function parameter 'path' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/GenModel.h:160:180: performance: Function parameter 'path' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/GenModel.h:161:180: performance: Function parameter 'path' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/GenModel.cpp:116:22: performance: Range variable 'name' should be declared as const reference. [iterateByValue]
IGoR-1.4.0/igor_src/GenModel.cpp:121:22: performance: Range variable 'name' should be declared as const reference. [iterateByValue]
IGoR-1.4.0/igor_src/GenModel.cpp:623:69: performance: Function parameter 'sequences' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/GenModel.cpp:630:133: performance: Function parameter 'seq_and_realizations' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/GenModel.cpp:719:57: warning: Uninitialized variable: j_gene_anchors [uninitvar]
IGoR-1.4.0/igor_src/GenModel.cpp:706:4: note: Assuming condition is false
IGoR-1.4.0/igor_src/GenModel.cpp:719:57: note: Uninitialized variable: j_gene_anchors
IGoR-1.4.0/igor_src/GenModel.cpp:720:31: warning: Uninitialized variable: v_gene_anchors [uninitvar]
IGoR-1.4.0/igor_src/GenModel.cpp:706:4: note: Assuming condition is false
IGoR-1.4.0/igor_src/GenModel.cpp:720:31: note: Uninitialized variable: v_gene_anchors
IGoR-1.4.0/igor_src/GenModel.cpp:470:20: style: Variable 'dur' is assigned a value that is never used. [unreadVariable]
IGoR-1.4.0/igor_src/GenModel.cpp:645:142: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
IGoR-1.4.0/igor_src/Genechoice.cpp:544:33: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Genechoice.cpp:649:33: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Genechoice.cpp:255:63: style: Checking if unsigned expression 'vd_length_best_proba_map.count(d_offset-v_3_off-1)' is less than zero. [unsignedLessThanZero]
IGoR-1.4.0/igor_src/Genechoice.cpp:261:63: style: Checking if unsigned expression 'vj_length_best_proba_map.count(j_offset-v_3_off-1)' is less than zero. [unsignedLessThanZero]
IGoR-1.4.0/igor_src/Genechoice.cpp:412:63: style: Checking if unsigned expression 'vd_length_best_proba_map.count(d_5_off-v_offset-1)' is less than zero. [unsignedLessThanZero]
IGoR-1.4.0/igor_src/Genechoice.cpp:412:124: style: Checking if unsigned expression 'dj_length_best_proba_map.count(j_offset-d_3_off-1)' is less than zero. [unsignedLessThanZero]
IGoR-1.4.0/igor_src/Genechoice.cpp:420:63: style: Checking if unsigned expression 'vd_length_best_proba_map.count(d_5_off-v_offset-1)' is less than zero. [unsignedLessThanZero]
IGoR-1.4.0/igor_src/Genechoice.cpp:426:64: style: Checking if unsigned expression 'dj_length_best_proba_map.count(j_offset-d_3_off-1)' is less than zero. [unsignedLessThanZero]
IGoR-1.4.0/igor_src/Genechoice.cpp:678:66: style: Checking if unsigned expression 'vd_length_best_proba_map.count(d_5_off-v_offset-1)' is less than zero. [unsignedLessThanZero]
IGoR-1.4.0/igor_src/Genechoice.cpp:678:135: style: Checking if unsigned expression 'dj_length_best_proba_map.count(j_offset-d_full_3_offset-1)' is less than zero. [unsignedLessThanZero]
IGoR-1.4.0/igor_src/Genechoice.cpp:686:66: style: Checking if unsigned expression 'vd_length_best_proba_map.count(d_5_off-v_offset-1)' is less than zero. [unsignedLessThanZero]
IGoR-1.4.0/igor_src/Genechoice.cpp:692:75: style: Checking if unsigned expression 'dj_length_best_proba_map.count(j_offset-d_full_3_offset-1)' is less than zero. [unsignedLessThanZero]
IGoR-1.4.0/igor_src/Genechoice.cpp:872:65: style: Checking if unsigned expression 'dj_length_best_proba_map.count(j_5_off-d_offset-1)' is less than zero. [unsignedLessThanZero]
IGoR-1.4.0/igor_src/Genechoice.cpp:878:63: style: Checking if unsigned expression 'vj_length_best_proba_map.count(j_5_off-v_offset-1)' is less than zero. [unsignedLessThanZero]
IGoR-1.4.0/igor_src/Genechoice.cpp:93:42: performance: Function parameter 'gene_name' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Genechoice.cpp:93:61: performance: Function parameter 'gene_sequence' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Genechoice.cpp:54:85: style: Parameter 'realizations' can be declared as reference to const [constParameterReference]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:190:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1085:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1101:80: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1504:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1642:113: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:71:24: style:inconclusive: Boolean expression 'apply_to==V_gene' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:71:70: style:inconclusive: Boolean expression 'apply_to==VDJ_genes' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:76:24: style:inconclusive: Boolean expression 'apply_to==D_gene' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:76:70: style:inconclusive: Boolean expression 'apply_to==VDJ_genes' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:81:24: style:inconclusive: Boolean expression 'apply_to==J_gene' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:81:70: style:inconclusive: Boolean expression 'apply_to==VDJ_genes' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:86:24: style:inconclusive: Boolean expression 'learn_on==V_gene' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:86:70: style:inconclusive: Boolean expression 'learn_on==VDJ_genes' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:91:24: style:inconclusive: Boolean expression 'learn_on==D_gene' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:91:70: style:inconclusive: Boolean expression 'learn_on==VDJ_genes' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:96:24: style:inconclusive: Boolean expression 'learn_on==J_gene' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:96:70: style:inconclusive: Boolean expression 'learn_on==VDJ_genes' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:205:3: style:inconclusive: Boolean expression 'this->learn_on==err_r.learn_on' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:206:3: style:inconclusive: Boolean expression 'this->mutation_Nmer_size==err_r.mutation_Nmer_size' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:207:3: style:inconclusive: Boolean expression 'identical_mut_probas' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:1046:25: style:inconclusive: Boolean expression 'learn_on==V_gene' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:1046:71: style:inconclusive: Boolean expression 'learn_on==VDJ_genes' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:1077:25: style:inconclusive: Boolean expression 'learn_on==D_gene' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:1077:71: style:inconclusive: Boolean expression 'learn_on==VDJ_genes' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:1110:25: style:inconclusive: Boolean expression 'learn_on==J_gene' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:1110:71: style:inconclusive: Boolean expression 'learn_on==VDJ_genes' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:83:9: style:inconclusive: Member variable 'Hypermutation_full_Nmer_errorrate::mutation_Nmer_size' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:31:250: note: Member variable 'Hypermutation_full_Nmer_errorrate::mutation_Nmer_size' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:83:9: note: Member variable 'Hypermutation_full_Nmer_errorrate::mutation_Nmer_size' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:81:13: style:inconclusive: Member variable 'Hypermutation_full_Nmer_errorrate::learn_on' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:31:283: note: Member variable 'Hypermutation_full_Nmer_errorrate::learn_on' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:81:13: note: Member variable 'Hypermutation_full_Nmer_errorrate::learn_on' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:95:9: style:inconclusive: Member variable 'Hypermutation_full_Nmer_errorrate::n_d_real' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:31:347: note: Member variable 'Hypermutation_full_Nmer_errorrate::n_d_real' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:95:9: note: Member variable 'Hypermutation_full_Nmer_errorrate::n_d_real' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:121:7: style:inconclusive: Member variable 'Hypermutation_full_Nmer_errorrate::vd_ins' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:33:18: note: Member variable 'Hypermutation_full_Nmer_errorrate::vd_ins' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:121:7: note: Member variable 'Hypermutation_full_Nmer_errorrate::vd_ins' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:118:7: style:inconclusive: Member variable 'Hypermutation_full_Nmer_errorrate::v_gene' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:33:48: note: Member variable 'Hypermutation_full_Nmer_errorrate::v_gene' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:118:7: note: Member variable 'Hypermutation_full_Nmer_errorrate::v_gene' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:1192:41: performance:inconclusive: Technically the member function 'Hypermutation_full_Nmer_errorrate::introduce_uniform_transversion' can be static (but you may consider moving to unnamed namespace). [functionStatic]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:79:7: note: Technically the member function 'Hypermutation_full_Nmer_errorrate::introduce_uniform_transversion' can be static (but you may consider moving to unnamed namespace).
