2025-04-13 22:23
ftp://ftp.de.debian.org/debian/pool/main/d/diamond-aligner/diamond-aligner_2.1.11.orig.tar.xz
cppcheck-options: --library=posix --library=gnu --library=bsd --library=openmp --library=bsd --library=zlib  --inconclusive --enable=style,information --inline-suppr --template=daca2 --disable=missingInclude --suppress=unmatchedSuppression --check-library --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning --suppress=normalCheckLevelConditionExpressions -D__GNUC__ --platform=unix64 -j3
platform: Linux-6.8.0-1022-oracle-aarch64-with-glibc2.39
python: 3.12.3
client-version: 1.3.67
compiler: g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
cppcheck: head 2.17.0
head-info: 52bfef4 (2025-04-13 21:41:34 +0200)
count: 2676 2419
elapsed-time: 11.1 7.5
head-timing-info:

old-timing-info:

head results:
diamond-2.1.11/src/align/alt_hsp.cpp:32:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable query_contexts [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/alt_hsp.cpp:43:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SUPER_HARD_MASK [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/alt_hsp.cpp:51:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable query_contexts [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/alt_hsp.cpp:74:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable query_contexts [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/alt_hsp.cpp:107:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable max_hsps [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/alt_hsp.cpp:18:12: style: Local variable 'active' shadows outer variable [shadowVariable]
diamond-2.1.11/src/align/alt_hsp.cpp:62:11: note: Shadowed declaration
diamond-2.1.11/src/align/alt_hsp.cpp:18:12: note: Shadow variable
diamond-2.1.11/src/align/target.h:107:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/culling.cpp:36:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable max_hsps [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/culling.cpp:44:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable max_hsps [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/culling.cpp:60:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable max_hsps [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/culling.cpp:84:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable evalue [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/culling.cpp:102:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MAX [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/culling.cpp:126:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MAX [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/culling.cpp:160:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable min_id [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/culling.cpp:172:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable no_self_hits [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/culling.cpp:193:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable min_id [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/legacy/query_mapper.h:171:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable query_contexts [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/legacy/query_mapper.h:197:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable query_translated [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/align.cpp:58:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable min_task_trace_pts [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/align.cpp:76:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable swipe_all [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/align.cpp:96:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable query_contexts [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/align.cpp:127:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable daa [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/align.cpp:168:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable swipe_all [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/align.cpp:229:113: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Hit [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/culling.cpp:159:9: style: Return value '!cluster_threshold' is always false [knownConditionTrueFalse]
diamond-2.1.11/src/align/culling.cpp:148:27: note: Assignment 'cluster_threshold=true', assigned value is 1
diamond-2.1.11/src/align/culling.cpp:159:9: note: Return value '!cluster_threshold' is always false
diamond-2.1.11/src/align/culling.cpp:173:17: style: Local variable 'seq' shadows outer variable [shadowVariable]
diamond-2.1.11/src/align/extend.h:61:11: note: Shadowed declaration
diamond-2.1.11/src/align/culling.cpp:173:17: note: Shadow variable
diamond-2.1.11/src/align/legacy/query_mapper.h:37:2: warning:inconclusive: Member variable 'SeedHit::frame_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/align/legacy/query_mapper.h:37:2: warning:inconclusive: Member variable 'SeedHit::subject_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/align/legacy/query_mapper.h:37:2: warning:inconclusive: Member variable 'SeedHit::subject_pos_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/align/legacy/query_mapper.h:37:2: warning:inconclusive: Member variable 'SeedHit::query_pos_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/align/legacy/query_mapper.h:37:2: warning:inconclusive: Member variable 'SeedHit::prefix_score' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/align/legacy/query_mapper.h:106:2: warning: Member variable 'Target::subject_block_id' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/align/legacy/query_mapper.h:106:2: warning: Member variable 'Target::filter_time' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/align/legacy/query_mapper.h:106:2: warning: Member variable 'Target::outranked' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/align/legacy/query_mapper.h:106:2: warning: Member variable 'Target::begin' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/align/legacy/query_mapper.h:106:2: warning: Member variable 'Target::end' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/align/legacy/query_mapper.h:110:2: warning: Member variable 'Target::filter_time' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/align/legacy/query_mapper.h:110:2: warning: Member variable 'Target::end' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/align/align.cpp:89:15: style:inconclusive: Technically the member function 'HitIterator::fetch' can be const. [functionConst]
diamond-2.1.11/src/align/align.cpp:167:10: style: Local variable 'dp_stat' shadows outer variable [shadowVariable]
diamond-2.1.11/src/align/align.cpp:48:8: note: Shadowed declaration
diamond-2.1.11/src/align/align.cpp:167:10: note: Shadow variable
diamond-2.1.11/src/align/align.cpp:265:43: style: Parameter 'tp' can be declared as reference to const [constParameterReference]
diamond-2.1.11/src/align/align.cpp:56:72: style: Parameter 'end' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/align/align.cpp:78:77: style: Parameter 'end' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/align/legacy/query_mapper.h:123:36: style: Parameter 'lhs' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/align/legacy/query_mapper.h:123:49: style: Parameter 'rhs' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/align/full_db.cpp:18:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable query_contexts [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/gapped_filter.cpp:51:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GAPPED_FILTER_HITS1 [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/gapped_filter.cpp:82:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable query_contexts [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/gapped_final.cpp:15:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NONE [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/gapped_final.cpp:32:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable min_id [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/gapped_final.cpp:48:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable query_contexts [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/gapped_final.cpp:66:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable max_hsps [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/gapped_score.cpp:43:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable padding [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/gapped_score.cpp:79:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable narrow_band_cov [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/gapped_score.cpp:96:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable max_hsps [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/gapped_score.cpp:120:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable query_contexts [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/gapped_score.cpp:185:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable block_id [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/global_ranking/extend.cpp:51:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable database_id [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/global_ranking/extend.cpp:83:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable statistics [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/global_ranking/extend.cpp:94:88: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEQS [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/global_ranking/extend.cpp:131:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable global_ranking_targets [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/global_ranking/extend.cpp:184:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEQS [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/global_ranking/global_ranking.h:51:2: warning: Member variable 'Hit::context' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/align/global_ranking/global_ranking.h:60:2: warning: Member variable 'Hit::context' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/align/global_ranking/global_ranking.h:60:2: style: Struct 'Hit' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/align/global_ranking/extend.cpp:137:6: style: Condition 'n' is always false [knownConditionTrueFalse]
diamond-2.1.11/src/align/global_ranking/extend.cpp:134:19: note: Assuming that condition 'table_end>table_begin' is not redundant
diamond-2.1.11/src/align/global_ranking/extend.cpp:135:29: note: Assignment 'n=table_end-table_begin', assigned value is less than 1
diamond-2.1.11/src/align/global_ranking/extend.cpp:137:6: note: Condition 'n' is always false
diamond-2.1.11/src/align/gapped_score.cpp:88:138: style:inconclusive: Function 'Match' argument 4 names different: declaration 'hsp' definition 'hsps'. [funcArgNamesDifferent]
diamond-2.1.11/src/align/extend.h:55:132: note: Function 'Match' argument 4 names different: declaration 'hsp' definition 'hsps'.
diamond-2.1.11/src/align/gapped_score.cpp:88:138: note: Function 'Match' argument 4 names different: declaration 'hsp' definition 'hsps'.
diamond-2.1.11/src/align/gapped_score.cpp:116:12: style: Local variable 'band' shadows outer function [shadowFunction]
diamond-2.1.11/src/align/def.h:10:5: note: Shadowed declaration
diamond-2.1.11/src/align/gapped_score.cpp:116:12: note: Shadow variable
diamond-2.1.11/src/align/gapped_score.cpp:220:29: style: Local variable 'cfg' shadows outer argument [shadowArgument]
diamond-2.1.11/src/align/gapped_score.cpp:176:275: note: Shadowed declaration
diamond-2.1.11/src/align/gapped_score.cpp:220:29: note: Shadow variable
diamond-2.1.11/src/align/gapped_score.cpp:147:23: warning:inconclusive: Either the condition 'd0!=2147483647' is redundant or there is signed integer underflow for expression 'd1-d0'. [integerOverflowCond]
diamond-2.1.11/src/align/gapped_score.cpp:134:26: note: Assignment 'd1=-2147483647-1', assigned value is -2147483648
diamond-2.1.11/src/align/gapped_score.cpp:138:41: note: Assuming container is not empty
diamond-2.1.11/src/align/gapped_score.cpp:156:12: note: Assuming that condition 'd0!=2147483647' is not redundant
diamond-2.1.11/src/align/gapped_score.cpp:147:23: note: Integer underflow
diamond-2.1.11/src/align/global_ranking/global_ranking.cpp:39:104: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ungapped_window [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/global_ranking/global_ranking.cpp:59:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable global_ranking_targets [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/global_ranking/global_ranking.cpp:80:3: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/align/global_ranking/global_ranking.cpp:72:71: style: Parameter 'out' can be declared as reference to const [constParameterReference]
diamond-2.1.11/src/align/global_ranking/global_ranking.cpp:72:87: style: Parameter 'ranking_db_filter' can be declared as reference to const [constParameterReference]
diamond-2.1.11/src/align/global_ranking/global_ranking.cpp:72:118: style: Parameter 'stat' can be declared as reference to const [constParameterReference]
diamond-2.1.11/src/align/load_hits.h:85:112: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable query_contexts [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/global_ranking/table.cpp:87:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable no_reextend [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/global_ranking/table.cpp:115:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable query_contexts [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/global_ranking/table.cpp:130:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable global_ranking_targets [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/global_ranking/table.cpp:150:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable log_stream [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/legacy/banded_swipe_pipeline.cpp:40:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable begin [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/legacy/banded_swipe_pipeline.cpp:50:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable frame_ [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/legacy/banded_swipe_pipeline.cpp:59:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable padding [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/legacy/banded_swipe_pipeline.cpp:78:63: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable begin [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/legacy/banded_swipe_pipeline.cpp:97:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable filter_score [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/legacy/banded_swipe_pipeline.cpp:113:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable frame_shift [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/legacy/banded_swipe_pipeline.cpp:123:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable filter_score [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/legacy/banded_swipe_pipeline.cpp:136:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable rank_ratio [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/legacy/banded_swipe_pipeline.cpp:162:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FORWARD [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/legacy/banded_swipe_pipeline.cpp:184:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable padding [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/load_hits.h:82:16: style: Variable 'target_len' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/align/load_hits.h:107:16: style: Variable 'target_len' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/align/legacy/banded_swipe_pipeline.cpp:40:63: debug: CheckClass::isMemberVar found used member variable 'begin' with varid 0 [varid0]
diamond-2.1.11/src/align/legacy/banded_swipe_pipeline.cpp:40:108: debug: CheckClass::isMemberVar found used member variable 'end' with varid 0 [varid0]
diamond-2.1.11/src/align/legacy/banded_swipe_pipeline.cpp:41:3: debug: CheckClass::isMemberVar found used member variable 'top_hit' with varid 0 [varid0]
diamond-2.1.11/src/align/legacy/banded_swipe_pipeline.cpp:50:25: debug: CheckClass::isMemberVar found used member variable 'top_hit' with varid 0 [varid0]
diamond-2.1.11/src/align/legacy/banded_swipe_pipeline.cpp:59:49: debug: CheckClass::isMemberVar found used member variable 'subject' with varid 0 [varid0]
diamond-2.1.11/src/align/legacy/banded_swipe_pipeline.cpp:78:63: debug: CheckClass::isMemberVar found used member variable 'begin' with varid 0 [varid0]
diamond-2.1.11/src/align/legacy/banded_swipe_pipeline.cpp:78:108: debug: CheckClass::isMemberVar found used member variable 'end' with varid 0 [varid0]
diamond-2.1.11/src/align/legacy/banded_swipe_pipeline.cpp:79:19: debug: CheckClass::isMemberVar found used member variable 'top_hit' with varid 0 [varid0]
diamond-2.1.11/src/align/legacy/banded_swipe_pipeline.cpp:97:3: debug: CheckClass::isMemberVar found used member variable 'filter_score' with varid 0 [varid0]
diamond-2.1.11/src/align/legacy/banded_swipe_pipeline.cpp:107:3: debug: CheckClass::isMemberVar found used member variable 'hsps' with varid 0 [varid0]
diamond-2.1.11/src/align/legacy/banded_swipe_pipeline.cpp:123:38: debug: CheckClass::isMemberVar found used member variable 'filter_score' with varid 0 [varid0]
diamond-2.1.11/src/align/legacy/banded_swipe_pipeline.cpp:127:38: debug: CheckClass::isMemberVar found used member variable 'filter_score' with varid 0 [varid0]
diamond-2.1.11/src/align/legacy/banded_swipe_pipeline.cpp:38:35: style: Parameter 'mapper' can be declared as reference to const [constParameterReference]
diamond-2.1.11/src/align/legacy/banded_swipe_pipeline.cpp:56:31: style: Parameter 'mapper' can be declared as reference to const [constParameterReference]
diamond-2.1.11/src/align/legacy/banded_swipe_pipeline.cpp:239:58: style: Parameter 't' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/align/legacy/query_mapper.cpp:71:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INTERVAL [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/legacy/query_mapper.cpp:80:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INTERVAL [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/legacy/query_mapper.cpp:104:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable log_query [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/legacy/query_mapper.cpp:123:90: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable subject_ [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/legacy/query_mapper.cpp:154:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/legacy/query_mapper.cpp:170:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable taxon_k [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/legacy/query_mapper.cpp:205:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FINISHED [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/legacy/query_mapper.cpp:233:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable subject_block_id [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/legacy/query_mapper.cpp:323:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/legacy/query_mapper.cpp:341:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable min_id [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/output.cpp:34:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ref_seqs [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/output.cpp:120:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable target_block_id [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/output.cpp:38:22: style: The scope of the variable 'hit_hsps' can be reduced. [variableScope]
diamond-2.1.11/src/align/output.cpp:38:31: style: Variable 'hit_hsps' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/align/legacy/query_mapper.cpp:89:14: warning: Member variable 'QueryMapper::unaligned_from' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/align/legacy/query_mapper.h:123:36: style: Parameter 'lhs' can be declared as pointer to const. However it seems that 'compare_score' is a callback function, if 'lhs' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
diamond-2.1.11/src/align/legacy/query_mapper.cpp:221:112: note: You might need to cast the function pointer here
diamond-2.1.11/src/align/legacy/query_mapper.h:123:36: note: Parameter 'lhs' can be declared as pointer to const
diamond-2.1.11/src/align/legacy/query_mapper.h:123:49: style: Parameter 'rhs' can be declared as pointer to const. However it seems that 'compare_score' is a callback function, if 'rhs' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
diamond-2.1.11/src/align/legacy/query_mapper.cpp:221:112: note: You might need to cast the function pointer here
diamond-2.1.11/src/align/legacy/query_mapper.h:123:49: note: Parameter 'rhs' can be declared as pointer to const
diamond-2.1.11/src/align/extend_chunk.h:2:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NONE [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/extend_chunk.h:31:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TARGET_HITS2 [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/extend.cpp:81:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable no_ranking [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/extend.cpp:96:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable min_id [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/extend.cpp:100:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NONE [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/extend.cpp:113:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable target_hard_cap [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/extend.cpp:125:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable evalue [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/extend.cpp:135:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable add_self_aln [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/extend.cpp:146:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable query_contexts [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/extend.cpp:258:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PARALLEL [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/legacy/query_mapper.cpp:197:27: style: Variable 'query_len' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/align/legacy/query_mapper.cpp:197:17: style: Variable 'query_len' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/align/legacy/query_mapper.cpp:225:17: style: Variable 'query_len' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/align/short.cpp:11:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TARGET_HITS0 [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/ungapped.cpp:58:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ref_seqs_unmasked [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/ungapped.cpp:134:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PARALLEL [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/basic/basic.cpp:121:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable codes [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/basic/basic.cpp:188:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable log_stream [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/basic/basic.cpp:281:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable background_freqs [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/basic/config.cpp:102:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable weight_ [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/basic/config.cpp:151:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NONE [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/basic/config.cpp:179:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GREEDY_VERTEX_COVER [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::threads_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::merge_seq_treshold' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::shapes' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::padding' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::output_threads' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::lowmem_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::chunk_size' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::min_identities_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::min_identities2' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::ungapped_xdrop' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::raw_ungapped_xdrop' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::min_compressed_identities' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::min_seed_score' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::seed_signatures' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::min_bit_score' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::run_len' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::max_seed_freq' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::long_mode' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::gapped_xdrop' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::max_evalue' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::gap_open' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::gap_extend' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::mismatch_penalty' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::match_reward' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::debug_log' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::verbose' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::quiet' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::salltitles' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::reward' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::penalty' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::min_id' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::compress_temp' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::forwardonly' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::fetch_size' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::db_size' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::query_cover' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::query_or_target_cover' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::mode_sensitive' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::verbosity' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::no_auto_append' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::rank_factor' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::rank_ratio' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::freq_sd_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::target_fetch_size' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::mode_more_sensitive' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::query_gencode' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::space_penalty' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::new_prefilter' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::reverse' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::comp_based_stats' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::neighborhood_score' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::seed_weight' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::report_unaligned' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::subject_cover' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::mode_very_sensitive' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::max_hsps' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::no_self_hits' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::query_bins_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::superblock' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::log_query' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::log_subject' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::threads_align' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::score_ratio' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::sallseqid' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::xml_blord_format' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::frame_shift' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::query_range_culling' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::query_range_cover' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::transcript_len_estimate' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::radix_cluster_buffered' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::join_split_size' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::join_split_key_len' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::radix_bits' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::join_ht_factor' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::sort_join' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::simple_freq' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::freq_treshold' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::use_dataset_field' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::store_query_quality' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::swipe_chunk_size' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::query_parallel_limit' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::long_reads' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::hardmasked' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::cbs_window' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::tantan_r' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::tantan_minMaskProb' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::no_unlink' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::no_dict' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::stop_match_score' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::tantan_maxRepeatOffset' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::tantan_ungapped' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::swipe_all' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::taxon_k' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::upgma_edge_limit' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::log_extend' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::chaining_maxgap' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::chaining_range_cover' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::no_swipe_realign' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::cut_bar' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::bootstrap' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::chaining_maxnodes' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::cutoff_score_8bit' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::inner_culling_overlap' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::min_band_overlap' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::min_realign_overhang' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::ungapped_window' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::gapped_filter_diag_score' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::gapped_filter_diag_bit_score' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::gapped_filter_evalue_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::gapped_filter_window' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::output_hits' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::ungapped_evalue_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::no_logfile' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::band_bin' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::col_bin' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::file_buffer_size' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::self' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::trace_pt_fetch_size' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::tile_size' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::short_query_ungapped_bitscore' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::short_query_max_len' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::gapped_filter_evalue1' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::ext_chunk_size' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::ext_min_yield' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::full_sw_len' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::relaxed_evalue_factor' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::raw' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::mode_ultra_sensitive' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::chaining_len_cap' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::chaining_min_nodes' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::fast_tsv' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::target_parallel_verbosity' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::global_ranking_targets' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::mode_mid_sensitive' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::no_ranking' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::query_memory' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::memory_intervals' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::seedhit_density' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::chunk_size_multiplier' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::ranking_score_drop_factor' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::ranking_cutoff_bitscore' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::left_most_interval' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::no_forward_fp' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::no_ref_masking' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::target_bias' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::check_multi_target' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::output_fp' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::family_cap' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::cbs_matrix_scale' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::query_count' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::cbs_err_tolerance' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::cbs_it_limit' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::query_match_distance_threshold' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::length_ratio_threshold' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::hash_join_swap' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::target_indexed' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::deque_bucket_size' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::mode_fast' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::log_evalue_scale' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::ungapped_evalue_short_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::max_swipe_dp' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::skip_missing_seqids' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::ignore_warnings' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::no_reextend' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::seed_cut_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::no_reorder' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::key2' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::freq_masking' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::max_motif_len' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::chaining_stacked_hsp_ratio' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::swipe_task_size' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::minimizer_window_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::lin_stage1' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::min_task_trace_pts' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::sketch_size' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::bootstrap_block' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::centroid_factor' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::timeout' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::target_hard_cap' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::mapany' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::reassign_overlap' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::reassign_ratio' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::reassign_max' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::add_self_aln' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::mode_faster' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::weighted_gvc' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::kmer_ranking' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::hamming_ext' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::strict_gvc' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::no_block_size_limit' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::mp_self' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::approx_backtrace' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::narrow_band_cov' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::narrow_band_factor' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::anchor_window' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::anchor_score' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::classic_band' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::no_8bit_extension' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::anchored_swipe' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::no_chaining_merge_hsps' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::pipeline_short' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::linsearch' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::tsv_read_size' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::zdrop' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::heartbeat' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::no_parse_seqids' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::sam_qlen_field' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::min_length_ratio' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::symmetric' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::no_gvc_reassign' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::max_indirection' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::mode_shapes30x10' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::include_lineage' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::mode_linclust_20' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::dbtype' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::sensitivity' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::multiprocessing' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::mp_init' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::mp_recover' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::mp_query_chunk' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::command' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::algo' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::cluster_restart' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::max_size_set' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::external' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::cluster_mcl_inflation' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::cluster_mcl_expansion' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::cluster_mcl_sparsity_switch' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::cluster_mcl_chunk_size' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::cluster_mcl_max_iter' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::cluster_mcl_stats' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::cluster_mcl_nonsymmetric' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.h:405:2: warning:inconclusive: Member variable 'Config::load_balancing' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/seed.h:52:1: style: The struct 'Seed' does not declare a constructor although it has private member variables which likely require initialization. [noConstructor]
diamond-2.1.11/src/basic/translated_position.h:27:2: warning:inconclusive: Member variable 'Frame::offset' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/translated_position.h:27:2: warning:inconclusive: Member variable 'Frame::strand' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/translated_position.h:56:2: warning:inconclusive: Member variable 'TranslatedPosition::translated' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/shape.h:33:2: warning: Member variable 'Shape::long_mask_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/value.h:123:2: style: Struct 'AlignMode' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/basic/sequence.h:58:2: style: Struct 'Sequence' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/basic/reduction.h:33:2: style: Struct 'Reduction' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/basic/sequence.h:199:5: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/basic/basic.cpp:284:5: style: Consider using std::transform algorithm instead of a raw loop. [useStlAlgorithm]
diamond-2.1.11/src/basic/hssp.cpp:46:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/basic/hssp.cpp:53:71: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRANSCRIPT [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/basic/hssp.cpp:111:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable translated [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/basic/hssp.cpp:153:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable op_frameshift_forward [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/basic/hssp.cpp:178:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable begin_ [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/basic/hssp.cpp:189:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end_ [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/basic/hssp.cpp:199:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable begin_ [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/basic/hssp.cpp:210:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end_ [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/basic/hssp.cpp:220:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/basic/hssp.cpp:262:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable op_match [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/basic/hssp.cpp:277:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gap_openings [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/basic/hssp.cpp:307:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bit_score [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/basic/hssp.cpp:363:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable begin_ [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/basic/hssp.cpp:372:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable query_len [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/basic/hssp.cpp:376:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable subject_len [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/basic/hssp.cpp:384:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end_ [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::merge_seq_treshold' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::shapes' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::padding' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::output_threads' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::lowmem_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::chunk_size' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::min_identities_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::min_identities2' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::min_compressed_identities' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::min_seed_score' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::seed_signatures' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::min_bit_score' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::run_len' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::max_seed_freq' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::long_mode' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::gapped_xdrop' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::max_evalue' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::mismatch_penalty' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::match_reward' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::debug_log' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::verbose' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::quiet' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::salltitles' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::reward' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::penalty' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::min_id' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::compress_temp' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::forwardonly' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::fetch_size' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::db_size' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::query_cover' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::query_or_target_cover' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::mode_sensitive' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::no_auto_append' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::rank_factor' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::rank_ratio' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::freq_sd_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::target_fetch_size' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::mode_more_sensitive' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::space_penalty' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::new_prefilter' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::reverse' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::neighborhood_score' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::seed_weight' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::report_unaligned' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::subject_cover' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::mode_very_sensitive' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::max_hsps' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::no_self_hits' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::query_bins_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::superblock' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::log_query' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::log_subject' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::threads_align' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::score_ratio' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::sallseqid' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::xml_blord_format' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::query_range_cover' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::transcript_len_estimate' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::radix_cluster_buffered' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::join_split_size' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::join_split_key_len' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::radix_bits' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::join_ht_factor' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::sort_join' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::simple_freq' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::freq_treshold' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::use_dataset_field' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::swipe_chunk_size' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::query_parallel_limit' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::long_reads' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::hardmasked' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::cbs_window' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::tantan_r' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::tantan_minMaskProb' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::no_unlink' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::no_dict' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::tantan_maxRepeatOffset' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::tantan_ungapped' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::swipe_all' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::taxon_k' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::upgma_edge_limit' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::log_extend' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::chaining_maxgap' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::chaining_range_cover' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::no_swipe_realign' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::cut_bar' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::bootstrap' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::chaining_maxnodes' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::cutoff_score_8bit' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::inner_culling_overlap' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::min_band_overlap' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::min_realign_overhang' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::ungapped_window' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::gapped_filter_diag_score' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::gapped_filter_diag_bit_score' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::gapped_filter_evalue_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::gapped_filter_window' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::output_hits' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::ungapped_evalue_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::no_logfile' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::band_bin' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::col_bin' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::file_buffer_size' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::self' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::trace_pt_fetch_size' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::tile_size' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::short_query_ungapped_bitscore' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::short_query_max_len' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::gapped_filter_evalue1' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::ext_chunk_size' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::ext_min_yield' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::full_sw_len' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::relaxed_evalue_factor' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::raw' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::mode_ultra_sensitive' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::chaining_len_cap' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::chaining_min_nodes' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::fast_tsv' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::target_parallel_verbosity' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::global_ranking_targets' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::mode_mid_sensitive' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::no_ranking' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::query_memory' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::memory_intervals' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::seedhit_density' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::chunk_size_multiplier' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::ranking_score_drop_factor' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::ranking_cutoff_bitscore' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::left_most_interval' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::no_forward_fp' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::no_ref_masking' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::target_bias' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::check_multi_target' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::output_fp' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::family_cap' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::query_count' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::cbs_err_tolerance' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::cbs_it_limit' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::query_match_distance_threshold' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::length_ratio_threshold' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::hash_join_swap' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::target_indexed' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::deque_bucket_size' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::mode_fast' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::log_evalue_scale' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::ungapped_evalue_short_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::max_swipe_dp' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::skip_missing_seqids' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::ignore_warnings' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::no_reextend' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::seed_cut_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::no_reorder' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::key2' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::freq_masking' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::max_motif_len' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::chaining_stacked_hsp_ratio' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::swipe_task_size' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::minimizer_window_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::lin_stage1' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::min_task_trace_pts' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::sketch_size' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::bootstrap_block' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::centroid_factor' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::timeout' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::target_hard_cap' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::mapany' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::reassign_overlap' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::reassign_ratio' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::reassign_max' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::add_self_aln' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::mode_faster' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::weighted_gvc' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::hamming_ext' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::strict_gvc' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::no_block_size_limit' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::mp_self' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::approx_backtrace' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::narrow_band_cov' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::narrow_band_factor' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::anchor_window' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::anchor_score' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::classic_band' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::no_8bit_extension' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::anchored_swipe' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::no_chaining_merge_hsps' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::pipeline_short' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::linsearch' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::tsv_read_size' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::zdrop' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::heartbeat' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::no_parse_seqids' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::sam_qlen_field' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::min_length_ratio' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::symmetric' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::no_gvc_reassign' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::max_indirection' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::mode_shapes30x10' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::include_lineage' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::mode_linclust_20' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::multiprocessing' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::mp_init' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::mp_recover' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::mp_query_chunk' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::cluster_restart' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::max_size_set' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::external' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::cluster_mcl_inflation' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::cluster_mcl_expansion' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::cluster_mcl_sparsity_switch' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::cluster_mcl_chunk_size' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::cluster_mcl_max_iter' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::cluster_mcl_stats' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::cluster_mcl_nonsymmetric' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:160:9: warning: Member variable 'Config::load_balancing' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/basic/config.cpp:516:9: style: Local variable 'query_match_distance_threshold' shadows outer variable [shadowVariable]
diamond-2.1.11/src/basic/config.h:256:9: note: Shadowed declaration
diamond-2.1.11/src/basic/config.cpp:516:9: note: Shadow variable
diamond-2.1.11/src/basic/config.cpp:517:9: style: Local variable 'length_ratio_threshold' shadows outer variable [shadowVariable]
diamond-2.1.11/src/basic/config.h:257:9: note: Shadowed declaration
diamond-2.1.11/src/basic/config.cpp:517:9: note: Shadow variable
diamond-2.1.11/src/basic/config.cpp:132:13: style: Variable 'i' can be declared as reference to const [constVariableReference]
diamond-2.1.11/src/basic/config.cpp:133:0: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
diamond-2.1.11/src/chaining/diag_graph.h:39:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/chaining/diag_graph.h:157:74: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/chaining/backtrace.cpp:22:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chaining_stacked_hsp_ratio [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/chaining/backtrace.cpp:39:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chaining_stacked_hsp_ratio [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/chaining/backtrace.cpp:101:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable op_insertion [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/chaining/backtrace.cpp:215:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable op_insertion [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/chaining/backtrace.cpp:327:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/chaining/greedy_align.cpp:79:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/chaining/greedy_align.cpp:88:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/chaining/greedy_align.cpp:99:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cmp_subject [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/chaining/greedy_align.cpp:118:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chaining_range_cover [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/chaining/greedy_align.cpp:272:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/chaining/greedy_align.cpp:288:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/chaining/greedy_align.cpp:366:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chaining_maxnodes [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/chaining/greedy_align.cpp:406:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/chaining/greedy_align.cpp:486:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chaining_maxgap [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/chaining/diag_graph.h:69:3: warning: Member variable 'Edge::path_max' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/chaining/diag_graph.h:69:3: warning: Member variable 'Edge::j' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/chaining/diag_graph.h:69:3: warning: Member variable 'Edge::path_min' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/chaining/diag_graph.h:69:3: warning: Member variable 'Edge::prefix_score_begin' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/chaining/diag_graph.h:69:3: warning: Member variable 'Edge::node_out' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/chaining/diag_graph.h:25:2: style: Struct 'DiagonalNode' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/chaining/hamming_ext.cpp:18:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable approx_min_id [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/chaining/hamming_ext.cpp:29:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cmp_score [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/chaining/hamming_ext.cpp:50:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hamming_ext [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/chaining/greedy_align.cpp:128:2: warning: Member variable 'Link::query_pos1' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/chaining/greedy_align.cpp:128:2: warning: Member variable 'Link::subject_pos2' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/chaining/greedy_align.cpp:128:2: warning: Member variable 'Link::query_pos2' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/chaining/greedy_align.cpp:128:2: warning: Member variable 'Link::score1' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/chaining/greedy_align.cpp:128:2: warning: Member variable 'Link::score2' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/chaining/greedy_align.cpp:131:2: warning: Member variable 'Link::subject_pos2' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/chaining/greedy_align.cpp:131:2: warning: Member variable 'Link::query_pos2' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/chaining/greedy_align.cpp:222:15: style:inconclusive: Technically the member function 'Chaining::Aligner::get_approximate_link' can be const. [functionConst]
diamond-2.1.11/src/chaining/aligner.h:13:6: note: Technically the member function 'Chaining::Aligner::get_approximate_link' can be const.