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:1192:41: note: Technically the member function 'Hypermutation_full_Nmer_errorrate::introduce_uniform_transversion' can be static (but you may consider moving to unnamed namespace).
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:53:2: warning: Class 'Hypermutation_full_Nmer_errorrate' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:53:2: warning: Class 'Hypermutation_full_Nmer_errorrate' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:71:24: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:71:47: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:71:70: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:76:24: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:76:47: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:76:70: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:81:24: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:81:47: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:81:70: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:86:24: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:86:47: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:86:70: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:91:24: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:91:47: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:91:70: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:96:24: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:96:47: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:96:70: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:1046:25: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:1046:48: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:1046:71: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:1077:25: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:1077:48: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:1077:71: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:1110:25: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:1110:48: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:1110:71: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Insertion.cpp:341:86: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:257:14: style: Local variable 'i' shadows outer variable [shadowVariable]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:142:14: note: Shadowed declaration
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:257:14: note: Shadow variable
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:258:15: style: Local variable 'j' shadows outer variable [shadowVariable]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:143:14: note: Shadowed declaration
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:258:15: note: Shadow variable
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:299:13: style: Local variable 'i' shadows outer variable [shadowVariable]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:142:14: note: Shadowed declaration
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:299:13: note: Shadow variable
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:300:14: style: Local variable 'j' shadows outer variable [shadowVariable]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:143:14: note: Shadowed declaration
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:300:14: note: Shadow variable
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:113:143: performance: Function parameter 'init_Nmer_mutations_probas' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:129:162: performance: Function parameter 'filename' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:133:143: performance: Function parameter 'init_Nmer_mutations_probas' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:133:177: performance: Function parameter 'filename' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:171:71: performance: Function parameter 'filename' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:193:117: performance: Function parameter 'err_r' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:1192:152: style: Parameter 'distribution' can be declared as reference to const [constParameterReference]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:353:33: error: Iterators of different containers '*mismatches_lists.at(J_gene_seq)' and '*mismatches_lists.at(V_gene_seq)' are used together. [mismatchingContainers]
IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:923:20: style: Variable 'dur' is assigned a value that is never used. [unreadVariable]
IGoR-1.4.0/igor_src/Insertion.cpp:31:12: warning: Member variable 'Insertion::memory_layer_proba_map_junction' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Insertion.cpp:52:12: warning: Member variable 'Insertion::memory_layer_proba_map_junction' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Insertion.cpp:61:12: warning: Member variable 'Insertion::memory_layer_proba_map_junction' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Insertion.h:90:6: style:inconclusive: Member variable 'Insertion::insertions' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/Insertion.cpp:52:121: note: Member variable 'Insertion::insertions' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Insertion.h:90:6: note: Member variable 'Insertion::insertions' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Insertion.h:88:9: style:inconclusive: Member variable 'Insertion::new_scenario_proba' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/Insertion.cpp:52:138: note: Member variable 'Insertion::new_scenario_proba' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Insertion.h:88:9: note: Member variable 'Insertion::new_scenario_proba' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Insertion.h:87:14: style:inconclusive: Member variable 'Insertion::base_index' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/Insertion.cpp:52:163: note: Member variable 'Insertion::base_index' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Insertion.h:87:14: note: Member variable 'Insertion::base_index' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Insertion.cpp:61:81: style: Parameter 'realizations' can be declared as reference to const [constParameterReference]
IGoR-1.4.0/igor_src/Model_Parms.cpp:333:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Model_Parms.cpp:519:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Model_Parms.cpp:573:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Model_marginals.cpp:99:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Model_marginals.cpp:1087:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Model_marginals.cpp:1135:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Model_marginals.cpp:1156:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Model_Parms.cpp:60:14: warning:inconclusive: Member variable 'Model_Parms::events' is not assigned in the copy constructor. Should it be copied? [missingMemberCopy]
IGoR-1.4.0/igor_src/Model_Parms.cpp:60:14: warning:inconclusive: Member variable 'Model_Parms::edges' is not assigned in the copy constructor. Should it be copied? [missingMemberCopy]
IGoR-1.4.0/igor_src/Utils.h:96:7: style:inconclusive: Technically the member function 'null_delete < Rec_Event >::operator()' can be const. [functionConst]
IGoR-1.4.0/igor_src/Model_Parms.cpp:131:24: style: Return value 'this->add_event(std::shared_ptr<Rec_Event>(event_point,null_delete < Rec_Event >()))' is always true [knownConditionTrueFalse]
IGoR-1.4.0/igor_src/Model_Parms.cpp:131:24: note: Calling function 'add_event' returns 1
IGoR-1.4.0/igor_src/Model_Parms.cpp:131:24: note: Return value 'this->add_event(std::shared_ptr<Rec_Event>(event_point,null_delete < Rec_Event >()))' is always true
IGoR-1.4.0/igor_src/Model_Parms.cpp:222:23: style: Return value 'this->add_edge(parent_smart_p,child_smart_p)' is always true [knownConditionTrueFalse]
IGoR-1.4.0/igor_src/Model_Parms.cpp:222:23: note: Calling function 'add_edge' returns 1
IGoR-1.4.0/igor_src/Model_Parms.cpp:222:23: note: Return value 'this->add_edge(parent_smart_p,child_smart_p)' is always true
IGoR-1.4.0/igor_src/Model_Parms.cpp:259:23: style: Return value 'this->add_edge(parent_smart_p,child_smart_p)' is always true [knownConditionTrueFalse]
IGoR-1.4.0/igor_src/Model_Parms.cpp:259:23: note: Calling function 'add_edge' returns 1
IGoR-1.4.0/igor_src/Model_Parms.cpp:259:23: note: Return value 'this->add_edge(parent_smart_p,child_smart_p)' is always true
IGoR-1.4.0/igor_src/Model_Parms.cpp:268:26: style: Return value 'this->remove_edge(parent_smart_p,child_smart_p)' is always true [knownConditionTrueFalse]
IGoR-1.4.0/igor_src/Model_Parms.cpp:268:26: note: Calling function 'remove_edge' returns 1
IGoR-1.4.0/igor_src/Model_Parms.cpp:268:26: note: Return value 'this->remove_edge(parent_smart_p,child_smart_p)' is always true
IGoR-1.4.0/igor_src/Model_Parms.cpp:309:26: style: Return value 'this->remove_edge(parent_smart_p,child_smart_p)' is always true [knownConditionTrueFalse]
IGoR-1.4.0/igor_src/Model_Parms.cpp:309:26: note: Calling function 'remove_edge' returns 1
IGoR-1.4.0/igor_src/Model_Parms.cpp:309:26: note: Return value 'this->remove_edge(parent_smart_p,child_smart_p)' is always true
IGoR-1.4.0/igor_src/Model_Parms.cpp:334:4: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