diamond-2.1.11/src/chaining/greedy_align.cpp:222:15: note: Technically the member function 'Chaining::Aligner::get_approximate_link' can be const.
diamond-2.1.11/src/chaining/greedy_align.cpp:87:21: style: The scope of the variable 'score' can be reduced. [variableScope]
diamond-2.1.11/src/chaining/greedy_align.cpp:229:49: style: The scope of the variable 'diff1' can be reduced. [variableScope]
diamond-2.1.11/src/chaining/greedy_align.cpp:241:45: style: Local variable 'edge' shadows outer variable [shadowVariable]
diamond-2.1.11/src/chaining/greedy_align.cpp:231:44: note: Shadowed declaration
diamond-2.1.11/src/chaining/greedy_align.cpp:241:45: note: Shadow variable
diamond-2.1.11/src/chaining/greedy_align.cpp:122:12: style: Consider using std::copy algorithm instead of a raw loop. [useStlAlgorithm]
diamond-2.1.11/src/chaining/greedy_align.cpp:270:106: error: Uninitialized variable: path_min [legacyUninitvar]
diamond-2.1.11/src/chaining/smith_waterman.cpp:22:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/chaining/greedy_align.cpp:229:55: style: Variable 'diff1' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/chaining/greedy_align.cpp:300:30: style: Variable 'shift' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/chaining/greedy_align.cpp:333:30: style: Variable 'shift' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/cluster/cluster.h:84:81: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable member_cover [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/cluster/cascaded/cascaded.h:57:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Data [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/cluster/cascaded/cascaded.h:75:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Data [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/cluster/cascaded/cascaded.cpp:62:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable command [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/cluster/cascaded/cascaded.cpp:130:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable approx_min_id [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/cluster/cluster.h:78:2: style: Struct 'Mapback' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/cluster/cascaded/cascaded.h:28:3: style: The destructor '~Cascaded' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/cluster/cluster.h:36:11: note: Virtual destructor in base class
diamond-2.1.11/src/cluster/cascaded/cascaded.h:28:3: note: Destructor in derived class
diamond-2.1.11/src/cluster/cascaded/cascaded.h:29:7: style: The function 'run' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/cluster/cluster.h:34:15: note: Virtual function in base class
diamond-2.1.11/src/cluster/cascaded/cascaded.h:29:7: note: Function in derived class
diamond-2.1.11/src/cluster/cascaded/cascaded.h:30:14: style: The function 'get_description' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/cluster/cluster.h:35:22: note: Virtual function in base class
diamond-2.1.11/src/cluster/cascaded/cascaded.h:30:14: note: Function in derived class
diamond-2.1.11/src/cluster/cascaded/cascaded.h:28:3: style: The destructor '~Cascaded' overrides a destructor in a base class but is identical to the overridden function [uselessOverride]
diamond-2.1.11/src/cluster/cluster.h:36:11: note: Virtual destructor in base class
diamond-2.1.11/src/cluster/cascaded/cascaded.h:28:3: note: Destructor in derived class
diamond-2.1.11/src/cluster/cluster.h:87:23: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/cluster/cascaded/cascaded.h:56:23: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/cluster/cascaded/cascaded.h:74:23: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/cluster/cascaded/cascaded.cpp:92:47: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/cluster/cascaded/cascaded.cpp:92:86: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/cluster/cascaded/helpers.cpp:32:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cluster_steps [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/cluster/cascaded/helpers.cpp:76:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable connected_component_depth [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/cluster/cascaded/recluster.cpp:53:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable member_cover [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/cluster/cascaded/recluster.cpp:145:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable message_stream [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/cluster/cascaded/wrapper.cpp:100:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Data [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/cluster/cascaded/wrapper.cpp:110:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable message_stream [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/cluster/cascaded/wrapper.cpp:162:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hamming_ext [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/cluster/cascaded/wrapper.cpp:51:2: warning: Member variable 'Config::block_size' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/cluster/cascaded/wrapper.cpp:51:2: style: Struct 'Config' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/cluster/cascaded/wrapper.cpp:93:2: style: Struct 'BestCentroid' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/cluster/cascaded/wrapper.cpp:99:23: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/cluster/cascaded/wrapper.cpp:222:22: style: Local variable 'i' shadows outer variable [shadowVariable]
diamond-2.1.11/src/cluster/cascaded/wrapper.cpp:190:7: note: Shadowed declaration
diamond-2.1.11/src/cluster/cascaded/wrapper.cpp:222:22: note: Shadow variable
diamond-2.1.11/src/cluster/cascaded/wrapper.cpp:51:35: style: Parameter 'db' can be declared as reference to const [constParameterReference]
diamond-2.1.11/src/cluster/cascaded/wrapper.cpp:66:38: style: struct member 'Config::block_size' is never used. [unusedStructMember]
diamond-2.1.11/src/cluster/cluster_registry.h:70:46: performance: Function parameter 'key' should be passed by const reference. [passedByValue]
diamond-2.1.11/src/cluster/cluster_registry.h:73:30: performance: Function parameter 'key' should be passed by const reference. [passedByValue]
diamond-2.1.11/src/cluster/external/make_seed_table.cpp:54:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FASTER [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/cluster/external/make_seed_table.cpp:45:7: performance:inconclusive: Technically the member function 'Cluster::SeedCallback::finish' can be static (but you may consider moving to unnamed namespace). [functionStatic]
diamond-2.1.11/src/cluster/output.cpp:80:94: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable comp_based_stats [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/cluster/output.cpp:107:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable output_sink [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/cluster/output.cpp:118:84: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DEFAULT_MEMORY_LIMIT [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/cluster/helpers.cpp:55:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cluster [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/cluster/helpers.cpp:83:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cluster [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/cluster/helpers.cpp:130:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable threads_ [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/cluster/helpers.cpp:167:94: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable threads_ [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/cluster/helpers.cpp:206:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable approx_min_id [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/cluster/helpers.cpp:225:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STRING [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/cluster/helpers.cpp:245:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STRING [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/cluster/helpers.cpp:139:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable threads_ [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/cluster/helpers.cpp:123:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable threads_ [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/cluster/helpers.cpp:216:2: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
diamond-2.1.11/src/cluster/helpers.cpp:219:2: note: Found duplicate branches for 'if' and 'else'.
diamond-2.1.11/src/cluster/helpers.cpp:216:2: note: Found duplicate branches for 'if' and 'else'.
diamond-2.1.11/src/cluster/helpers.cpp:213:113: style: Same value in both branches of ternary operator. [duplicateValueTernary]
diamond-2.1.11/src/cluster/helpers.cpp:171:52: style: Parameter 'oid_to_centroid_oid' can be declared as reference to const [constParameterReference]
diamond-2.1.11/src/cluster/helpers.cpp:78:22: style: Variable 'lines' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/cluster/helpers.cpp:78:16: style: Variable 'lines' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/cluster/realign.cpp:44:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable output_format [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/cluster/reassign.cpp:43:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable message_stream [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/cluster/realign.cpp:49:0: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
diamond-2.1.11/src/contrib/dna/timer.h:98:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/dna/build_score.cpp:52:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable eBlastTypeBlastn [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/dna/alignment.cpp:42:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NUCLEOTIDE_COUNT [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/dna/build_score.cpp:86:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NCBIMATH_LN2 [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/dna/alignment.cpp:97:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Alignment [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/dna/alignment.cpp:124:74: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Alignment [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/dna/alignment.cpp:227:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable op_deletion [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/dna/alignment.cpp:119:5: style: Assignment of function parameter has no effect outside the function. [uselessAssignmentArg]
diamond-2.1.11/src/contrib/dna/timer.h:95:10: style:inconclusive: Technically the member function 'Dna::TotalTime::print' can be const. [functionConst]
diamond-2.1.11/src/contrib/dna/alignment.cpp:119:10: style: Variable 'band' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/contrib/dna/chain.cpp:74:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable i [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/dna/chain.cpp:142:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable best_hsp_only [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/dna/dna_index.cpp:45:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seedp [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/dna/dna_index.cpp:87:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seedp [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/dna/dna_index.cpp:104:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable threads_ [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/dna/dna_index.cpp:113:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seedp [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/dna/dna_index.cpp:131:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable threads_ [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/dna/dna_index.cpp:141:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable seedp [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/dna/dna_index.cpp:158:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable repetitive_cutoff [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/dna/chain.cpp:74:20: style: Consider using std::transform algorithm instead of a raw loop. [useStlAlgorithm]
diamond-2.1.11/src/contrib/dna/extension.cpp:80:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NUCLEOTIDE_COUNT [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/dna/extension.cpp:135:71: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Alignment [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/dna/extension.cpp:237:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable op_deletion [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/dna/extension.cpp:278:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable max_evalue [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/dna/extension.cpp:381:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chaining_out [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/dna/extension.cpp:263:33: style: Parameter 'end' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/contrib/dna/extension_chain.cpp:32:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable span [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/dna/extension_chain.cpp:52:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable i [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/dna/extension_chain.cpp:90:71: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable j [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/dna/extension_chain.cpp:127:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable i [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/dna/extension_chain.cpp:286:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable i [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/dna/extension_chain.cpp:450:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chaining_out [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/dna/extension_seed_matches.cpp:29:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable shapes [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/dna/extension_seed_matches.cpp:54:21: style: Array index 'right_i' is used before limits check. [arrayIndexThenCheck]
diamond-2.1.11/src/contrib/dna/seed_set_dna.cpp:36:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable shapes [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/dna/seed_set_dna.h:47:9: style:inconclusive: Member variable 'SeedMatch::j_' is in the wrong place in the initializer list. [initializerList]
diamond-2.1.11/src/contrib/dna/seed_set_dna.cpp:58:1: note: Member variable 'SeedMatch::j_' is in the wrong place in the initializer list.
diamond-2.1.11/src/contrib/dna/seed_set_dna.h:47:9: note: Member variable 'SeedMatch::j_' is in the wrong place in the initializer list.
diamond-2.1.11/src/contrib/dna/seed_set_dna.cpp:32:110: style:inconclusive: Function 'seed_lookup' argument 4 names different: declaration 'it_param' definition 'window_size'. [funcArgNamesDifferent]
diamond-2.1.11/src/contrib/dna/seed_set_dna.h:51:110: note: Function 'seed_lookup' argument 4 names different: declaration 'it_param' definition 'window_size'.
diamond-2.1.11/src/contrib/dna/seed_set_dna.cpp:32:110: note: Function 'seed_lookup' argument 4 names different: declaration 'it_param' definition 'window_size'.
diamond-2.1.11/src/contrib/dna/extension_chain.cpp:269:89: style: Parameter 'chainingParameters' can be declared as reference to const [constParameterReference]
diamond-2.1.11/src/contrib/dna/setup.cpp:28:71: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sequence_type [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/dna/smith_watermann.cpp:77:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bit_score [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/mcl/clustering_variables.h:67:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable begin_ [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/mcl/clustering_variables.h:79:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end_ [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/mcl/clustering_variables.h:91:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable begin_ [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/mcl/clustering_variables.h:103:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable end_ [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/mcl/clustering_format.cpp:43:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable hsp_values [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/mcl/clustering_variables.h:332:35: performance: Function parameter 'key' should be passed by const reference. [passedByValue]
diamond-2.1.11/src/contrib/mcl/clustering_variables.h:335:30: performance: Function parameter 'key' should be passed by const reference. [passedByValue]
diamond-2.1.11/src/contrib/mcl/recursive_parser.h:30:7: style:inconclusive: Technically the member function 'RecursiveParser::peek' can be const. [functionConst]
diamond-2.1.11/src/contrib/mcl/recursive_parser.h:34:7: style:inconclusive: Technically the member function 'RecursiveParser::peek' can be const. [functionConst]
diamond-2.1.11/src/contrib/mcl/recursive_parser.h:200:25: performance: Function 'variables()' should return member 'vars_' by const reference. [returnByReference]
diamond-2.1.11/src/contrib/mcl/recursive_parser.h:71:8: style: Instance of 'std::runtime_error' object is destroyed immediately. [unusedScopedObject]
diamond-2.1.11/src/data/sequence_file.h:266:1: error: There is an unknown macro here somewhere. Configuration is required. If DEFINE_ENUM_FLAG_OPERATORS is a macro then please configure it. [unknownMacro]
diamond-2.1.11/src/contrib/mcl/mcl.cpp:67:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cluster_mcl_chunk_size [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/mcl/mcl.cpp:180:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cluster_mcl_nonsymmetric [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/mcl/mcl.cpp:363:65: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable database [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:135:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:173:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:215:82: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable rhs [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:221:82: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable rhs [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:230:82: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable rhs [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:292:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:345:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/masking/def.h:29:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/masking/def.h:35:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/sequence_file.h:201:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable OId [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/block/block_wrapper.cpp:111:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DELIMITER [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/flags.h:23:2: warning:inconclusive: Member variable 'PackedLocId::block_id' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/data/flags.h:24:2: warning: Member variable 'PackedLocId::block_id' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/data/sequence_file.h:98:3: warning:inconclusive: Member variable 'SeqInfo::pos' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/data/sequence_file.h:98:3: warning:inconclusive: Member variable 'SeqInfo::seq_len' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/data/flags.h:11:7: performance:inconclusive: Technically the member function 'NoFilter::contains' can be static (but you may consider moving to unnamed namespace). [functionStatic]
diamond-2.1.11/src/data/sequence_set.h:39:11: warning: The struct 'SequenceSet' defines member function with name 'operator[]' also defined in its parent struct 'StringSetBase < Letter , Sequence :: DELIMITER , 1 >'. [duplInheritedMember]
diamond-2.1.11/src/data/string_set.h:162:11: note: Parent function 'StringSetBase < Letter , Sequence :: DELIMITER , 1 >::operator[]'
diamond-2.1.11/src/data/sequence_set.h:39:11: note: Derived function 'SequenceSet::operator[]'
diamond-2.1.11/src/data/sequence_set.h:31:2: style: Struct 'SequenceSet' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/data/sequence_set.h:32:2: style: Struct 'SequenceSet' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/data/taxonomy_nodes.h:35:2: style: Struct 'Rank' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/data/taxonomy_nodes.h:38:2: style: Struct 'Rank' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/data/taxonomy_nodes.h:62:2: style: Struct 'TaxonomyNodes' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/basic/packed_loc.h:38:5: style: Struct 'packed_uint40_t' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/data/flags.h:24:2: style: Struct 'PackedLocId' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/data/block/block.h:40:2: style: Struct 'Block' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/data/block/block_wrapper.h:8:2: style: Struct 'BlockWrapper' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/data/block/block_wrapper.h:37:11: style: The destructor '~BlockWrapper' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/data/sequence_file.h:157:11: note: Virtual destructor in base class
diamond-2.1.11/src/data/block/block_wrapper.h:37:11: note: Destructor in derived class
diamond-2.1.11/src/data/sequence_file.h:200:14: style: Variable 'v' can be declared as reference to const [constVariableReference]
diamond-2.1.11/src/data/sequence_file.h:202:14: style: Variable 'v' can be declared as reference to const [constVariableReference]
diamond-2.1.11/src/data/sequence_file.h:204:14: style: Variable 'v' can be declared as reference to const [constVariableReference]
diamond-2.1.11/src/data/sequence_file.h:206:14: style: Variable 'v' can be declared as reference to const [constVariableReference]
diamond-2.1.11/src/data/sequence_file.h:208:14: style: Variable 'v' can be declared as reference to const [constVariableReference]
diamond-2.1.11/src/data/seed_histogram.h:64:5: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
diamond-2.1.11/src/data/sequence_file.h:201:6: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
diamond-2.1.11/src/data/sequence_file.h:203:6: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
diamond-2.1.11/src/data/sequence_file.h:205:6: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
diamond-2.1.11/src/data/sequence_file.h:207:6: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
diamond-2.1.11/src/data/sequence_file.h:209:6: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
diamond-2.1.11/src/data/dmnd/dmnd.cpp:110:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/dmnd/dmnd.cpp:115:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/dmnd/dmnd.cpp:121:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NO_COMPATIBILITY_CHECK [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/dmnd/dmnd.cpp:141:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TAXON_MAPPING [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/dmnd/dmnd.cpp:190:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable magic_number [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/dmnd/dmnd.cpp:222:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable file_buffer_size [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/dmnd/dmnd.cpp:364:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SIZE [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/dmnd/dmnd.cpp:413:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable message_stream [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/dmnd/dmnd.cpp:524:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DELIMITER [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/dmnd/dmnd.cpp:555:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TAXON_MAPPING [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/dmnd/dmnd.cpp:593:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable file_name [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/dmnd/dmnd.cpp:644:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ACC_TO_OID_MAPPING [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/align/extend.cpp:247:184: style: Redundant condition: config.mapany. '!config.mapany || (config.mapany && matches.empty())' is equivalent to '!config.mapany || matches.empty()' [redundantCondition]
diamond-2.1.11/src/align/extend.cpp:179:18: style: Local variable 'first_round_hspv' shadows outer function [shadowFunction]
diamond-2.1.11/src/align/extend.cpp:99:18: note: Shadowed declaration
diamond-2.1.11/src/align/extend.cpp:179:18: note: Shadow variable
diamond-2.1.11/src/data/dmnd/dmnd.h:33:2: warning: Member variable 'ReferenceHeader::pos_array_offset' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/data/dmnd/dmnd.h:143:14: style: Virtual function 'build_version' is called from constructor 'DatabaseFile(const std::string&file_name,Metadata metadata=Metadata()' at line 147. Dynamic binding is not used. [virtualCallInConstructor]
diamond-2.1.11/src/data/dmnd/dmnd.cpp:147:51: note: Calling build_version
diamond-2.1.11/src/data/dmnd/dmnd.h:143:14: note: build_version is a virtual function
diamond-2.1.11/src/data/dmnd/dmnd.h:105:15: style: Virtual function 'init_seq_access' is called from constructor 'DatabaseFile(const std::string&file_name,Metadata metadata=Metadata()' at line 165. Dynamic binding is not used. [virtualCallInConstructor]
diamond-2.1.11/src/data/dmnd/dmnd.cpp:165:3: note: Calling read_seqid_list
diamond-2.1.11/src/data/dmnd/dmnd.cpp:651:2: note: Calling init_seq_access
diamond-2.1.11/src/data/dmnd/dmnd.h:105:15: note: init_seq_access is a virtual function
diamond-2.1.11/src/data/dmnd/dmnd.h:101:15: style: Virtual function 'close' is called from destructor '~DatabaseFile()' at line 569. Dynamic binding is not used. [virtualCallInConstructor]
diamond-2.1.11/src/data/dmnd/dmnd.cpp:569:2: note: Calling close
diamond-2.1.11/src/data/dmnd/dmnd.h:101:15: note: close is a virtual function
diamond-2.1.11/src/data/dmnd/dmnd.h:84:2: style: Struct 'DatabaseFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/data/dmnd/dmnd.h:85:2: style: Struct 'DatabaseFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/data/fasta/fasta_file.h:13:2: style: Struct 'FastaFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/data/dmnd/dmnd.h:144:11: style: The destructor '~DatabaseFile' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/data/sequence_file.h:157:11: note: Virtual destructor in base class
diamond-2.1.11/src/data/dmnd/dmnd.h:144:11: note: Destructor in derived class
diamond-2.1.11/src/data/fasta/fasta_file.h:42:11: style: The destructor '~FastaFile' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/data/sequence_file.h:157:11: note: Virtual destructor in base class
diamond-2.1.11/src/data/fasta/fasta_file.h:42:11: note: Destructor in derived class
diamond-2.1.11/src/data/dmnd/dmnd.cpp:583:2: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
diamond-2.1.11/src/data/dmnd/dmnd.cpp:244:22: style: The scope of the variable 'n' can be reduced. [variableScope]
diamond-2.1.11/src/data/dmnd/dmnd.cpp:244:41: style: The scope of the variable 'total_seqs' can be reduced. [variableScope]
diamond-2.1.11/src/data/dmnd/dmnd.cpp:133:42: style:inconclusive: Function 'DatabaseFile' argument 1 names different: declaration 'file_name' definition 'input_file'. [funcArgNamesDifferent]
diamond-2.1.11/src/data/dmnd/dmnd.h:84:34: note: Function 'DatabaseFile' argument 1 names different: declaration 'file_name' definition 'input_file'.
diamond-2.1.11/src/data/dmnd/dmnd.cpp:133:42: note: Function 'DatabaseFile' argument 1 names different: declaration 'file_name' definition 'input_file'.
diamond-2.1.11/src/data/dmnd/dmnd.cpp:244:9: style: Local variable 'letters' shadows outer function [shadowFunction]
diamond-2.1.11/src/data/dmnd/dmnd.h:138:18: note: Shadowed declaration
diamond-2.1.11/src/data/dmnd/dmnd.cpp:244:9: note: Shadow variable
diamond-2.1.11/src/data/dmnd/dmnd.cpp:426:9: style: Local variable 'letters' shadows outer function [shadowFunction]
diamond-2.1.11/src/data/dmnd/dmnd.h:138:18: note: Shadowed declaration
diamond-2.1.11/src/data/dmnd/dmnd.cpp:426:9: note: Shadow variable
diamond-2.1.11/src/data/frequent_seeds.cpp:44:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/frequent_seeds.cpp:82:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEED_MASK [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/frequent_seeds.cpp:101:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable threads_ [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/mcl/sparse.h:26:36: performance:inconclusive: Technically the member function 'Workflow::Cluster::MCL::sparse_matrix_multiply' can be static (but you may consider moving to unnamed namespace). [functionStatic]
diamond-2.1.11/src/contrib/mcl/mcl.h:75:32: note: Technically the member function 'Workflow::Cluster::MCL::sparse_matrix_multiply' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/contrib/mcl/sparse.h:26:36: note: Technically the member function 'Workflow::Cluster::MCL::sparse_matrix_multiply' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/contrib/mcl/sparse.h:90:36: performance:inconclusive: Technically the member function 'Workflow::Cluster::MCL::sparse_matrix_get_gamma' can be static (but you may consider moving to unnamed namespace). [functionStatic]
diamond-2.1.11/src/contrib/mcl/mcl.h:76:32: note: Technically the member function 'Workflow::Cluster::MCL::sparse_matrix_get_gamma' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/contrib/mcl/sparse.h:90:36: note: Technically the member function 'Workflow::Cluster::MCL::sparse_matrix_get_gamma' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/contrib/mcl/sparse.h:109:12: performance:inconclusive: Technically the member function 'Workflow::Cluster::MCL::sparse_matrix_get_norm' can be static (but you may consider moving to unnamed namespace). [functionStatic]
diamond-2.1.11/src/contrib/mcl/mcl.h:77:8: note: Technically the member function 'Workflow::Cluster::MCL::sparse_matrix_get_norm' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/contrib/mcl/sparse.h:109:12: note: Technically the member function 'Workflow::Cluster::MCL::sparse_matrix_get_norm' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/contrib/mcl/mcl.cpp:64:11: performance:inconclusive: Technically the member function 'Workflow::Cluster::MCL::print_stats' can be static (but you may consider moving to unnamed namespace). [functionStatic]
diamond-2.1.11/src/contrib/mcl/mcl.h:78:7: note: Technically the member function 'Workflow::Cluster::MCL::print_stats' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/contrib/mcl/mcl.cpp:64:11: note: Technically the member function 'Workflow::Cluster::MCL::print_stats' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/contrib/mcl/mcl.cpp:212:33: performance:inconclusive: Technically the member function 'Workflow::Cluster::MCL::get_sparse_matrix_and_clear' can be static (but you may consider moving to unnamed namespace). [functionStatic]
diamond-2.1.11/src/contrib/mcl/mcl.h:85:29: note: Technically the member function 'Workflow::Cluster::MCL::get_sparse_matrix_and_clear' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/contrib/mcl/mcl.cpp:212:33: note: Technically the member function 'Workflow::Cluster::MCL::get_sparse_matrix_and_clear' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/contrib/mcl/mcl.cpp:227:22: performance:inconclusive: Technically the member function 'Workflow::Cluster::MCL::get_dense_matrix_and_clear' can be static (but you may consider moving to unnamed namespace). [functionStatic]
diamond-2.1.11/src/contrib/mcl/mcl.h:86:18: note: Technically the member function 'Workflow::Cluster::MCL::get_dense_matrix_and_clear' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/contrib/mcl/mcl.cpp:227:22: note: Technically the member function 'Workflow::Cluster::MCL::get_dense_matrix_and_clear' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:395:11: style:inconclusive: Either there is a missing 'override', or the member function 'SparseMatrixStream < float >::getNumberOfElements' can be const. [functionConst]
diamond-2.1.11/src/contrib/mcl/mcl.h:60:2: style: Struct 'Clustering_format' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/contrib/mcl/mcl.h:98:3: style: The destructor '~MCL' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/cluster/cluster.h:36:11: note: Virtual destructor in base class
diamond-2.1.11/src/contrib/mcl/mcl.h:98:3: note: Destructor in derived class
diamond-2.1.11/src/contrib/mcl/mcl.h:99:7: style: The function 'run' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/cluster/cluster.h:34:15: note: Virtual function in base class
diamond-2.1.11/src/contrib/mcl/mcl.h:99:7: note: Function in derived class
diamond-2.1.11/src/contrib/mcl/mcl.h:100:9: style: The function 'get_description' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/cluster/cluster.h:35:22: note: Virtual function in base class
diamond-2.1.11/src/contrib/mcl/mcl.h:100:9: note: Function in derived class
diamond-2.1.11/src/contrib/mcl/mcl.h:98:3: style: The destructor '~MCL' overrides a destructor in a base class but is identical to the overridden function [uselessOverride]
diamond-2.1.11/src/cluster/cluster.h:36:11: note: Virtual destructor in base class
diamond-2.1.11/src/contrib/mcl/mcl.h:98:3: note: Destructor in derived class
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:79:14: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:80:14: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:82:14: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:111:16: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:112:16: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:129:29: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:131:31: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:133:27: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:162:29: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:164:31: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:174:13: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:176:13: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:297:11: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:299:11: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:308:12: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:310:12: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:350:12: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:352:12: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:365:13: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:367:13: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:82:14: portability:inconclusive: Casting from double * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast]
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:133:27: portability: Casting between const char * and double * which have an incompatible binary data representation. [invalidPointerCast]
diamond-2.1.11/src/data/frequent_seeds.cpp:96:21: performance:inconclusive: Technically the member function 'FrequentSeeds::build' can be static (but you may consider moving to unnamed namespace). [functionStatic]
diamond-2.1.11/src/data/frequent_seeds.h:33:7: note: Technically the member function 'FrequentSeeds::build' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/data/frequent_seeds.cpp:96:21: note: Technically the member function 'FrequentSeeds::build' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/data/frequent_seeds.cpp:122:29: style: Variable 'end' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/data/queries.cpp:36:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable query_translated [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/queries.cpp:51:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable query_translated [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/contrib/mcl/mcl.cpp:454:41: style: Local variable 't' shadows outer variable [shadowVariable]
diamond-2.1.11/src/contrib/mcl/mcl.cpp:442:40: note: Shadowed declaration
diamond-2.1.11/src/contrib/mcl/mcl.cpp:454:41: note: Shadow variable
diamond-2.1.11/src/contrib/mcl/mcl.cpp:473:41: style: Local variable 't' shadows outer variable [shadowVariable]
diamond-2.1.11/src/contrib/mcl/mcl.cpp:442:40: note: Shadowed declaration
diamond-2.1.11/src/contrib/mcl/mcl.cpp:473:41: note: Shadow variable
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:173:13: style: Local variable 'os' shadows outer variable [shadowVariable]
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:76:17: note: Shadowed declaration
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:173:13: note: Shadow variable
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:349:11: style: Local variable 'n' shadows outer variable [shadowVariable]
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:54:9: note: Shadowed declaration
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:349:11: note: Shadow variable
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:229:60: performance: Function parameter 'graph_file_name' should be passed by const reference. [passedByValue]
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:86:60: style: Parameter 'indexToSetId' can be declared as reference to const [constParameterReference]
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:180:61: style: Parameter 'split' can be declared as reference to const [constParameterReference]
diamond-2.1.11/src/contrib/mcl/mcl.cpp:173:9: style: Variable 'uints' can be declared as const array [constVariable]
diamond-2.1.11/src/contrib/mcl/mcl.cpp:117:43: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
diamond-2.1.11/src/contrib/mcl/mcl.cpp:507:44: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
diamond-2.1.11/src/contrib/mcl/sparse_matrix_stream.h:183:13: style: Consider using std::transform algorithm instead of a raw loop. [useStlAlgorithm]
diamond-2.1.11/src/contrib/mcl/mcl.cpp:69:14: style: Variable 'inflation' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/contrib/mcl/mcl.cpp:582:9: style: Unused variable: n [unusedVariable]
diamond-2.1.11/src/data/seed_set.h:56:2: style: Struct 'HashedSeedSet' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/data/seed_histogram.cpp:65:8: performance:inconclusive: Technically the member function 'SeedHistogram::Callback::finish' can be static (but you may consider moving to unnamed namespace). [functionStatic]
diamond-2.1.11/src/data/enum_seeds.h:17:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable query_contexts [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/enum_seeds.h:46:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable query_contexts [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/enum_seeds.h:74:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable query_contexts [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/enum_seeds.h:103:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable query_contexts [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/enum_seeds.h:126:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable shapes [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/enum_seeds.h:180:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NONE [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/seed_array.cpp:49:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SeedOffset [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/seed_array.cpp:156:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stats_ [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/seed_array.cpp:236:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable threads_ [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/seed_array.cpp:85:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Entry [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/seed_set.cpp:68:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable shapes [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/seed_set.cpp:114:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable log_stream [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/seed_set.cpp:137:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable log_stream [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/sequence_set.cpp:39:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable verbose_stream [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/sequence_set.cpp:95:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable query_translated [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/sequence_set.cpp:110:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STD [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/sequence_set.cpp:119:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STD [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/sequence_set.cpp:140:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable id_delimiters [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/seed_array.cpp:210:3: warning: Struct 'OnePassBuildCallback < packed_uint40_t >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
diamond-2.1.11/src/data/seed_array.cpp:210:3: warning: Struct 'OnePassBuildCallback < packed_uint40_t >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
diamond-2.1.11/src/data/seed_array.cpp:210:3: warning: Struct 'OnePassBuildCallback < PackedLocId >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
diamond-2.1.11/src/data/seed_array.cpp:210:3: warning: Struct 'OnePassBuildCallback < PackedLocId >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
diamond-2.1.11/src/data/seed_array.cpp:121:3: warning: Struct 'BuildCallback < packed_uint40_t >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
diamond-2.1.11/src/data/seed_array.cpp:121:3: warning: Struct 'BuildCallback < packed_uint40_t >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
diamond-2.1.11/src/data/seed_array.cpp:121:3: warning: Struct 'BuildCallback < PackedLocId >' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
diamond-2.1.11/src/data/seed_array.cpp:121:3: warning: Struct 'BuildCallback < PackedLocId >' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
diamond-2.1.11/src/data/seed_array.cpp:143:8: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/data/enum_seeds.h:124:21: style: The scope of the variable 'errmsg' can be reduced. [variableScope]
diamond-2.1.11/src/data/seed_set.cpp:59:7: performance:inconclusive: Technically the member function 'SeedSetCallback::finish' can be static (but you may consider moving to unnamed namespace). [functionStatic]
diamond-2.1.11/src/data/seed_set.cpp:88:7: performance:inconclusive: Technically the member function 'HashedSeedSetCallback::finish' can be static (but you may consider moving to unnamed namespace). [functionStatic]
diamond-2.1.11/src/data/seed_array.cpp:230:124: style:inconclusive: Function 'SeedArray < packed_uint40_t >' argument 5 names different: declaration 'cfg' definition 'enum_cfg'. [funcArgNamesDifferent]
diamond-2.1.11/src/data/seed_array.h:82:105: note: Function 'SeedArray < packed_uint40_t >' argument 5 names different: declaration 'cfg' definition 'enum_cfg'.