IGoR-1.4.0/igor_src/Model_Parms.cpp:348:4: style: Throwing a copy of the caught exception instead of rethrowing the original exception. [exceptRethrowCopy]
IGoR-1.4.0/igor_src/Model_Parms.cpp:146:28: style: Checking if unsigned expression 'edges.count(event_name)' is less than zero. [unsignedLessThanZero]
IGoR-1.4.0/igor_src/Model_Parms.cpp:162:28: style: Checking if unsigned expression 'edges.count(event_name)' is less than zero. [unsignedLessThanZero]
IGoR-1.4.0/igor_src/Model_Parms.cpp:196:28: style: Checking if unsigned expression 'edges.count(event_name)' is less than zero. [unsignedLessThanZero]
IGoR-1.4.0/igor_src/Model_Parms.cpp:204:50: style: Checking if unsigned expression 'ancestor_set.count(exploratory_list.front())' is less than zero. [unsignedLessThanZero]
IGoR-1.4.0/igor_src/Model_Parms.cpp:229:43: style: Checking if unsigned expression 'edges.count(parent_point->get_name())' is less than zero. [unsignedLessThanZero]
IGoR-1.4.0/igor_src/Model_Parms.cpp:232:42: style: Checking if unsigned expression 'edges.count(child_point->get_name())' is less than zero. [unsignedLessThanZero]
IGoR-1.4.0/igor_src/Model_Parms.cpp:45:55: performance: Function parameter 'event_list' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Model_Parms.cpp:145:69: performance: Function parameter 'event_name' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Model_Parms.cpp:161:70: performance: Function parameter 'event_name' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Model_Parms.cpp:190:71: performance: Function parameter 'event_name' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Model_Parms.cpp:256:43: performance: Function parameter 'parent_name' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Model_Parms.cpp:256:71: performance: Function parameter 'child_name' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Model_Parms.cpp:306:46: performance: Function parameter 'parent_name' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Model_Parms.cpp:306:74: performance: Function parameter 'child_name' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Model_Parms.cpp:358:46: performance: Function parameter 'ev1_name' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Model_Parms.cpp:358:71: performance: Function parameter 'ev2_name' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Model_Parms.cpp:379:43: performance: Function parameter 'parent_name' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Model_Parms.cpp:379:71: performance: Function parameter 'child_name' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Model_Parms.cpp:70:29: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
IGoR-1.4.0/igor_src/Model_Parms.cpp:78:29: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
IGoR-1.4.0/igor_src/Model_Parms.cpp:244:56: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
IGoR-1.4.0/igor_src/Model_Parms.cpp:280:30: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
IGoR-1.4.0/igor_src/Model_Parms.cpp:293:31: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
IGoR-1.4.0/igor_src/Model_Parms.cpp:285:17: warning: Either the condition is redundant or function 'erase()' is called on the iterator 'iter' which is out of bounds. [eraseIteratorOutOfBoundsCond]
IGoR-1.4.0/igor_src/Model_Parms.cpp:298:16: warning: Either the condition is redundant or function 'erase()' is called on the iterator 'iter' which is out of bounds. [eraseIteratorOutOfBoundsCond]
IGoR-1.4.0/igor_src/Model_Parms.cpp:627:18: style: Variable 'test' is assigned a value that is never used. [unreadVariable]
IGoR-1.4.0/igor_src/Model_Parms.cpp:627:13: style: Variable 'test' is assigned a value that is never used. [unreadVariable]
IGoR-1.4.0/igor_src/Model_Parms.cpp:69:113: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:92:24: style:inconclusive: Boolean expression 'apply_to==V_gene' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:92:70: style:inconclusive: Boolean expression 'apply_to==VDJ_genes' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:97:24: style:inconclusive: Boolean expression 'apply_to==D_gene' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:97:70: style:inconclusive: Boolean expression 'apply_to==VDJ_genes' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:102:24: style:inconclusive: Boolean expression 'apply_to==J_gene' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:102:70: style:inconclusive: Boolean expression 'apply_to==VDJ_genes' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:107:24: style:inconclusive: Boolean expression 'learn_on==V_gene' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:107:70: style:inconclusive: Boolean expression 'learn_on==VDJ_genes' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:112:24: style:inconclusive: Boolean expression 'learn_on==D_gene' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:112:70: style:inconclusive: Boolean expression 'learn_on==VDJ_genes' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:117:24: style:inconclusive: Boolean expression 'learn_on==J_gene' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:117:70: style:inconclusive: Boolean expression 'learn_on==VDJ_genes' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:217:3: style:inconclusive: Boolean expression 'this->learn_on==err_r.learn_on' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:218:3: style:inconclusive: Boolean expression 'this->mutation_Nmer_size==err_r.mutation_Nmer_size' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:219:3: style:inconclusive: Boolean expression 'this->mu==err_r.mu' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1503:25: style:inconclusive: Boolean expression 'learn_on==V_gene' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1503:71: style:inconclusive: Boolean expression 'learn_on==VDJ_genes' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1535:25: style:inconclusive: Boolean expression 'learn_on==D_gene' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1535:71: style:inconclusive: Boolean expression 'learn_on==VDJ_genes' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1568:25: style:inconclusive: Boolean expression 'learn_on==J_gene' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1568:71: style:inconclusive: Boolean expression 'learn_on==VDJ_genes' is used in bitwise operation. Did you mean '||'? [bitwiseOnBoolean]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1241:116: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1422:118: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:90:13: style:inconclusive: Member variable 'Hypermutation_global_errorrate::learn_on' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:43:199: note: Member variable 'Hypermutation_global_errorrate::learn_on' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:90:13: note: Member variable 'Hypermutation_global_errorrate::learn_on' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:114:9: style:inconclusive: Member variable 'Hypermutation_global_errorrate::n_d_real' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:43:348: note: Member variable 'Hypermutation_global_errorrate::n_d_real' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:114:9: note: Member variable 'Hypermutation_global_errorrate::n_d_real' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:140:7: style:inconclusive: Member variable 'Hypermutation_global_errorrate::vd_ins' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:45:18: note: Member variable 'Hypermutation_global_errorrate::vd_ins' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:140:7: note: Member variable 'Hypermutation_global_errorrate::vd_ins' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:137:7: style:inconclusive: Member variable 'Hypermutation_global_errorrate::v_gene' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:45:48: note: Member variable 'Hypermutation_global_errorrate::v_gene' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:137:7: note: Member variable 'Hypermutation_global_errorrate::v_gene' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1788:40: style:inconclusive: Technically the member function 'Hypermutation_global_errorrate::compute_Nmer_unorm_score' can be const. [functionConst]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:84:9: note: Technically the member function 'Hypermutation_global_errorrate::compute_Nmer_unorm_score' can be const.
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1788:40: note: Technically the member function 'Hypermutation_global_errorrate::compute_Nmer_unorm_score' can be const.
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1797:38: performance:inconclusive: Technically the member function 'Hypermutation_global_errorrate::introduce_uniform_transversion' can be static (but you may consider moving to unnamed namespace). [functionStatic]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:88:7: note: Technically the member function 'Hypermutation_global_errorrate::introduce_uniform_transversion' can be static (but you may consider moving to unnamed namespace).
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1797:38: note: Technically the member function 'Hypermutation_global_errorrate::introduce_uniform_transversion' can be static (but you may consider moving to unnamed namespace).