diamond-2.1.11/src/data/seed_array.cpp:230:124: note: Function 'SeedArray < packed_uint40_t >' argument 5 names different: declaration 'cfg' definition 'enum_cfg'.
diamond-2.1.11/src/data/seed_array.cpp:230:124: style:inconclusive: Function 'SeedArray < PackedLocId >' argument 5 names different: declaration 'cfg' definition 'enum_cfg'. [funcArgNamesDifferent]
diamond-2.1.11/src/data/seed_array.h:82:105: note: Function 'SeedArray < PackedLocId >' argument 5 names different: declaration 'cfg' definition 'enum_cfg'.
diamond-2.1.11/src/data/seed_array.cpp:230:124: note: Function 'SeedArray < PackedLocId >' argument 5 names different: declaration 'cfg' definition 'enum_cfg'.
diamond-2.1.11/src/data/seed_set.cpp:80:2: style: Struct 'HashedSeedSetCallback' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/data/seed_array.h:115:7: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
diamond-2.1.11/src/data/seed_set.cpp:124:7: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/data/seed_set.cpp:126:7: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/data/seed_set.cpp:128:26: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/data/seed_set.cpp:132:28: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/data/seed_set.cpp:133:22: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/data/enum_seeds.h:26:16: style: Variable 'ptr' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/data/enum_seeds.h:26:12: style: Variable 'ptr' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/data/taxon_list.cpp:61:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable prot_accession2taxid [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/taxon_list.cpp:140:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable no_parse_seqids [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/taxonomy.cpp:56:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable r [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/taxonomy.cpp:62:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable namesdmp [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/taxonomy.cpp:88:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable message_stream [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/dp/flags.h:29:1: error: There is an unknown macro here somewhere. Configuration is required. If DEFINE_ENUM_FLAG_OPERATORS is a macro then please configure it. [unknownMacro]
diamond-2.1.11/src/data/taxonomy_nodes.cpp:60:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable message_stream [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/dp/scan_diags.cpp:302:1: error: There is an unknown macro here somewhere. Configuration is required. If DISPATCH_6V is a macro then please configure it. [unknownMacro]
diamond-2.1.11/src/dp/score_vector.h:135:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CHANNELS [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/dp/score_profile.cpp:18:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AMINO_ACID_COUNT [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/dp/score_profile.h:45:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AMINO_ACID_COUNT [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/dp/score_profile.h:52:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AMINO_ACID_COUNT [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/data/taxonomy_nodes.cpp:147:19: style: Variable 'max' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/dp/score_profile.h:32:2: style: Struct 'LongScoreProfile < int8_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/dp/score_profile.h:32:2: style: Struct 'LongScoreProfile < int16_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/dp/ungapped_simd.cpp:31:104: style: Parameter 'out' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/examples/wfa_adapt.c:40:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable wavefront_aligner_attr_default [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/examples/wfa_adapt.c:58:18: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/examples/wfa_basic.c:40:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable wavefront_aligner_attr_default [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:254:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:271:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:297:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:320:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:399:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:557:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/examples/wfa_bindings.cpp:45:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MemoryHigh [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/examples/wfa_lambda.cpp:58:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MemoryHigh [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.cpp:282:16: style:inconclusive: Technically the member function 'wfa::WFAligner::getAlignmentStatus' can be const. [functionConst]
diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.hpp:178:7: note: Technically the member function 'wfa::WFAligner::getAlignmentStatus' can be const.
diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.cpp:282:16: note: Technically the member function 'wfa::WFAligner::getAlignmentStatus' can be const.
diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.cpp:285:16: style:inconclusive: Technically the member function 'wfa::WFAligner::getAlignmentScore' can be const. [functionConst]
diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.hpp:179:7: note: Technically the member function 'wfa::WFAligner::getAlignmentScore' can be const.
diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.cpp:285:16: note: Technically the member function 'wfa::WFAligner::getAlignmentScore' can be const.
diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.cpp:288:17: style:inconclusive: Technically the member function 'wfa::WFAligner::getAlignment' can be const. [functionConst]
diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.hpp:180:8: note: Technically the member function 'wfa::WFAligner::getAlignment' can be const.
diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.cpp:288:17: note: Technically the member function 'wfa::WFAligner::getAlignment' can be const.
diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.cpp:294:24: style:inconclusive: Technically the member function 'wfa::WFAligner::getAlignment' can be const. [functionConst]
diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.hpp:183:15: note: Technically the member function 'wfa::WFAligner::getAlignment' can be const.
diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.cpp:294:24: note: Technically the member function 'wfa::WFAligner::getAlignment' can be const.
diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.cpp:335:18: performance:inconclusive: Technically the member function 'wfa::WFAligner::strStatus' can be static (but you may consider moving to unnamed namespace). [functionStatic]
diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.hpp:198:9: note: Technically the member function 'wfa::WFAligner::strStatus' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.cpp:335:18: note: Technically the member function 'wfa::WFAligner::strStatus' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/lib/WFA2-lib.diamond/examples/wfa_lambda.cpp:49:11: style: Parameter 'arguments' can be declared as pointer to const. However it seems that 'match_function' is a callback function, if 'arguments' is declared with const you might also need to cast function pointer(s). [constParameterCallback]
diamond-2.1.11/src/lib/WFA2-lib.diamond/examples/wfa_lambda.cpp:60:24: note: You might need to cast the function pointer here
diamond-2.1.11/src/lib/WFA2-lib.diamond/examples/wfa_lambda.cpp:49:11: note: Parameter 'arguments' can be declared as pointer to const
diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.hpp:206:3: style: Class 'WFAligner' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.hpp:218:3: style: Class 'WFAlignerIndel' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.hpp:227:3: style: Class 'WFAlignerEdit' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.cpp:188:18: style: Parameter 'pattern' can be declared as reference to const [constParameterReference]
diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.cpp:189:18: style: Parameter 'text' can be declared as reference to const [constParameterReference]
diamond-2.1.11/src/lib/WFA2-lib.diamond/examples/wfa_repeated.c:40:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable wavefront_aligner_attr_default [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:122:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable mem_ptr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:132:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable segment_ptr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:188:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:265:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIu64 [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:179:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable segment_ptr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:194:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable segment_ptr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:279:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:357:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:391:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:500:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIu64 [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:520:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIu64 [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:554:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIu64 [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:592:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIu64 [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:76:3: warning: If memory allocation fails, then there is a possible null pointer dereference: segment [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:74:67: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:74:39: note: Assignment 'segment=(struct mm_stack_segment_t*)malloc(sizeof(struct mm_stack_segment_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:76:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:76:19: warning: If memory allocation fails, then there is a possible null pointer dereference: mm_stack [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:99:52: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:99:32: note: Assignment 'mm_stack=(struct mm_stack_t*)malloc(sizeof(struct mm_stack_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:104:24: note: Calling function 'mm_stack_segment_new', 1st argument 'mm_stack' value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:76:19: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:77:3: warning: If memory allocation fails, then there is a possible null pointer dereference: segment [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:74:67: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:74:39: note: Assignment 'segment=(struct mm_stack_segment_t*)malloc(sizeof(struct mm_stack_segment_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:77:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:77:28: warning: If memory allocation fails, then there is a possible null pointer dereference: mm_stack [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:99:52: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:99:32: note: Assignment 'mm_stack=(struct mm_stack_t*)malloc(sizeof(struct mm_stack_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:104:24: note: Calling function 'mm_stack_segment_new', 1st argument 'mm_stack' value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:77:28: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:78:3: warning: If memory allocation fails, then there is a possible null pointer dereference: segment [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:74:67: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:74:39: note: Assignment 'segment=(struct mm_stack_segment_t*)malloc(sizeof(struct mm_stack_segment_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:78:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:80:17: warning: If memory allocation fails, then there is a possible null pointer dereference: mm_stack [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:99:52: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:99:32: note: Assignment 'mm_stack=(struct mm_stack_t*)malloc(sizeof(struct mm_stack_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:104:24: note: Calling function 'mm_stack_segment_new', 1st argument 'mm_stack' value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:80:17: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:101:3: warning: If memory allocation fails, then there is a possible null pointer dereference: mm_stack [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:99:52: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:99:32: note: Assignment 'mm_stack=(struct mm_stack_t*)malloc(sizeof(struct mm_stack_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:101:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:102:3: warning: If memory allocation fails, then there is a possible null pointer dereference: mm_stack [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:99:52: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:99:32: note: Assignment 'mm_stack=(struct mm_stack_t*)malloc(sizeof(struct mm_stack_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:102:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:106:3: warning: If memory allocation fails, then there is a possible null pointer dereference: mm_stack [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:99:52: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:99:32: note: Assignment 'mm_stack=(struct mm_stack_t*)malloc(sizeof(struct mm_stack_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:106:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:108:3: warning: If memory allocation fails, then there is a possible null pointer dereference: mm_stack [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:99:52: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:99:32: note: Assignment 'mm_stack=(struct mm_stack_t*)malloc(sizeof(struct mm_stack_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:108:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:110:3: warning: If memory allocation fails, then there is a possible null pointer dereference: mm_stack [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:99:52: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:99:32: note: Assignment 'mm_stack=(struct mm_stack_t*)malloc(sizeof(struct mm_stack_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:110:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:209:26: warning: If memory allocation fails, then there is a possible null pointer dereference: memory_base [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:208:25: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:208:25: note: Assignment 'memory_base=malloc(num_bytes_allocated)', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:209:26: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:229:29: style: Variable 'current_segment' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:203:35: portability: 'segment->memory' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:216:38: portability: 'memory_base' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_stack.c:217:35: portability: 'memory_aligned' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/profiler_counter.c:106:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable METRIC_FACTOR_1G [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/profiler_counter.c:183:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable METRIC_FACTOR_1G [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/profiler_counter.c:225:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable METRIC_FACTOR_1G [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:766:17: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:770:17: warning: %d in format string (no. 1) requires 'int' but the argument type is 'unsigned int'. [invalidPrintfArgType_sint]
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:66:3: warning: If memory allocation fails, then there is a possible null pointer dereference: cigar [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:64:32: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:64:32: note: Assignment 'cigar=malloc(sizeof(struct cigar_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:66:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:67:3: warning: If memory allocation fails, then there is a possible null pointer dereference: cigar [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:64:32: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:64:32: note: Assignment 'cigar=malloc(sizeof(struct cigar_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:67:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:67:30: warning: If memory allocation fails, then there is a possible null pointer dereference: cigar [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:64:32: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:64:32: note: Assignment 'cigar=malloc(sizeof(struct cigar_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:67:30: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:68:3: warning: If memory allocation fails, then there is a possible null pointer dereference: cigar [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:64:32: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:64:32: note: Assignment 'cigar=malloc(sizeof(struct cigar_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:68:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:69:3: warning: If memory allocation fails, then there is a possible null pointer dereference: cigar [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:64:32: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:64:32: note: Assignment 'cigar=malloc(sizeof(struct cigar_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:69:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:70:3: warning: If memory allocation fails, then there is a possible null pointer dereference: cigar [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:64:32: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:64:32: note: Assignment 'cigar=malloc(sizeof(struct cigar_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:70:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:71:3: warning: If memory allocation fails, then there is a possible null pointer dereference: cigar [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:64:32: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:64:32: note: Assignment 'cigar=malloc(sizeof(struct cigar_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:71:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:72:3: warning: If memory allocation fails, then there is a possible null pointer dereference: cigar [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:64:32: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:64:32: note: Assignment 'cigar=malloc(sizeof(struct cigar_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:72:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:74:3: warning: If memory allocation fails, then there is a possible null pointer dereference: cigar [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:64:32: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:64:32: note: Assignment 'cigar=malloc(sizeof(struct cigar_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:74:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:75:3: warning: If memory allocation fails, then there is a possible null pointer dereference: cigar [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:64:32: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:64:32: note: Assignment 'cigar=malloc(sizeof(struct cigar_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:75:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:701:23: warning: If memory allocation fails, then there is a possible null pointer dereference: buffer [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:699:30: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:699:30: note: Assignment 'buffer=malloc(2*(cigar->end_offset-cigar->begin_offset)+10)', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:701:23: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:749:23: warning: If memory allocation fails, then there is a possible null pointer dereference: buffer [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:747:30: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:747:30: note: Assignment 'buffer=malloc(2*(cigar->end_offset-cigar->begin_offset))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:749:23: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:793:37: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:791:27: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:791:27: note: Assignment 'mem=calloc(3*max_buffer_length,1)', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:792:27: note: pattern_alg is assigned 'mem' here.