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:43:235: warning: Class 'Hypermutation_global_errorrate' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:43:235: warning: Class 'Hypermutation_global_errorrate' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:92:24: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:92:47: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:92:70: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:97:24: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:97:47: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:97:70: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:102:24: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:102:47: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:102:70: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:107:24: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:107:47: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:107:70: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:112:24: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:112:47: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:112:70: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:117:24: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:117:47: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:117:70: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1503:25: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1503:48: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1503:71: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1535:25: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1535:48: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1535:71: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1568:25: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1568:48: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1568:71: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1077:10: style: The scope of the variable 'rand_contribution' can be reduced. [variableScope]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1406:9: style: The scope of the variable 'current_Nmer_P_SHM' can be reduced. [variableScope]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1407:9: style: The scope of the variable 'current_Nmer_P_bg' can be reduced. [variableScope]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1408:9: style: The scope of the variable 'current_Nmer_unorm_score' can be reduced. [variableScope]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:259:14: style: Local variable 'i' shadows outer variable [shadowVariable]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:161:14: note: Shadowed declaration
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:259:14: note: Shadow variable
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:260:15: style: Local variable 'j' shadows outer variable [shadowVariable]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:162:14: note: Shadowed declaration
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:260:15: note: Shadow variable
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:280:13: style: Local variable 'i' shadows outer variable [shadowVariable]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:161:14: note: Shadowed declaration
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:280:13: note: Shadow variable
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:281:14: style: Local variable 'j' shadows outer variable [shadowVariable]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:162:14: note: Shadowed declaration
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:281:14: note: Shadow variable
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:134:166: performance: Function parameter 'ei_contributions' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:147:156: performance: Function parameter 'filename' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:151:165: performance: Function parameter 'ei_contributions' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:151:189: performance: Function parameter 'filename' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:189:68: performance: Function parameter 'filename' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:213:108: performance: Function parameter 'err_r' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1797:149: style: Parameter 'distribution' can be declared as reference to const [constParameterReference]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1788:70: style: Parameter 'base_4_address' can be declared as pointer to const [constParameterPointer]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1788:93: style: Parameter 'ei_nucleotide_contributions_p' can be declared as pointer to const [constParameterPointer]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:333:33: error: Iterators of different containers '*mismatches_lists.at(J_gene_seq)' and '*mismatches_lists.at(V_gene_seq)' are used together. [mismatchingContainers]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1067:20: style: Variable 'dur' is assigned a value that is never used. [unreadVariable]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1115:16: style: Variable 'j_norm' is assigned a value that is never used. [unreadVariable]
IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1227:65: style: Variable 'H_data[(3*mutation_Nmer_size+1)*(3*mutation_Nmer_size+1)-1]' is assigned a value that is never used. [unreadVariable]
IGoR-1.4.0/igor_src/Pgencounter.cpp:55:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Pgencounter.cpp:149:118: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Model_marginals.cpp:48:18: warning:inconclusive: Member variable 'Model_marginals::debug_marg_name' is not assigned in the copy constructor. Should it be copied? [missingMemberCopy]
IGoR-1.4.0/igor_src/Model_marginals.cpp:681:35: warning:inconclusive: Member variable 'Model_marginals::debug_marg_name' is not assigned a value in 'Model_marginals::operator='. [operatorEqVarError]
IGoR-1.4.0/igor_src/Model_marginals.cpp:33:2: performance: Variable 'marginal_array_smart_p' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
IGoR-1.4.0/igor_src/Model_marginals.cpp:355:25: style:inconclusive: Technically the member function 'Model_marginals::compute_size' can be const. [functionConst]
IGoR-1.4.0/igor_src/Model_marginals.h:66:9: note: Technically the member function 'Model_marginals::compute_size' can be const.
IGoR-1.4.0/igor_src/Model_marginals.cpp:355:25: note: Technically the member function 'Model_marginals::compute_size' can be const.
IGoR-1.4.0/igor_src/Model_marginals.cpp:373:25: performance:inconclusive: Technically the member function 'Model_marginals::get_event_size' can be static (but you may consider moving to unnamed namespace). [functionStatic]
IGoR-1.4.0/igor_src/Model_marginals.h:67:9: note: Technically the member function 'Model_marginals::get_event_size' can be static (but you may consider moving to unnamed namespace).
IGoR-1.4.0/igor_src/Model_marginals.cpp:373:25: note: Technically the member function 'Model_marginals::get_event_size' can be static (but you may consider moving to unnamed namespace).
IGoR-1.4.0/igor_src/Model_marginals.cpp:715:34: style:inconclusive: Technically the member function 'Model_marginals::operator+' can be const. [functionConst]
IGoR-1.4.0/igor_src/Model_marginals.h:74:18: note: Technically the member function 'Model_marginals::operator+' can be const.
IGoR-1.4.0/igor_src/Model_marginals.cpp:715:34: note: Technically the member function 'Model_marginals::operator+' can be const.
IGoR-1.4.0/igor_src/Model_marginals.cpp:720:34: style:inconclusive: Technically the member function 'Model_marginals::operator-' can be const. [functionConst]
IGoR-1.4.0/igor_src/Model_marginals.h:75:18: note: Technically the member function 'Model_marginals::operator-' can be const.
IGoR-1.4.0/igor_src/Model_marginals.cpp:720:34: note: Technically the member function 'Model_marginals::operator-' can be const.
IGoR-1.4.0/igor_src/Model_marginals.h:108:2: style: Class 'Model_marginals' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
IGoR-1.4.0/igor_src/Model_marginals.cpp:65:62: performance: Function parameter 'ev1_name' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Model_marginals.cpp:65:88: performance: Function parameter 'ev2_name' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Model_marginals.cpp:393:132: performance: Function parameter 'event_name' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Model_marginals.cpp:397:132: performance: Function parameter 'event_name' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Model_marginals.cpp:423:21: performance: Range variable 'ev_name' should be declared as const reference. [iterateByValue]
IGoR-1.4.0/igor_src/Model_marginals.cpp:792:170: performance: Function parameter 'model_queue' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Model_marginals.cpp:883:162: performance: Function parameter 'index_map' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Model_marginals.cpp:1198:45: performance: Function parameter 'event_1' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Model_marginals.cpp:1198:75: performance: Function parameter 'event_2' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Model_marginals.cpp:1316:57: performance: Function parameter 'event_1' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Model_marginals.cpp:1316:87: performance: Function parameter 'event_2' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Model_marginals.cpp:98:20: style: Variable 'e' can be declared as reference to const [constVariableReference]
IGoR-1.4.0/igor_src/Model_marginals.cpp:902:135: style: Parameter 'related_events' can be declared as reference to const [constParameterReference]
IGoR-1.4.0/igor_src/Model_marginals.cpp:537:39: performance: Searching before insertion is not necessary. [stlFindInsert]
IGoR-1.4.0/igor_src/Model_marginals.cpp:541:62: performance: Searching before insertion is not necessary. [stlFindInsert]
IGoR-1.4.0/igor_src/Model_marginals.cpp:152:33: style: Consider using std::transform algorithm instead of a raw loop. [useStlAlgorithm]
IGoR-1.4.0/igor_src/Model_marginals.cpp:198:23: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
IGoR-1.4.0/igor_src/Model_marginals.cpp:252:35: style: Consider using std::transform algorithm instead of a raw loop. [useStlAlgorithm]
IGoR-1.4.0/igor_src/Model_marginals.cpp:268:33: style: Consider using std::transform algorithm instead of a raw loop. [useStlAlgorithm]
IGoR-1.4.0/igor_src/Model_marginals.cpp:378:13: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
IGoR-1.4.0/igor_src/Model_marginals.cpp:425:18: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
IGoR-1.4.0/igor_src/Model_marginals.cpp:865:16: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
IGoR-1.4.0/igor_src/Model_marginals.cpp:1253:30: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
IGoR-1.4.0/igor_src/Model_marginals.cpp:1279:30: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
IGoR-1.4.0/igor_src/Model_marginals.cpp:1258:65: error: Uninitialized variable: event_2_iterator [uninitvar]
IGoR-1.4.0/igor_src/Model_marginals.cpp:1253:19: note: Assuming condition is false
IGoR-1.4.0/igor_src/Model_marginals.cpp:1258:65: note: Uninitialized variable: event_2_iterator
IGoR-1.4.0/igor_src/Model_marginals.cpp:1046:17: error: Memory is allocated but not initialized: summed_probas[i/event_size] [uninitdata]
IGoR-1.4.0/igor_src/Model_marginals.cpp:261:115: style: Variable 'new_marginals_inverse_offset_map' is assigned a value that is never used. [unreadVariable]
IGoR-1.4.0/igor_src/Model_marginals.cpp:357:54: style: Variable 'edges' is assigned a value that is never used. [unreadVariable]
IGoR-1.4.0/igor_src/Model_marginals.cpp:357:48: style: Variable 'edges' is assigned a value that is never used. [unreadVariable]
IGoR-1.4.0/igor_src/Model_marginals.cpp:952:37: style: Variable 'events' is assigned a value that is never used. [unreadVariable]
IGoR-1.4.0/igor_src/Model_marginals.cpp:952:30: style: Variable 'events' is assigned a value that is never used. [unreadVariable]
IGoR-1.4.0/igor_src/Pgencounter.h:45:2: style: Class 'Pgen_counter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
IGoR-1.4.0/igor_src/Model_marginals.cpp:989:37: style: Variable 'events' is assigned a value that is never used. [unreadVariable]
IGoR-1.4.0/igor_src/Model_marginals.cpp:978:20: style: Variable 'dur' is assigned a value that is never used. [unreadVariable]
IGoR-1.4.0/igor_src/Model_marginals.cpp:989:30: style: Variable 'events' is assigned a value that is never used. [unreadVariable]
IGoR-1.4.0/igor_src/Model_marginals.cpp:1080:36: style: Unused variable: rank_map [unusedVariable]
IGoR-1.4.0/igor_src/Model_marginals.cpp:1081:30: style: Unused variable: processed_events [unusedVariable]
IGoR-1.4.0/igor_src/Pgencounter.h:47:11: style: The destructor '~Pgen_counter' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Counter.h:50:11: note: Virtual destructor in base class
IGoR-1.4.0/igor_src/Pgencounter.h:47:11: note: Destructor in derived class
IGoR-1.4.0/igor_src/Pgencounter.h:49:14: style: The function 'type' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Counter.h:52:22: note: Virtual function in base class
IGoR-1.4.0/igor_src/Pgencounter.h:49:14: note: Function in derived class
IGoR-1.4.0/igor_src/Pgencounter.h:51:7: style: The function 'initialize_counter' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Counter.h:54:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Pgencounter.h:51:7: note: Function in derived class
IGoR-1.4.0/igor_src/Pgencounter.h:53:7: style: The function 'count_scenario' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Counter.h:56:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Pgencounter.h:53:7: note: Function in derived class
IGoR-1.4.0/igor_src/Pgencounter.h:55:7: style: The function 'dump_sequence_data' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Counter.h:62:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Pgencounter.h:55:7: note: Function in derived class
IGoR-1.4.0/igor_src/Pgencounter.h:57:7: style: The function 'add_checked' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Counter.h:60:15: note: Virtual function in base class
IGoR-1.4.0/igor_src/Pgencounter.h:57:7: note: Function in derived class
IGoR-1.4.0/igor_src/Pgencounter.h:59:27: style: The function 'copy' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
IGoR-1.4.0/igor_src/Counter.h:69:35: note: Virtual function in base class
IGoR-1.4.0/igor_src/Pgencounter.h:59:27: note: Function in derived class
IGoR-1.4.0/igor_src/Pgencounter.cpp:34:40: performance: Function parameter 'path' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Pgencounter.cpp:37:40: performance: Function parameter 'path' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Singleerrorrate.cpp:283:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Utils.cpp:364:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Utils.cpp:414:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Utils.cpp:440:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/Rec_Event.cpp:41:12: warning: Member variable 'Rec_Event::viterbi_run' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Rec_Event.cpp:41:12: warning: Member variable 'Rec_Event::initialized' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Rec_Event.cpp:41:12: warning: Member variable 'Rec_Event::event_marginal_size' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Rec_Event.cpp:41:12: warning: Member variable 'Rec_Event::current_downstream_proba_memory_layers' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Rec_Event.cpp:34:12: warning: Member variable 'Rec_Event::viterbi_run' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Rec_Event.cpp:34:12: warning: Member variable 'Rec_Event::initialized' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Rec_Event.cpp:34:12: warning: Member variable 'Rec_Event::event_marginal_size' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Rec_Event.cpp:34:12: warning: Member variable 'Rec_Event::current_downstream_proba_memory_layers' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Rec_Event.cpp:37:12: warning: Member variable 'Rec_Event::viterbi_run' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Rec_Event.cpp:37:12: warning: Member variable 'Rec_Event::initialized' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Rec_Event.cpp:37:12: warning: Member variable 'Rec_Event::event_marginal_size' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Rec_Event.cpp:37:12: warning: Member variable 'Rec_Event::current_downstream_proba_memory_layers' is not initialized in the constructor. [uninitMemberVar]
IGoR-1.4.0/igor_src/Rec_Event.h:209:9: style:inconclusive: Member variable 'Rec_Event::scenario_downstream_upper_bound_proba' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/Rec_Event.cpp:34:304: note: Member variable 'Rec_Event::scenario_downstream_upper_bound_proba' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Rec_Event.h:209:9: note: Member variable 'Rec_Event::scenario_downstream_upper_bound_proba' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Rec_Event.h:208:9: style:inconclusive: Member variable 'Rec_Event::event_upper_bound_proba' is in the wrong place in the initializer list. [initializerList]
IGoR-1.4.0/igor_src/Rec_Event.cpp:34:346: note: Member variable 'Rec_Event::event_upper_bound_proba' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Rec_Event.h:208:9: note: Member variable 'Rec_Event::event_upper_bound_proba' is in the wrong place in the initializer list.
IGoR-1.4.0/igor_src/Rec_Event.cpp:273:17: performance:inconclusive: Technically the member function 'Rec_Event::iterate_initialize_Len_proba_wrap_up' can be static (but you may consider moving to unnamed namespace). [functionStatic]
IGoR-1.4.0/igor_src/Rec_Event.h:184:7: note: Technically the member function 'Rec_Event::iterate_initialize_Len_proba_wrap_up' can be static (but you may consider moving to unnamed namespace).
IGoR-1.4.0/igor_src/Rec_Event.cpp:273:17: note: Technically the member function 'Rec_Event::iterate_initialize_Len_proba_wrap_up' can be static (but you may consider moving to unnamed namespace).
IGoR-1.4.0/igor_src/Rec_Event.cpp:107:17: style:inconclusive: Technically the member function 'Rec_Event::iterate_wrap_up' can be const. [functionConst]
IGoR-1.4.0/igor_src/Rec_Event.h:223:7: note: Technically the member function 'Rec_Event::iterate_wrap_up' can be const.
IGoR-1.4.0/igor_src/Rec_Event.cpp:107:17: note: Technically the member function 'Rec_Event::iterate_wrap_up' can be const.