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:793:37: note: Null pointer addition
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:114:20: style: Parameter 'cigar' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:127:20: style: Parameter 'cigar_src' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:130:15: style: Variable 'operations_src' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:139:20: style: Parameter 'cigar_src' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:144:15: style: Variable 'operations_src' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:245:20: style: Parameter 'cigar' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:261:20: style: Parameter 'cigar' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:262:31: style: Parameter 'penalties' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:307:33: style: Parameter 'penalties' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:347:20: style: Parameter 'cigar_a' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:348:20: style: Parameter 'cigar_b' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:354:15: style: Variable 'operations_a' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:355:15: style: Variable 'operations_b' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:626:15: style: Variable 'operations' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:786:15: style: Variable 'operations' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/profiler_timer.c:55:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CLOCK_REALTIME [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/profiler_timer.c:125:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIu64 [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/profiler_timer.c:152:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRIu64 [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:116:48: warning: If memory allocation fails, then there is a possible null pointer dereference: mm_allocator [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:155:64: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:155:40: note: Assignment 'mm_allocator=(struct mm_allocator_t*)malloc(sizeof(struct mm_allocator_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:164:28: note: Calling function 'mm_allocator_segment_new', 1st argument 'mm_allocator' value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:116:48: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:117:3: warning: If memory allocation fails, then there is a possible null pointer dereference: segment [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:114:75: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:114:43: note: Assignment 'segment=(struct mm_allocator_segment_t*)malloc(sizeof(struct mm_allocator_segment_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:117:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:119:3: warning: If memory allocation fails, then there is a possible null pointer dereference: segment [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:114:75: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:114:43: note: Assignment 'segment=(struct mm_allocator_segment_t*)malloc(sizeof(struct mm_allocator_segment_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:119:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:119:19: warning: If memory allocation fails, then there is a possible null pointer dereference: mm_allocator [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:155:64: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:155:40: note: Assignment 'mm_allocator=(struct mm_allocator_t*)malloc(sizeof(struct mm_allocator_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:164:28: note: Calling function 'mm_allocator_segment_new', 1st argument 'mm_allocator' value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:119:19: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:120:3: warning: If memory allocation fails, then there is a possible null pointer dereference: segment [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:114:75: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:114:43: note: Assignment 'segment=(struct mm_allocator_segment_t*)malloc(sizeof(struct mm_allocator_segment_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:120:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:120:28: warning: If memory allocation fails, then there is a possible null pointer dereference: mm_allocator [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:155:64: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:155:40: note: Assignment 'mm_allocator=(struct mm_allocator_t*)malloc(sizeof(struct mm_allocator_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:164:28: note: Calling function 'mm_allocator_segment_new', 1st argument 'mm_allocator' value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:120:28: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:121:3: warning: If memory allocation fails, then there is a possible null pointer dereference: segment [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:114:75: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:114:43: note: Assignment 'segment=(struct mm_allocator_segment_t*)malloc(sizeof(struct mm_allocator_segment_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:121:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:123:3: warning: If memory allocation fails, then there is a possible null pointer dereference: segment [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:114:75: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:114:43: note: Assignment 'segment=(struct mm_allocator_segment_t*)malloc(sizeof(struct mm_allocator_segment_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:123:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:125:17: warning: If memory allocation fails, then there is a possible null pointer dereference: mm_allocator [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:155:64: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:155:40: note: Assignment 'mm_allocator=(struct mm_allocator_t*)malloc(sizeof(struct mm_allocator_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:164:28: note: Calling function 'mm_allocator_segment_new', 1st argument 'mm_allocator' value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:125:17: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:156:3: warning: If memory allocation fails, then there is a possible null pointer dereference: mm_allocator [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:155:64: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:155:40: note: Assignment 'mm_allocator=(struct mm_allocator_t*)malloc(sizeof(struct mm_allocator_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:156:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:158:3: warning: If memory allocation fails, then there is a possible null pointer dereference: mm_allocator [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:155:64: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:155:40: note: Assignment 'mm_allocator=(struct mm_allocator_t*)malloc(sizeof(struct mm_allocator_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:158:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:159:3: warning: If memory allocation fails, then there is a possible null pointer dereference: mm_allocator [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:155:64: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:155:40: note: Assignment 'mm_allocator=(struct mm_allocator_t*)malloc(sizeof(struct mm_allocator_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:159:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:160:3: warning: If memory allocation fails, then there is a possible null pointer dereference: mm_allocator [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:155:64: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:155:40: note: Assignment 'mm_allocator=(struct mm_allocator_t*)malloc(sizeof(struct mm_allocator_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:160:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:167:3: warning: If memory allocation fails, then there is a possible null pointer dereference: mm_allocator [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:155:64: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:155:40: note: Assignment 'mm_allocator=(struct mm_allocator_t*)malloc(sizeof(struct mm_allocator_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:167:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:169:3: warning: If memory allocation fails, then there is a possible null pointer dereference: mm_allocator [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:155:64: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:155:40: note: Assignment 'mm_allocator=(struct mm_allocator_t*)malloc(sizeof(struct mm_allocator_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:169:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:170:3: warning: If memory allocation fails, then there is a possible null pointer dereference: mm_allocator [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:155:64: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:155:40: note: Assignment 'mm_allocator=(struct mm_allocator_t*)malloc(sizeof(struct mm_allocator_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:170:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:320:26: warning: If memory allocation fails, then there is a possible null pointer dereference: memory_base [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:319:37: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:319:37: note: Assignment 'memory_base=malloc(num_bytes_allocated)', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:320:26: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:322:40: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:319:37: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:319:37: note: Assignment 'memory_base=malloc(num_bytes_allocated)', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:322:40: note: Null pointer addition
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:400:29: style: Local variable 'request' shadows outer variable [shadowVariable]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:387:33: note: Shadowed declaration
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:400:29: note: Shadow variable
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:383:37: style: Parameter 'mm_reference' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:400:29: style: Variable 'request' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:422:17: style: Parameter 'memory' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:460:37: style: Variable 'request' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:475:37: style: Variable 'request' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:497:35: style: Parameter 'request' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:519:32: style: Parameter 'request' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:292:47: portability: 'segment->memory' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:295:40: portability: 'memory_base' is of type 'void * const'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:295:75: portability: 'memory_base+sizeof(struct mm_allocator_reference_t)' is of type 'void * const'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:297:39: portability: 'memory_aligned' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:300:95: portability: 'memory_aligned' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:322:40: portability: 'memory_base' is of type 'void * const'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:322:75: portability: 'memory_base+sizeof(struct mm_allocator_reference_t)' is of type 'void * const'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:324:39: portability: 'memory_aligned' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:327:95: portability: 'memory_aligned' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:427:41: portability: 'memory' is of type 'void * const'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:115:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable wavefront_aligner_attr_default [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:155:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable wavefront_aligner_attr_default [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:252:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BUFFER_SIZE_1M [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:344:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:351:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:444:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:455:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:507:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/benchmark/benchmark_check.c:56:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark_params.c:109:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark_params.c:188:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable required_argument [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:324:19: warning: Identical condition 'line1_length==-1', second condition is always false [identicalConditionAfterEarlyExit]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:322:19: note: If condition 'line1_length==-1' is true, the function will return/exit
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:324:19: note: Testing identical condition 'line1_length==-1'
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:125:37: style: Condition 'endsfree' is always false [knownConditionTrueFalse]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:110:25: note: Assignment 'endsfree=pattern_begin_free>0||pattern_end_free>0||text_begin_free>0||text_end_free>0', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:125:37: note: Condition 'endsfree' is always false
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:144:12: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: wf_plot [nullPointerOutOfResources]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:142:32: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:142:32: note: Assignment 'wf_plot=fopen("test.wfa","w")', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:144:12: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:386:10: warning:inconclusive: If resource allocation fails, then there is a possible null pointer dereference: wf_plot [nullPointerOutOfResources]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:384:30: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:384:30: note: Assignment 'wf_plot=fopen(filename,"w")', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:386:10: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:109:25: style: The comparison 'pattern_begin_free > 0' is always false. [knownConditionTrueFalse]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:104:34: note: 'pattern_begin_free' is assigned value '0' here.
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:109:25: note: The comparison 'pattern_begin_free > 0' is always false.
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:109:28: style: Same expression on both sides of '||' because 'pattern_begin_free>0' and 'pattern_end_free>0' represent the same value. [knownConditionTrueFalse]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:104:34: note: 'pattern_begin_free' is assigned value '0' here.
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:105:32: note: 'pattern_end_free' is assigned value '0' here.
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:109:28: note: Same expression on both sides of '||' because 'pattern_begin_free>0' and 'pattern_end_free>0' represent the same value.
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:109:47: style: The comparison 'pattern_end_free > 0' is always false. [knownConditionTrueFalse]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:105:32: note: 'pattern_end_free' is assigned value '0' here.
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:109:47: note: The comparison 'pattern_end_free > 0' is always false.
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:109:50: style: Same expression on both sides of '||' because 'text_begin_free>0' and 'pattern_end_free>0' represent the same value. [knownConditionTrueFalse]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:104:34: note: 'pattern_begin_free' is assigned value '0' here.
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:106:31: note: 'text_begin_free' is assigned value '0' here.
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:105:32: note: 'pattern_end_free' is assigned value '0' here.
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:109:50: note: Same expression on both sides of '||' because 'text_begin_free>0' and 'pattern_end_free>0' represent the same value.
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:110:22: style: The comparison 'text_begin_free > 0' is always false. [knownConditionTrueFalse]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:106:31: note: 'text_begin_free' is assigned value '0' here.
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:110:22: note: The comparison 'text_begin_free > 0' is always false.
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:110:25: style: Same expression on both sides of '||' because 'text_end_free>0' and 'text_begin_free>0' represent the same value. [knownConditionTrueFalse]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:104:34: note: 'pattern_begin_free' is assigned value '0' here.
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:107:29: note: 'text_end_free' is assigned value '0' here.
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:106:31: note: 'text_begin_free' is assigned value '0' here.
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:110:25: note: Same expression on both sides of '||' because 'text_end_free>0' and 'text_begin_free>0' represent the same value.
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:110:41: style: The comparison 'text_end_free > 0' is always false. [knownConditionTrueFalse]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:107:29: note: 'text_end_free' is assigned value '0' here.
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:110:41: note: The comparison 'text_end_free > 0' is always false.
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/benchmark/benchmark_edit.c:154:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable compute_score [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:544:34: style: Variable 'offset' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark.c:520:52: style: Variable 'seqs_batch' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/benchmark/benchmark_gap_affine.c:151:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable compute_score [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/benchmark/benchmark_gap_affine2p.c:92:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable compute_score [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/benchmark/benchmark_gap_linear.c:91:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable compute_score [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/benchmark/benchmark_indel.c:61:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable compute_score [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/benchmark/benchmark_utils.c:192:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALIGN_DEBUG_CHECK_SCORE [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/benchmark/benchmark_utils.c:122:26: style: Parameter 'align_input' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/edit/edit_bpm.c:78:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT64_LENGTH [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/edit/edit_bpm.c:150:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT64_LENGTH [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/edit/edit_bpm.c:179:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT64_LENGTH [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/edit/edit_bpm.c:294:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UINT64_LENGTH [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/edit/edit_dp.c:67:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/edit/edit_dp.c:40:27: style: Parameter 'score_matrix' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/gap_affine/affine_matrix.c:88:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable M [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/gap_affine/affine_matrix.c:118:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable M [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/edit/edit_bpm.c:236:14: style: Array index 'last' is used before limits check. [arrayIndexThenCheck]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/edit/edit_bpm.c:281:17: style: Parameter 'text' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/edit/edit_bpm.c:283:15: style: Variable 'pattern' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/edit/edit_bpm.c:92:37: portability: 'memory' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/edit/edit_bpm.c:93:35: portability: 'memory' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/edit/edit_bpm.c:94:35: portability: 'memory' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/edit/edit_bpm.c:95:44: portability: 'memory' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/edit/edit_bpm.c:96:39: portability: 'memory' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/edit/edit_bpm.c:97:44: portability: 'memory' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark_params.c:293:24: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark_params.c:295:18: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark_params.c:297:18: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark_params.c:302:24: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark_params.c:304:18: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark_params.c:306:18: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark_params.c:308:18: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark_params.c:313:24: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark_params.c:315:18: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark_params.c:317:18: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark_params.c:319:18: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark_params.c:321:18: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark_params.c:323:18: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark_params.c:349:26: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark_params.c:350:20: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark_params.c:352:20: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark_params.c:354:20: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark_params.c:356:20: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark_params.c:397:24: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark_params.c:400:18: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark_params.c:403:18: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark_params.c:350:18: style: Redundant initialization for 'sentinel'. The initialized value is overwritten before it is read. [redundantInitialization]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark_params.c:349:24: note: sentinel is initialized
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark_params.c:350:18: note: sentinel is overwritten
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark_params.c:186:17: style: Variable 'long_options' can be declared as const array [constVariable]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark_params.c:293:13: style: Variable 'sentinel' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark_params.c:302:13: style: Variable 'sentinel' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark_params.c:313:13: style: Variable 'sentinel' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark_params.c:349:15: style: Variable 'sentinel' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/align_benchmark_params.c:397:13: style: Variable 'sentinel' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/gap_affine/swg.c:58:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable affine_matrix_M [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/gap_affine/swg.c:119:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable D [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/gap_affine/swg.c:179:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable D [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/gap_affine/swg.c:260:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable D [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/gap_affine2p/affine2p_dp.c:52:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable affine2p_matrix_M [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/gap_affine2p/affine2p_matrix.c:133:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/gap_affine2p/affine2p_matrix.c:75:28: style: Parameter 'affine2p_cell' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/gap_linear/nw.c:39:27: style: Parameter 'score_matrix' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/gap_linear/nw.c:40:31: style: Parameter 'penalties' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/gap_affine2p/affine2p_dp.c:40:33: style: Parameter 'penalties' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/gap_affine/swg.c:41:28: style: Parameter 'affine_matrix' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/gap_affine/swg.c:42:31: style: Parameter 'penalties' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/indel/indel_dp.c:61:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/bitmap.c:44:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bitmap_t [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/bitmap.c:68:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BITMAP_BLOCK_ELEMENTS [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/bitmap.c:77:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BITMAP_BLOCK_ELEMENTS [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/bitmap.c:87:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BITMAP_BLOCK_ELEMENTS [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/bitmap.c:118:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BITMAP_BLOCK_ELEMENTS [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/align_benchmark/indel/indel_dp.c:38:27: style: Parameter 'score_matrix' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/bitmap.c:102:21: style: Parameter 'bitmap' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/bitmap.c:115:21: style: Parameter 'bitmap' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/bitmap.c:121:25: style: Variable 'bitmap_block' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:85:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAND_MAX [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:284:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:299:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable required_argument [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/commons.c:42:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAND_MAX [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:42:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sequence_buffer_t [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:86:84: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sequence_offset_t [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:44:3: warning: If memory allocation fails, then there is a possible null pointer dereference: sequence_buffer [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:42:52: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:42:52: note: Assignment 'sequence_buffer=malloc(sizeof(sequence_buffer_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:44:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:46:3: warning: If memory allocation fails, then there is a possible null pointer dereference: sequence_buffer [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:42:52: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:42:52: note: Assignment 'sequence_buffer=malloc(sizeof(sequence_buffer_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:46:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:47:3: warning: If memory allocation fails, then there is a possible null pointer dereference: sequence_buffer [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:42:52: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:42:52: note: Assignment 'sequence_buffer=malloc(sizeof(sequence_buffer_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:47:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:48:3: warning: If memory allocation fails, then there is a possible null pointer dereference: sequence_buffer [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:42:52: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:42:52: note: Assignment 'sequence_buffer=malloc(sizeof(sequence_buffer_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:48:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:51:3: warning: If memory allocation fails, then there is a possible null pointer dereference: sequence_buffer [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:42:52: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:42:52: note: Assignment 'sequence_buffer=malloc(sizeof(sequence_buffer_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:51:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:52:3: warning: If memory allocation fails, then there is a possible null pointer dereference: sequence_buffer [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:42:52: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:42:52: note: Assignment 'sequence_buffer=malloc(sizeof(sequence_buffer_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:52:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:53:3: warning: If memory allocation fails, then there is a possible null pointer dereference: sequence_buffer [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:42:52: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:42:52: note: Assignment 'sequence_buffer=malloc(sizeof(sequence_buffer_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:53:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:55:3: warning: If memory allocation fails, then there is a possible null pointer dereference: sequence_buffer [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:42:52: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:42:52: note: Assignment 'sequence_buffer=malloc(sizeof(sequence_buffer_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:55:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:56:3: warning: If memory allocation fails, then there is a possible null pointer dereference: sequence_buffer [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:42:52: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:42:52: note: Assignment 'sequence_buffer=malloc(sizeof(sequence_buffer_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:56:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:99:17: style: Parameter 'pattern' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/sequence_buffer.c:101:17: style: Parameter 'text' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:333:26: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:335:20: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:54:3: warning: If memory allocation fails, then there is a possible null pointer dereference: heatmap [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:52:48: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:52:30: note: Assignment 'heatmap=(struct heatmap_t*)malloc(sizeof(struct