IGoR-1.4.0/igor_src/Utils.cpp:435:25: style: C-style pointer casting [cstyleCast]
IGoR-1.4.0/igor_src/Utils.cpp:500:9: style: The scope of the variable 'codonPos' can be reduced. [variableScope]
IGoR-1.4.0/igor_src/Utils.cpp:503:9: style: The scope of the variable 'strCodon' can be reduced. [variableScope]
IGoR-1.4.0/igor_src/Utils.cpp:504:9: style: The scope of the variable 'AA' can be reduced. [variableScope]
IGoR-1.4.0/igor_src/Utils.cpp:506:7: style: The scope of the variable 'stopCodonQ' can be reduced. [variableScope]
IGoR-1.4.0/igor_src/Utils.cpp:103:39: performance: Function parameter 'str' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Utils.cpp:145:35: performance: Function parameter 'str' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Utils.cpp:355:51: performance: Function parameter 'total_string' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Utils.cpp:355:78: performance: Function parameter 'separator' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Utils.cpp:383:83: performance: Function parameter 'prefix_message' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Utils.cpp:407:67: performance: Function parameter 'prefix_message' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Utils.cpp:499:25: performance: Function parameter 'seq' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Utils.h:111:27: style: Parameter 'arr' can be declared as const array [constParameter]
IGoR-1.4.0/igor_src/Utils.cpp:503:18: style: Variable 'strCodon' is assigned a value that is never used. [unreadVariable]
IGoR-1.4.0/igor_src/Utils.cpp:504:12: style: Variable 'AA' is assigned a value that is never used. [unreadVariable]
IGoR-1.4.0/igor_src/Utils.cpp:506:18: style: Variable 'stopCodonQ' is assigned a value that is never used. [unreadVariable]
IGoR-1.4.0/igor_src/Utils.cpp:514:16: style: Variable 'stopCodonQ' is assigned a value that is never used. [unreadVariable]
IGoR-1.4.0/igor_src/Rec_Event.cpp:37:99: style: Parameter 'realizations' can be declared as reference to const [constParameterReference]
IGoR-1.4.0/igor_src/Rec_Event.cpp:254:67: style: Parameter 'tmp_err_w_proba' can be declared as reference to const [constParameterReference]
IGoR-1.4.0/igor_src/Rec_Event.cpp:71:0: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
IGoR-1.4.0/igor_src/Rec_Event.cpp:257:29: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
IGoR-1.4.0/igor_src/Singleerrorrate.cpp:102:11: style: The scope of the variable 'd_gene_seq' can be reduced. [variableScope]
IGoR-1.4.0/igor_src/Singleerrorrate.cpp:155:9: style: The scope of the variable 'rand_err' can be reduced. [variableScope]
IGoR-1.4.0/igor_src/Singleerrorrate.cpp:42:20: style: Local variable 'temp' shadows outer variable [shadowVariable]
IGoR-1.4.0/igor_src/Singleerrorrate.h:78:14: note: Shadowed declaration
IGoR-1.4.0/igor_src/Singleerrorrate.cpp:42:20: note: Shadow variable
IGoR-1.4.0/igor_src/Singleerrorrate.cpp:226:6: style: Local variable 'number_errors' shadows outer variable [shadowVariable]
IGoR-1.4.0/igor_src/Singleerrorrate.h:75:6: note: Shadowed declaration
IGoR-1.4.0/igor_src/Singleerrorrate.cpp:226:6: note: Shadow variable
IGoR-1.4.0/igor_src/Singleerrorrate.cpp:41:67: performance: Function parameter 'err_r' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Singleerrorrate.cpp:47:69: performance: Function parameter 'err_r' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/Rec_Event.cpp:157:170: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
IGoR-1.4.0/igor_src/main.cpp:66:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/main.cpp:266:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
IGoR-1.4.0/igor_src/main.cpp:289:4: warning: Return value of function std::freopen() is not used. [ignoredReturnValue]
IGoR-1.4.0/igor_src/main.cpp:209:10: style: The scope of the variable 'v_align_filename' can be reduced. [variableScope]
IGoR-1.4.0/igor_src/main.cpp:222:10: style: The scope of the variable 'd_align_filename' can be reduced. [variableScope]
IGoR-1.4.0/igor_src/main.cpp:235:10: style: The scope of the variable 'j_align_filename' can be reduced. [variableScope]
IGoR-1.4.0/igor_src/main.cpp:247:8: style: The scope of the variable 'b_feature' can be reduced. [variableScope]
IGoR-1.4.0/igor_src/main.cpp:1520:31: style: Local variable 'v_genomic' shadows outer variable [shadowVariable]
IGoR-1.4.0/igor_src/main.cpp:149:30: note: Shadowed declaration
IGoR-1.4.0/igor_src/main.cpp:1520:31: note: Shadow variable
IGoR-1.4.0/igor_src/main.cpp:1522:31: style: Local variable 'd_genomic' shadows outer variable [shadowVariable]
IGoR-1.4.0/igor_src/main.cpp:150:30: note: Shadowed declaration
IGoR-1.4.0/igor_src/main.cpp:1522:31: note: Shadow variable
IGoR-1.4.0/igor_src/main.cpp:1524:31: style: Local variable 'j_genomic' shadows outer variable [shadowVariable]
IGoR-1.4.0/igor_src/main.cpp:151:30: note: Shadowed declaration
IGoR-1.4.0/igor_src/main.cpp:1524:31: note: Shadow variable
IGoR-1.4.0/igor_src/main.cpp:63:66: performance: Function parameter 'error_messages' should be passed by const reference. [passedByValue]
IGoR-1.4.0/igor_src/main.cpp:65:13: performance: Range variable 'error_message' should be declared as const reference. [iterateByValue]
IGoR-1.4.0/igor_src/main.cpp:1805:20: performance: Range variable 'unknown_gene' should be declared as const reference. [iterateByValue]
IGoR-1.4.0/igor_src/main.cpp:1843:19: performance: Range variable 'unknown_gene' should be declared as const reference. [iterateByValue]
IGoR-1.4.0/igor_src/main.cpp:1881:19: performance: Range variable 'unknown_gene' should be declared as const reference. [iterateByValue]
IGoR-1.4.0/igor_src/main.cpp:1913:20: performance: Range variable 'unknown_gene' should be declared as const reference. [iterateByValue]
IGoR-1.4.0/igor_src/main.cpp:1951:19: performance: Range variable 'unknown_gene' should be declared as const reference. [iterateByValue]
IGoR-1.4.0/igor_src/main.cpp:79:72: style: Parameter 'e' can be declared as reference to const [constParameterReference]
IGoR-1.4.0/igor_src/main.cpp:87:87: style: Parameter 'e' can be declared as reference to const [constParameterReference]
IGoR-1.4.0/igor_src/main.cpp:1295:25: style: Variable 'ev_real' can be declared as reference to const [constVariableReference]
IGoR-1.4.0/igor_src/main.cpp:1336:25: style: Variable 'ev_real' can be declared as reference to const [constVariableReference]
IGoR-1.4.0/igor_src/main.cpp:1377:25: style: Variable 'ev_real' can be declared as reference to const [constVariableReference]
IGoR-1.4.0/igor_src/main.cpp:1799:66: performance: Searching before insertion is not necessary. [stlFindInsert]
IGoR-1.4.0/igor_src/main.cpp:1875:65: performance: Searching before insertion is not necessary. [stlFindInsert]
IGoR-1.4.0/igor_src/main.cpp:1907:66: performance: Searching before insertion is not necessary. [stlFindInsert]
IGoR-1.4.0/igor_src/main.cpp:2116:129: warning: Uninitialized variable: v_queue_pos [uninitvar]
IGoR-1.4.0/igor_src/main.cpp:2105:11: note: Assuming condition is false
IGoR-1.4.0/igor_src/main.cpp:2116:129: note: Uninitialized variable: v_queue_pos
IGoR-1.4.0/igor_src/main.cpp:2117:58: warning: Uninitialized variable: j_queue_pos [uninitvar]
IGoR-1.4.0/igor_src/main.cpp:2105:11: note: Assuming condition is false
IGoR-1.4.0/igor_src/main.cpp:2117:58: note: Uninitialized variable: j_queue_pos
IGoR-1.4.0/igor_src/main.cpp:1984:31: style: Variable 'cl_path_ref_genome' is assigned a value that is never used. [unreadVariable]
diff:
head IGoR-1.4.0/igor_src/Aligner.cpp:606:15: performance:inconclusive: Technically the member function 'Aligner::write_alignments_seq_csv' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     IGoR-1.4.0/igor_src/Aligner.h:128:7: note: Technically the member function 'Aligner::write_alignments_seq_csv' can be static (but you may consider moving to unnamed namespace).
     IGoR-1.4.0/igor_src/Aligner.cpp:606:15: note: Technically the member function 'Aligner::write_alignments_seq_csv' can be static (but you may consider moving to unnamed namespace).
head IGoR-1.4.0/igor_src/Aligner.cpp:752:44: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/Aligner.cpp:859:14: performance:inconclusive: Technically the member function 'Aligner::incorporate_in_dels' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     IGoR-1.4.0/igor_src/Aligner.h:132:6: note: Technically the member function 'Aligner::incorporate_in_dels' can be static (but you may consider moving to unnamed namespace).
     IGoR-1.4.0/igor_src/Aligner.cpp:859:14: note: Technically the member function 'Aligner::incorporate_in_dels' can be static (but you may consider moving to unnamed namespace).