heatmap_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:54:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:55:3: warning: If memory allocation fails, then there is a possible null pointer dereference: heatmap [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:52:48: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:52:30: note: Assignment 'heatmap=(struct heatmap_t*)malloc(sizeof(struct heatmap_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:55:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:56:3: warning: If memory allocation fails, then there is a possible null pointer dereference: heatmap [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:52:48: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:52:30: note: Assignment 'heatmap=(struct heatmap_t*)malloc(sizeof(struct heatmap_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:56:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/vector.c:52:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:57:3: warning: If memory allocation fails, then there is a possible null pointer dereference: heatmap [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:52:48: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:52:30: note: Assignment 'heatmap=(struct heatmap_t*)malloc(sizeof(struct heatmap_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:57:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/vector.c:80:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:58:3: warning: If memory allocation fails, then there is a possible null pointer dereference: heatmap [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:52:48: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:52:30: note: Assignment 'heatmap=(struct heatmap_t*)malloc(sizeof(struct heatmap_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:58:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:73:3: warning: If memory allocation fails, then there is a possible null pointer dereference: heatmap [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:52:48: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:52:30: note: Assignment 'heatmap=(struct heatmap_t*)malloc(sizeof(struct heatmap_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:73:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:73:35: warning: If memory allocation fails, then there is a possible null pointer dereference: heatmap [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:52:48: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:52:30: note: Assignment 'heatmap=(struct heatmap_t*)malloc(sizeof(struct heatmap_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:73:35: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:103:5: warning: If memory allocation fails, then there is a possible null pointer dereference: sequence [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:362:31: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:362:31: note: Assignment 'seqlong=malloc(seqlong_length+1)', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:370:30: note: Calling function 'sequence_generate_random', 1st argument 'seqlong' value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:103:5: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:75:14: warning: If memory allocation fails, then there is a possible null pointer dereference: heatmap [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:52:48: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:52:30: note: Assignment 'heatmap=(struct heatmap_t*)malloc(sizeof(struct heatmap_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:75:14: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:105:3: warning: If memory allocation fails, then there is a possible null pointer dereference: sequence [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:362:31: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:362:31: note: Assignment 'seqlong=malloc(seqlong_length+1)', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:370:30: note: Calling function 'sequence_generate_random', 1st argument 'seqlong' value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:105:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:76:5: warning: If memory allocation fails, then there is a possible null pointer dereference: heatmap [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:52:48: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:52:30: note: Assignment 'heatmap=(struct heatmap_t*)malloc(sizeof(struct heatmap_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:76:5: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:117:11: warning: If memory allocation fails, then there is a possible null pointer dereference: seqshort [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:363:32: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:363:32: note: Assignment 'seqshort=malloc(seqshort_length+1+num_errors+parameters.indels_num*parameters.indels_length)', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:372:64: note: Calling function 'sequence_extract', 3rd argument 'seqshort' value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:117:11: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:76:39: warning: If memory allocation fails, then there is a possible null pointer dereference: heatmap [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:52:48: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:52:30: note: Assignment 'heatmap=(struct heatmap_t*)malloc(sizeof(struct heatmap_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:76:39: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:86:29: warning: If memory allocation fails, then there is a possible null pointer dereference: heatmap [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:52:48: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:52:30: note: Assignment 'heatmap=(struct heatmap_t*)malloc(sizeof(struct heatmap_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:79:17: note: Calling function 'heatmap_clear', 1st argument 'heatmap' value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:86:29: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:117:27: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:362:31: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:362:31: note: Assignment 'seqlong=malloc(seqlong_length+1)', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:372:41: note: Calling function 'sequence_extract', 1st argument 'seqlong' value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:117:27: note: Null pointer addition
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:87:24: warning: If memory allocation fails, then there is a possible null pointer dereference: heatmap [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:52:48: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:52:30: note: Assignment 'heatmap=(struct heatmap_t*)malloc(sizeof(struct heatmap_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:79:17: note: Calling function 'heatmap_clear', 1st argument 'heatmap' value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:87:24: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:88:27: warning: If memory allocation fails, then there is a possible null pointer dereference: heatmap [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:52:48: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:52:30: note: Assignment 'heatmap=(struct heatmap_t*)malloc(sizeof(struct heatmap_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:79:17: note: Calling function 'heatmap_clear', 1st argument 'heatmap' value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:88:27: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:111:17: style: Parameter 'seqlong' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:126:24: style: Parameter 'errors_log' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:298:17: style: Variable 'long_options' can be declared as const array [constVariable]
diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:333:15: style: Variable 'sentinel' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/vector.c:48:3: warning: If memory allocation fails, then there is a possible null pointer dereference: vector_buffer [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/vector.c:47:53: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/vector.c:47:35: note: Assignment 'vector_buffer=(struct vector_t*)malloc(sizeof(struct vector_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/vector.c:48:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/vector.c:49:3: warning: If memory allocation fails, then there is a possible null pointer dereference: vector_buffer [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/vector.c:47:53: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/vector.c:47:35: note: Assignment 'vector_buffer=(struct vector_t*)malloc(sizeof(struct vector_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/vector.c:49:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/vector.c:50:3: warning: If memory allocation fails, then there is a possible null pointer dereference: vector_buffer [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/vector.c:47:53: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/vector.c:47:35: note: Assignment 'vector_buffer=(struct vector_t*)malloc(sizeof(struct vector_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/vector.c:50:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/vector.c:51:8: warning: If memory allocation fails, then there is a possible null pointer dereference: vector_buffer [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/vector.c:47:53: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/vector.c:47:35: note: Assignment 'vector_buffer=(struct vector_t*)malloc(sizeof(struct vector_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/vector.c:51:8: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/vector.c:110:21: style: Parameter 'vector_from' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/vector.c:119:21: style: Parameter 'vector_src' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/vector.c:86:26: portability: 'vector->memory' is of type 'void *'. When using void pointers in calculations, the behaviour is undefined. [arithOperationsOnVoidPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront.c:168:24: style: Parameter 'wavefront' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_align.c:74:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_align.c:252:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_aligner.c:110:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BUFFER_SIZE_256M [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_aligner.c:134:71: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BUFFER_SIZE_4M [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_aligner.c:318:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable affine2p_matrix_M [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_align.c:248:35: style: Variable 'align_status' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_backtrace_buffer.c:64:71: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BUFFER_SIZE_8M [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_backtrace_buffer.c:145:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BUFFER_SIZE_8M [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_backtrace_buffer.c:165:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BUFFER_SIZE_8M [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_backtrace_buffer.c:169:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BUFFER_SIZE_8M [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_backtrace_buffer.c:176:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BUFFER_SIZE_8M [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_backtrace_buffer.c:186:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BUFFER_SIZE_8M [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_backtrace_buffer.c:199:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BUFFER_SIZE_8M [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_backtrace_buffer.c:212:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BUFFER_SIZE_8M [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_backtrace_buffer.c:230:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BUFFER_SIZE_8M [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_backtrace_buffer.c:248:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BUFFER_SIZE_8M [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_backtrace_buffer.c:333:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable affine_matrix_M [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_backtrace_buffer.c:409:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable block_bm_ptr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_backtrace_buffer.c:468:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BUFFER_SIZE_8M [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_aligner.c:192:32: style: Variable 'wf_heuristic' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_aligner.c:257:32: style: Variable 'penalties' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_aligner.c:391:32: style: Variable 'sequences' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_aligner.c:681:32: style: Parameter 'wf_aligner' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_aligner.c:705:32: style: Parameter 'wf_aligner' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_aligner.c:721:32: style: Parameter 'wf_aligner' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_backtrace.c:297:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_backtrace.c:347:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable affine2p_matrix_M [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_backtrace_buffer.c:437:30: style: Local variable 'block_idx' shadows outer variable [shadowVariable]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_backtrace_buffer.c:408:26: note: Shadowed declaration
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_backtrace_buffer.c:437:30: note: Shadow variable
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_backtrace_buffer.c:144:34: style: Parameter 'bt_buffer' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_backtrace_buffer.c:149:34: style: Parameter 'bt_buffer' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_backtrace_buffer.c:168:34: style: Parameter 'bt_buffer' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_backtrace_buffer.c:289:19: style: Variable 'palignment_blocks' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_backtrace_buffer.c:332:19: style: Variable 'palignment_blocks' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_backtrace_buffer.c:378:24: style: Parameter 'offsets' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_backtrace_buffer.c:379:27: style: Parameter 'bt_block_idxs' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_backtrace_buffer.c:414:25: style: Variable 'bt_block' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_backtrace_offload.c:102:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_backtrace_offload.c:158:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_backtrace_offload.c:40:24: style: Parameter 'out_offsets' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialign.c:62:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialign.c:106:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialign.c:203:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable affine2p_matrix_I1 [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialign.c:304:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable affine2p_matrix_M [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialign.c:355:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable affine2p_matrix_D2 [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialign.c:478:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:60:3: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_bialigner [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:44:53: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:44:53: note: Assignment 'wf_bialigner=malloc(sizeof(struct wavefront_bialigner_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:60:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:61:3: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_bialigner [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:44:53: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:44:53: note: Assignment 'wf_bialigner=malloc(sizeof(struct wavefront_bialigner_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:61:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:62:3: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_bialigner [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:44:53: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:44:53: note: Assignment 'wf_bialigner=malloc(sizeof(struct wavefront_bialigner_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:62:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:63:3: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_bialigner [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:44:53: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:44:53: note: Assignment 'wf_bialigner=malloc(sizeof(struct wavefront_bialigner_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:63:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:64:3: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_bialigner [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:44:53: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:44:53: note: Assignment 'wf_bialigner=malloc(sizeof(struct wavefront_bialigner_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:64:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:65:3: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_bialigner [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:44:53: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:44:53: note: Assignment 'wf_bialigner=malloc(sizeof(struct wavefront_bialigner_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:65:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:69:3: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_bialigner [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:44:53: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:44:53: note: Assignment 'wf_bialigner=malloc(sizeof(struct wavefront_bialigner_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:69:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:70:3: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_bialigner [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:44:53: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:44:53: note: Assignment 'wf_bialigner=malloc(sizeof(struct wavefront_bialigner_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:70:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:71:3: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_bialigner [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:44:53: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:44:53: note: Assignment 'wf_bialigner=malloc(sizeof(struct wavefront_bialigner_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:71:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:41:37: style: Parameter 'attributes' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialigner.c:163:34: style: Parameter 'heuristic' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_components.c:178:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gap_linear [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_components.c:216:73: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable wavefront_t [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_components.c:394:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable BT_BLOCK_IDX_NULL [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_components.c:458:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_components.c:48:35: style: Parameter 'wf_components' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_components.c:63:35: style: Parameter 'wf_components' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_components.c:82:35: style: Parameter 'wf_components' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_components.c:102:35: style: Parameter 'wf_components' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_components.c:385:22: style: Variable 'offsets' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_backtrace.c:229:32: style: Variable 'sequences' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_backtrace.c:328:32: style: Variable 'sequences' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_backtrace.c:546:21: style: Variable 'init_block' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_backtrace.c:549:34: style: Variable 'backtrace_init_pos' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_backtrace.c:279:26: style: Variable 'backtrace_type' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_backtrace.c:434:26: style: Variable 'backtrace_type' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute_affine.c:64:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRAGMA_LOOP_VECTORIZE [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute_affine.c:128:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRAGMA_LOOP_VECTORIZE [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute.c:441:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialign.c:56:36: style: Parameter 'breakpoint' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialign.c:82:29: style: Parameter 'form' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialign.c:157:29: style: Parameter 'form' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialign.c:199:32: style: Variable 'sequences' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialign.c:266:32: style: Variable 'sequences' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialign.c:422:29: style: Variable 'system' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialign.c:428:32: style: Variable 'sequences' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialign.c:552:29: style: Parameter 'global_form' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialign.c:567:29: style: Parameter 'global_form' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialign.c:589:32: style: Variable 'sequences' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialign.c:667:32: style: Variable 'sequences' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_bialign.c:711:34: style: Variable 'sequences' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute_affine.c:50:32: style: Variable 'sequences' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute_affine.c:96:32: style: Variable 'sequences' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute_affine.c:197:28: style: Parameter 'wavefront_set' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute.c:128:27: style: Variable 'alg_form' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute.c:129:32: style: Variable 'penalties' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute.c:150:27: style: Variable 'alg_form' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute.c:151:32: style: Variable 'penalties' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute.c:179:27: style: Variable 'alg_form' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute.c:180:32: style: Variable 'penalties' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute.c:222:27: style: Variable 'alg_form' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute.c:223:32: style: Variable 'penalties' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute.c:580:32: style: Variable 'sequences' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute.c:583:22: style: Variable 'offsets' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute_edit.c:58:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRAGMA_LOOP_VECTORIZE [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute_edit.c:86:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRAGMA_LOOP_VECTORIZE [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute_edit.c:125:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRAGMA_LOOP_VECTORIZE [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute_edit.c:168:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRAGMA_LOOP_VECTORIZE [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute_affine2p.c:70:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRAGMA_LOOP_VECTORIZE [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute_affine2p.c:163:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRAGMA_LOOP_VECTORIZE [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute_linear.c:60:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRAGMA_LOOP_VECTORIZE [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute_linear.c:101:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRAGMA_LOOP_VECTORIZE [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute_edit.c:46:24: style: Parameter 'wf_prev' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute_edit.c:51:32: style: Variable 'sequences' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute_edit.c:74:24: style: Parameter 'wf_prev' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute_edit.c:79:32: style: Variable 'sequences' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute_edit.c:106:24: style: Parameter 'wf_prev' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute_edit.c:112:32: style: Variable 'sequences' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute_edit.c:149:24: style: Parameter 'wf_prev' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute_edit.c:155:32: style: Variable 'sequences' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute_edit.c:223:32: style: Variable 'sequences' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute_edit.c:226:22: style: Variable 'offsets' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute_linear.c:50:32: style: Variable 'sequences' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute_linear.c:84:32: style: Variable 'sequences' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute_linear.c:134:28: style: Parameter 'wavefront_set' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_debug.c:215:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_debug.c:224:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_debug.c:236:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_debug.c:44:32: style: Variable 'sequences' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_debug.c:51:18: style: Variable 'cigar' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_debug.c:52:15: style: Variable 'operations' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_debug.c:128:32: style: Variable 'sequences' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_display.c:174:24: style: Parameter 'wavefront' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_display.c:175:17: style: Parameter 'wavefront_id' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute_affine2p.c:51:32: style: Variable 'sequences' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute_affine2p.c:116:32: style: Variable 'sequences' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_compute_affine2p.c:288:28: style: Parameter 'wavefront_set' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_extend.c:54:32: style: Variable 'seqs' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_extend.c:136:32: style: Variable 'seqs' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_extend.c:226:32: style: Variable 'seqs' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_extend_kernels.c:55:9: style: Variable 'pattern_ptr' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_extend_kernels.c:56:9: style: Variable 'text_ptr' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_extend_kernels.c:73:13: style: Variable 'pattern_blocks' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_extend_kernels.c:74:13: style: Variable 'text_blocks' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_penalties.c:70:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_penalties.c:102:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_penalties.c:139:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_pcigar.c:230:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable affine_matrix_M [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_penalties.c:65:31: style: Parameter 'linear_penalties' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_penalties.c:97:31: style: Parameter 'affine_penalties' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_penalties.c:134:33: style: Parameter 'affine2p_penalties' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_penalties.c:179:34: style: Parameter 'wf_penalties' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_pcigar.c:84:24: style: Variable 'op' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_pcigar.c:102:13: style: Variable 'pattern_blocks' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_pcigar.c:103:13: style: Variable 'text_blocks' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_pcigar.c:161:15: style: Variable 'pattern' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_pcigar.c:163:15: style: Variable 'text' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_pcigar.c:165:15: style: Variable 'cigar_buffer_base' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_pcigar.c:194:24: style: Variable 'op' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_pcigar.c:213:15: style: Variable 'pattern' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_pcigar.c:215:15: style: Variable 'text' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_pcigar.c:249:24: style: Variable 'op' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_pcigar.c:75:12: error: Shifting 32-bit value by 32 bits is undefined behaviour [shiftTooManyBits]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_pcigar.c:73:28: note: Assignment 'free_slots=((pcigar)!=0)?__builtin_clz(pcigar)/2:16', assigned value is 16
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_pcigar.c:75:12: note: Shift
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_pcigar.c:171:12: error: Shifting 32-bit value by 32 bits is undefined behaviour [shiftTooManyBits]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_pcigar.c:169:28: note: Assignment 'free_slots=((pcigar)!=0)?__builtin_clz(pcigar)/2:16', assigned value is 16
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_pcigar.c:171:12: note: Shift
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_pcigar.c:223:12: error: Shifting 32-bit value by 32 bits is undefined behaviour [shiftTooManyBits]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_pcigar.c:221:28: note: Assignment 'free_slots=((pcigar)!=0)?__builtin_clz(pcigar)/2:16', assigned value is 16
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_pcigar.c:223:12: note: Shift
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_heuristic.c:184:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRAGMA_LOOP_VECTORIZE [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_heuristic.c:203:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRAGMA_LOOP_VECTORIZE [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_heuristic.c:222:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRAGMA_LOOP_VECTORIZE [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_heuristic.c:311:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PRAGMA_LOOP_VECTORIZE [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:52:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable heatmap_value [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_slab.c:288:29: style: Parameter 'wavefront_slab' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:150:17: warning: Identical condition 'offset<0', second condition is always false [identicalConditionAfterEarlyExit]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:148:19: note: 'h_local' is assigned value 'offset' here.