2.17.0 IGoR-1.4.0/igor_src/Aligner.h:128:7: performance:inconclusive: Technically the member function 'Aligner::write_alignments_seq_csv' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     IGoR-1.4.0/igor_src/Aligner.cpp:606:15: note: Technically the member function 'Aligner::write_alignments_seq_csv' can be static (but you may consider moving to unnamed namespace).
     IGoR-1.4.0/igor_src/Aligner.h:128:7: note: Technically the member function 'Aligner::write_alignments_seq_csv' can be static (but you may consider moving to unnamed namespace).
2.17.0 IGoR-1.4.0/igor_src/Aligner.h:132:6: performance:inconclusive: Technically the member function 'Aligner::incorporate_in_dels' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     IGoR-1.4.0/igor_src/Aligner.cpp:859:14: note: Technically the member function 'Aligner::incorporate_in_dels' can be static (but you may consider moving to unnamed namespace).
     IGoR-1.4.0/igor_src/Aligner.h:132:6: note: Technically the member function 'Aligner::incorporate_in_dels' can be static (but you may consider moving to unnamed namespace).
head IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:266:64: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
head IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:323:54: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
head IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:474:28: performance:inconclusive: Technically the member function 'Coverage_err_counter::deallocate_coverage_and_errors_arrays' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     IGoR-1.4.0/igor_src/Coverageerrcounter.h:67:7: note: Technically the member function 'Coverage_err_counter::deallocate_coverage_and_errors_arrays' can be static (but you may consider moving to unnamed namespace).
     IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:474:28: note: Technically the member function 'Coverage_err_counter::deallocate_coverage_and_errors_arrays' can be static (but you may consider moving to unnamed namespace).
head IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:54:47: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:54:70: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:59:48: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:59:71: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:641:28: style:inconclusive: Technically the member function 'Coverage_err_counter::symmetrize_counter_array_recurs' can be const. [functionConst]
     IGoR-1.4.0/igor_src/Coverageerrcounter.h:73:7: note: Technically the member function 'Coverage_err_counter::symmetrize_counter_array_recurs' can be const.
     IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:641:28: note: Technically the member function 'Coverage_err_counter::symmetrize_counter_array_recurs' can be const.
head IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:64:48: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:64:71: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
2.17.0 IGoR-1.4.0/igor_src/Coverageerrcounter.h:67:7: performance:inconclusive: Technically the member function 'Coverage_err_counter::deallocate_coverage_and_errors_arrays' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:474:28: note: Technically the member function 'Coverage_err_counter::deallocate_coverage_and_errors_arrays' can be static (but you may consider moving to unnamed namespace).
     IGoR-1.4.0/igor_src/Coverageerrcounter.h:67:7: note: Technically the member function 'Coverage_err_counter::deallocate_coverage_and_errors_arrays' can be static (but you may consider moving to unnamed namespace).
2.17.0 IGoR-1.4.0/igor_src/Coverageerrcounter.h:73:7: style:inconclusive: Technically the member function 'Coverage_err_counter::symmetrize_counter_array_recurs' can be const. [functionConst]
     IGoR-1.4.0/igor_src/Coverageerrcounter.cpp:641:28: note: Technically the member function 'Coverage_err_counter::symmetrize_counter_array_recurs' can be const.
     IGoR-1.4.0/igor_src/Coverageerrcounter.h:73:7: note: Technically the member function 'Coverage_err_counter::symmetrize_counter_array_recurs' can be const.
head IGoR-1.4.0/igor_src/ExtractFeatures.cpp:215:25: style:inconclusive: Technically the member function 'ExtractFeatures::generateCDR3_csv_line' can be const. [functionConst]
     IGoR-1.4.0/igor_src/ExtractFeatures.h:70:12: note: Technically the member function 'ExtractFeatures::generateCDR3_csv_line' can be const.
     IGoR-1.4.0/igor_src/ExtractFeatures.cpp:215:25: note: Technically the member function 'ExtractFeatures::generateCDR3_csv_line' can be const.
2.17.0 IGoR-1.4.0/igor_src/ExtractFeatures.h:70:12: style:inconclusive: Technically the member function 'ExtractFeatures::generateCDR3_csv_line' can be const. [functionConst]
     IGoR-1.4.0/igor_src/ExtractFeatures.cpp:215:25: note: Technically the member function 'ExtractFeatures::generateCDR3_csv_line' can be const.
     IGoR-1.4.0/igor_src/ExtractFeatures.h:70:12: note: Technically the member function 'ExtractFeatures::generateCDR3_csv_line' can be const.
head IGoR-1.4.0/igor_src/GenModel.cpp:623:16: performance:inconclusive: Technically the member function 'GenModel::write_seq2txt' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     IGoR-1.4.0/igor_src/GenModel.h:168:7: note: Technically the member function 'GenModel::write_seq2txt' can be static (but you may consider moving to unnamed namespace).
     IGoR-1.4.0/igor_src/GenModel.cpp:623:16: note: Technically the member function 'GenModel::write_seq2txt' can be static (but you may consider moving to unnamed namespace).
2.17.0 IGoR-1.4.0/igor_src/GenModel.h:168:7: performance:inconclusive: Technically the member function 'GenModel::write_seq2txt' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     IGoR-1.4.0/igor_src/GenModel.cpp:623:16: note: Technically the member function 'GenModel::write_seq2txt' can be static (but you may consider moving to unnamed namespace).
     IGoR-1.4.0/igor_src/GenModel.h:168:7: note: Technically the member function 'GenModel::write_seq2txt' can be static (but you may consider moving to unnamed namespace).
head IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:1046:48: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:1046:71: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:1077:48: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:1077:71: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:1110:48: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:1110:71: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:1192:41: performance:inconclusive: Technically the member function 'Hypermutation_full_Nmer_errorrate::introduce_uniform_transversion' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:79:7: note: Technically the member function 'Hypermutation_full_Nmer_errorrate::introduce_uniform_transversion' can be static (but you may consider moving to unnamed namespace).
     IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:1192:41: note: Technically the member function 'Hypermutation_full_Nmer_errorrate::introduce_uniform_transversion' can be static (but you may consider moving to unnamed namespace).
head IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:71:47: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:71:70: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:76:47: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:76:70: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:81:47: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:81:70: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:86:47: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:86:70: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:91:47: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:91:70: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:96:47: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:96:70: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
2.17.0 IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:79:7: performance:inconclusive: Technically the member function 'Hypermutation_full_Nmer_errorrate::introduce_uniform_transversion' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.cpp:1192:41: note: Technically the member function 'Hypermutation_full_Nmer_errorrate::introduce_uniform_transversion' can be static (but you may consider moving to unnamed namespace).
     IGoR-1.4.0/igor_src/HypermutationfullNmererrorrate.h:79:7: note: Technically the member function 'Hypermutation_full_Nmer_errorrate::introduce_uniform_transversion' can be static (but you may consider moving to unnamed namespace).
head IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:102:47: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:102:70: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:107:47: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:107:70: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:112:47: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:112:70: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:117:47: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:117:70: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1503:48: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1503:71: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1535:48: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1535:71: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1568:48: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1568:71: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1788:40: style:inconclusive: Technically the member function 'Hypermutation_global_errorrate::compute_Nmer_unorm_score' can be const. [functionConst]
     IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:84:9: note: Technically the member function 'Hypermutation_global_errorrate::compute_Nmer_unorm_score' can be const.
     IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1788:40: note: Technically the member function 'Hypermutation_global_errorrate::compute_Nmer_unorm_score' can be const.
head IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1797:38: performance:inconclusive: Technically the member function 'Hypermutation_global_errorrate::introduce_uniform_transversion' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:88:7: note: Technically the member function 'Hypermutation_global_errorrate::introduce_uniform_transversion' can be static (but you may consider moving to unnamed namespace).
     IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1797:38: note: Technically the member function 'Hypermutation_global_errorrate::introduce_uniform_transversion' can be static (but you may consider moving to unnamed namespace).
head IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:92:47: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:92:70: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:97:47: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
head IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:97:70: style: Boolean result is used in bitwise operation. Clarify expression with parentheses. [clarifyCondition]
2.17.0 IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:84:9: style:inconclusive: Technically the member function 'Hypermutation_global_errorrate::compute_Nmer_unorm_score' can be const. [functionConst]
     IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1788:40: note: Technically the member function 'Hypermutation_global_errorrate::compute_Nmer_unorm_score' can be const.
     IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:84:9: note: Technically the member function 'Hypermutation_global_errorrate::compute_Nmer_unorm_score' can be const.
2.17.0 IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:88:7: performance:inconclusive: Technically the member function 'Hypermutation_global_errorrate::introduce_uniform_transversion' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.cpp:1797:38: note: Technically the member function 'Hypermutation_global_errorrate::introduce_uniform_transversion' can be static (but you may consider moving to unnamed namespace).
     IGoR-1.4.0/igor_src/Hypermutationglobalerrorrate.h:88:7: note: Technically the member function 'Hypermutation_global_errorrate::introduce_uniform_transversion' can be static (but you may consider moving to unnamed namespace).
head IGoR-1.4.0/igor_src/Model_Parms.cpp:627:13: style: Variable 'test' is assigned a value that is never used. [unreadVariable]
head IGoR-1.4.0/igor_src/Model_marginals.cpp:355:25: style:inconclusive: Technically the member function 'Model_marginals::compute_size' can be const. [functionConst]
     IGoR-1.4.0/igor_src/Model_marginals.h:66:9: note: Technically the member function 'Model_marginals::compute_size' can be const.
     IGoR-1.4.0/igor_src/Model_marginals.cpp:355:25: note: Technically the member function 'Model_marginals::compute_size' can be const.
head IGoR-1.4.0/igor_src/Model_marginals.cpp:357:48: style: Variable 'edges' is assigned a value that is never used. [unreadVariable]
head IGoR-1.4.0/igor_src/Model_marginals.cpp:373:25: performance:inconclusive: Technically the member function 'Model_marginals::get_event_size' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     IGoR-1.4.0/igor_src/Model_marginals.h:67:9: note: Technically the member function 'Model_marginals::get_event_size' can be static (but you may consider moving to unnamed namespace).
     IGoR-1.4.0/igor_src/Model_marginals.cpp:373:25: note: Technically the member function 'Model_marginals::get_event_size' can be static (but you may consider moving to unnamed namespace).
head IGoR-1.4.0/igor_src/Model_marginals.cpp:715:34: style:inconclusive: Technically the member function 'Model_marginals::operator+' can be const. [functionConst]
     IGoR-1.4.0/igor_src/Model_marginals.h:74:18: note: Technically the member function 'Model_marginals::operator+' can be const.
     IGoR-1.4.0/igor_src/Model_marginals.cpp:715:34: note: Technically the member function 'Model_marginals::operator+' can be const.
head IGoR-1.4.0/igor_src/Model_marginals.cpp:720:34: style:inconclusive: Technically the member function 'Model_marginals::operator-' can be const. [functionConst]
     IGoR-1.4.0/igor_src/Model_marginals.h:75:18: note: Technically the member function 'Model_marginals::operator-' can be const.
     IGoR-1.4.0/igor_src/Model_marginals.cpp:720:34: note: Technically the member function 'Model_marginals::operator-' can be const.
head IGoR-1.4.0/igor_src/Model_marginals.cpp:952:30: style: Variable 'events' is assigned a value that is never used. [unreadVariable]
head IGoR-1.4.0/igor_src/Model_marginals.cpp:989:30: style: Variable 'events' is assigned a value that is never used. [unreadVariable]
2.17.0 IGoR-1.4.0/igor_src/Model_marginals.h:66:9: style:inconclusive: Technically the member function 'Model_marginals::compute_size' can be const. [functionConst]
     IGoR-1.4.0/igor_src/Model_marginals.cpp:355:25: note: Technically the member function 'Model_marginals::compute_size' can be const.
     IGoR-1.4.0/igor_src/Model_marginals.h:66:9: note: Technically the member function 'Model_marginals::compute_size' can be const.
2.17.0 IGoR-1.4.0/igor_src/Model_marginals.h:67:9: performance:inconclusive: Technically the member function 'Model_marginals::get_event_size' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     IGoR-1.4.0/igor_src/Model_marginals.cpp:373:25: note: Technically the member function 'Model_marginals::get_event_size' can be static (but you may consider moving to unnamed namespace).
     IGoR-1.4.0/igor_src/Model_marginals.h:67:9: note: Technically the member function 'Model_marginals::get_event_size' can be static (but you may consider moving to unnamed namespace).
2.17.0 IGoR-1.4.0/igor_src/Model_marginals.h:74:18: style:inconclusive: Technically the member function 'Model_marginals::operator+' can be const. [functionConst]
     IGoR-1.4.0/igor_src/Model_marginals.cpp:715:34: note: Technically the member function 'Model_marginals::operator+' can be const.
     IGoR-1.4.0/igor_src/Model_marginals.h:74:18: note: Technically the member function 'Model_marginals::operator+' can be const.
2.17.0 IGoR-1.4.0/igor_src/Model_marginals.h:75:18: style:inconclusive: Technically the member function 'Model_marginals::operator-' can be const. [functionConst]
     IGoR-1.4.0/igor_src/Model_marginals.cpp:720:34: note: Technically the member function 'Model_marginals::operator-' can be const.
     IGoR-1.4.0/igor_src/Model_marginals.h:75:18: note: Technically the member function 'Model_marginals::operator-' can be const.
head IGoR-1.4.0/igor_src/Rec_Event.cpp:107:17: style:inconclusive: Technically the member function 'Rec_Event::iterate_wrap_up' can be const. [functionConst]
     IGoR-1.4.0/igor_src/Rec_Event.h:223:7: note: Technically the member function 'Rec_Event::iterate_wrap_up' can be const.
     IGoR-1.4.0/igor_src/Rec_Event.cpp:107:17: note: Technically the member function 'Rec_Event::iterate_wrap_up' can be const.
head IGoR-1.4.0/igor_src/Rec_Event.cpp:273:17: performance:inconclusive: Technically the member function 'Rec_Event::iterate_initialize_Len_proba_wrap_up' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     IGoR-1.4.0/igor_src/Rec_Event.h:184:7: note: Technically the member function 'Rec_Event::iterate_initialize_Len_proba_wrap_up' can be static (but you may consider moving to unnamed namespace).
     IGoR-1.4.0/igor_src/Rec_Event.cpp:273:17: note: Technically the member function 'Rec_Event::iterate_initialize_Len_proba_wrap_up' can be static (but you may consider moving to unnamed namespace).
2.17.0 IGoR-1.4.0/igor_src/Rec_Event.h:184:7: performance:inconclusive: Technically the member function 'Rec_Event::iterate_initialize_Len_proba_wrap_up' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     IGoR-1.4.0/igor_src/Rec_Event.cpp:273:17: note: Technically the member function 'Rec_Event::iterate_initialize_Len_proba_wrap_up' can be static (but you may consider moving to unnamed namespace).
     IGoR-1.4.0/igor_src/Rec_Event.h:184:7: note: Technically the member function 'Rec_Event::iterate_initialize_Len_proba_wrap_up' can be static (but you may consider moving to unnamed namespace).
2.17.0 IGoR-1.4.0/igor_src/Rec_Event.h:223:7: style:inconclusive: Technically the member function 'Rec_Event::iterate_wrap_up' can be const. [functionConst]
     IGoR-1.4.0/igor_src/Rec_Event.cpp:107:17: note: Technically the member function 'Rec_Event::iterate_wrap_up' can be const.
     IGoR-1.4.0/igor_src/Rec_Event.h:223:7: note: Technically the member function 'Rec_Event::iterate_wrap_up' can be const.


DONE