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:145:16: note: If condition 'offset<0' is true, the function will return/exit
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:150:17: note: Testing identical condition 'offset<0'
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:47:22: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_plot [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:62: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:37: note: Assignment 'wf_plot=(struct wavefront_plot_t*)malloc(sizeof(struct wavefront_plot_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:101:36: note: Calling function 'wavefront_plot_heatmaps_allocate', 1st argument 'wf_plot' value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:47:22: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:47:50: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_plot [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:62: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:37: note: Assignment 'wf_plot=(struct wavefront_plot_t*)malloc(sizeof(struct wavefront_plot_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:101:36: note: Calling function 'wavefront_plot_heatmaps_allocate', 1st argument 'wf_plot' value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:47:50: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:48:22: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_plot [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:62: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:37: note: Assignment 'wf_plot=(struct wavefront_plot_t*)malloc(sizeof(struct wavefront_plot_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:101:36: note: Calling function 'wavefront_plot_heatmaps_allocate', 1st argument 'wf_plot' value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:48:22: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:48:65: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_plot [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:62: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:37: note: Assignment 'wf_plot=(struct wavefront_plot_t*)malloc(sizeof(struct wavefront_plot_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:101:36: note: Calling function 'wavefront_plot_heatmaps_allocate', 1st argument 'wf_plot' value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:48:65: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:49:22: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_plot [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:62: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:37: note: Assignment 'wf_plot=(struct wavefront_plot_t*)malloc(sizeof(struct wavefront_plot_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:101:36: note: Calling function 'wavefront_plot_heatmaps_allocate', 1st argument 'wf_plot' value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:49:22: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:49:50: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_plot [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:62: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:37: note: Assignment 'wf_plot=(struct wavefront_plot_t*)malloc(sizeof(struct wavefront_plot_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:101:36: note: Calling function 'wavefront_plot_heatmaps_allocate', 1st argument 'wf_plot' value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:49:50: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:50:22: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_plot [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:62: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:37: note: Assignment 'wf_plot=(struct wavefront_plot_t*)malloc(sizeof(struct wavefront_plot_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:101:36: note: Calling function 'wavefront_plot_heatmaps_allocate', 1st argument 'wf_plot' value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:50:22: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:50:62: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_plot [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:62: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:37: note: Assignment 'wf_plot=(struct wavefront_plot_t*)malloc(sizeof(struct wavefront_plot_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:101:36: note: Calling function 'wavefront_plot_heatmaps_allocate', 1st argument 'wf_plot' value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:50:62: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:52:3: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_plot [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:62: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:37: note: Assignment 'wf_plot=(struct wavefront_plot_t*)malloc(sizeof(struct wavefront_plot_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:101:36: note: Calling function 'wavefront_plot_heatmaps_allocate', 1st argument 'wf_plot' value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:52:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:55:3: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_plot [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:62: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:37: note: Assignment 'wf_plot=(struct wavefront_plot_t*)malloc(sizeof(struct wavefront_plot_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:101:36: note: Calling function 'wavefront_plot_heatmaps_allocate', 1st argument 'wf_plot' value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:55:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:57:3: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_plot [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:62: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:37: note: Assignment 'wf_plot=(struct wavefront_plot_t*)malloc(sizeof(struct wavefront_plot_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:101:36: note: Calling function 'wavefront_plot_heatmaps_allocate', 1st argument 'wf_plot' value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:57:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:58:3: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_plot [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:62: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:37: note: Assignment 'wf_plot=(struct wavefront_plot_t*)malloc(sizeof(struct wavefront_plot_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:101:36: note: Calling function 'wavefront_plot_heatmaps_allocate', 1st argument 'wf_plot' value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:58:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:59:3: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_plot [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:62: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:37: note: Assignment 'wf_plot=(struct wavefront_plot_t*)malloc(sizeof(struct wavefront_plot_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:101:36: note: Calling function 'wavefront_plot_heatmaps_allocate', 1st argument 'wf_plot' value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:59:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:60:3: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_plot [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:62: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:37: note: Assignment 'wf_plot=(struct wavefront_plot_t*)malloc(sizeof(struct wavefront_plot_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:101:36: note: Calling function 'wavefront_plot_heatmaps_allocate', 1st argument 'wf_plot' value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:60:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:61:7: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_plot [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:62: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:37: note: Assignment 'wf_plot=(struct wavefront_plot_t*)malloc(sizeof(struct wavefront_plot_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:101:36: note: Calling function 'wavefront_plot_heatmaps_allocate', 1st argument 'wf_plot' value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:61:7: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:63:3: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_plot [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:62: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:37: note: Assignment 'wf_plot=(struct wavefront_plot_t*)malloc(sizeof(struct wavefront_plot_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:101:36: note: Calling function 'wavefront_plot_heatmaps_allocate', 1st argument 'wf_plot' value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:61:32: note: Assuming condition is false
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:63:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:65:3: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_plot [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:62: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:37: note: Assignment 'wf_plot=(struct wavefront_plot_t*)malloc(sizeof(struct wavefront_plot_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:101:36: note: Calling function 'wavefront_plot_heatmaps_allocate', 1st argument 'wf_plot' value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:61:32: note: Assuming condition is false
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:65:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:67:7: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_plot [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:62: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:37: note: Assignment 'wf_plot=(struct wavefront_plot_t*)malloc(sizeof(struct wavefront_plot_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:101:36: note: Calling function 'wavefront_plot_heatmaps_allocate', 1st argument 'wf_plot' value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:61:32: note: Assuming condition is false
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:67:7: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:94:3: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_plot [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:62: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:37: note: Assignment 'wf_plot=(struct wavefront_plot_t*)malloc(sizeof(struct wavefront_plot_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:94:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:95:3: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_plot [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:62: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:37: note: Assignment 'wf_plot=(struct wavefront_plot_t*)malloc(sizeof(struct wavefront_plot_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:95:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:96:3: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_plot [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:62: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:37: note: Assignment 'wf_plot=(struct wavefront_plot_t*)malloc(sizeof(struct wavefront_plot_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:96:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:97:3: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_plot [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:62: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:37: note: Assignment 'wf_plot=(struct wavefront_plot_t*)malloc(sizeof(struct wavefront_plot_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:97:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:98:3: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_plot [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:62: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:37: note: Assignment 'wf_plot=(struct wavefront_plot_t*)malloc(sizeof(struct wavefront_plot_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:98:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:99:3: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_plot [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:62: note: Assuming allocation function fails
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:37: note: Assignment 'wf_plot=(struct wavefront_plot_t*)malloc(sizeof(struct wavefront_plot_t))', assigned value is 0
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:99:3: note: Null pointer dereference
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:44:32: style: Variable 'attributes' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:90:34: style: Parameter 'attributes' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:133:32: style: Variable 'sequences' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_heuristic.c:544:15: style: The comparison 'lo_base == mwavefront->lo' is always true because 'lo_base' and 'mwavefront->lo' represent the same value. [knownConditionTrueFalse]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_heuristic.c:524:33: note: 'lo_base' is assigned value 'mwavefront->lo' here.
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_heuristic.c:544:15: note: The comparison 'lo_base == mwavefront->lo' is always true because 'lo_base' and 'mwavefront->lo' represent the same value.
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_heuristic.c:544:44: style: The comparison 'hi_base == mwavefront->hi' is always true because 'hi_base' and 'mwavefront->hi' represent the same value. [knownConditionTrueFalse]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_heuristic.c:523:33: note: 'hi_base' is assigned value 'mwavefront->hi' here.
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_heuristic.c:544:44: note: The comparison 'hi_base == mwavefront->hi' is always true because 'hi_base' and 'mwavefront->hi' represent the same value.
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_heuristic.c:83:15: style:inconclusive: Function 'wavefront_heuristic_set_zdrop' argument 2 names different: declaration 'ydrop' definition 'zdrop'. [funcArgNamesDifferent]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_heuristic.h:94:15: note: Function 'wavefront_heuristic_set_zdrop' argument 2 names different: declaration 'ydrop' definition 'zdrop'.
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_heuristic.c:83:15: note: Function 'wavefront_heuristic_set_zdrop' argument 2 names different: declaration 'ydrop' definition 'zdrop'.
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_heuristic.c:163:24: style: Parameter 'wavefront_src' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_heuristic.c:177:24: style: Parameter 'wavefront' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_heuristic.c:194:24: style: Parameter 'wavefront' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_heuristic.c:213:24: style: Parameter 'wavefront' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_heuristic.c:262:32: style: Variable 'sequences' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_heuristic.c:299:24: style: Parameter 'wavefront' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_heuristic.c:458:32: style: Variable 'wf_heuristic' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_heuristic.c:467:32: style: Variable 'sequences' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_heuristic.c:573:34: style: Parameter 'wf_heuristic' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_termination.c:43:32: style: Variable 'sequences' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_termination.c:122:32: style: Variable 'sequences' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/alp/njn_ioutil.hpp:120:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable skipws [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_unialign.c:78:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_unialign.c:112:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:144:29: style: Virtual function 'setValueFct' is called from constructor 'DynProgProb(ValueFct*valueFct_=0,long dimInputProb_=0,const double*inputProb_=0,long valueLower_=0,long valueUpper_=0,const double*prob_=0)' at line 84. Dynamic binding is not used. [virtualCallInConstructor]
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:84:13: note: Calling setValueFct
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:144:29: note: setValueFct is a virtual function
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:149:22: style: Virtual function 'setInput' is called from constructor 'DynProgProb(ValueFct*valueFct_=0,long dimInputProb_=0,const double*inputProb_=0,long valueLower_=0,long valueUpper_=0,const double*prob_=0)' at line 85. Dynamic binding is not used. [virtualCallInConstructor]
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:85:13: note: Calling setInput
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:149:22: note: setInput is a virtual function
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:135:22: style: Virtual function 'clear' is called from constructor 'DynProgProb(ValueFct*valueFct_=0,long dimInputProb_=0,const double*inputProb_=0,long valueLower_=0,long valueUpper_=0,const double*prob_=0)' at line 87. Dynamic binding is not used. [virtualCallInConstructor]
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:87:13: note: Calling clear
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:135:22: note: clear is a virtual function
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:116:29: style: Virtual function 'copy' is called from copy constructor 'DynProgProb(const DynProgProb&dynProgProb_)' at line 95. Dynamic binding is not used. [virtualCallInConstructor]
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:95:13: note: Calling copy
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:116:29: note: copy is a virtual function
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:202:22: style: Virtual function 'free2' is called from destructor '~DynProgProb()' at line 100. Dynamic binding is not used. [virtualCallInConstructor]
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:100:13: note: Calling free2
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:202:22: note: free2 is a virtual function
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:195:22: style: Virtual function 'freeInput' is called from destructor '~DynProgProb()' at line 101. Dynamic binding is not used. [virtualCallInConstructor]
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:101:13: note: Calling freeInput
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:195:22: note: freeInput is a virtual function
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:67:16: style: Class 'DynProgProb' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:98:25: style: The destructor '~DynProgProb' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/lib/alp/njn_dynprogprobproto.hpp:65:18: note: Virtual destructor in base class
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:98:25: note: Destructor in derived class
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:104:24: style: The function 'operatorbool' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/lib/alp/njn_dynprogprobproto.hpp:67:24: note: Virtual function in base class
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:104:24: note: Function in derived class
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:142:29: style: The function 'clear' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/lib/alp/njn_dynprogprobproto.hpp:69:22: note: Virtual function in base class
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:142:29: note: Function in derived class
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:153:22: style: The function 'update' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/lib/alp/njn_dynprogprobproto.hpp:71:22: note: Virtual function in base class
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:153:22: note: Function in derived class
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:158:31: style: The function 'getProb' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/lib/alp/njn_dynprogprobproto.hpp:73:31: note: Virtual function in base class
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:158:31: note: Function in derived class
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:167:31: style: The function 'getStep' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/lib/alp/njn_dynprogprobproto.hpp:75:31: note: Virtual function in base class
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:167:31: note: Function in derived class
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:172:33: style: The function 'getValueLower' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/lib/alp/njn_dynprogprobproto.hpp:77:33: note: Virtual function in base class
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:172:33: note: Function in derived class
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:173:33: style: The function 'getValueUpper' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/lib/alp/njn_dynprogprobproto.hpp:78:33: note: Virtual function in base class
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:173:33: note: Function in derived class
diamond-2.1.11/src/lib/alp/njn_dynprogprob.cpp:131:11: style:inconclusive: Function 'copy' argument 7 names different: declaration 'valueFct_' definition 'newStateFct_'. [funcArgNamesDifferent]
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:131:19: note: Function 'copy' argument 7 names different: declaration 'valueFct_' definition 'newStateFct_'.
diamond-2.1.11/src/lib/alp/njn_dynprogprob.cpp:131:11: note: Function 'copy' argument 7 names different: declaration 'valueFct_' definition 'newStateFct_'.
diamond-2.1.11/src/lib/alp/njn_ioutil.hpp:114:25: style: Unused variable: line [unusedVariable]
diamond-2.1.11/src/lib/alp/njn_dynprogprob.cpp:268:28: style: Variable 'array' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/lib/alp/njn_dynprogprob.cpp:291:28: style: Variable 'array' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/lib/alp/njn_dynprogproblim.hpp:67:16: style: Class 'DynProgProbLim' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/lib/alp/njn_dynprogproblim.hpp:88:25: style: The destructor '~DynProgProbLim' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:98:25: note: Virtual destructor in base class
diamond-2.1.11/src/lib/alp/njn_dynprogproblim.hpp:88:25: note: Destructor in derived class
diamond-2.1.11/src/lib/alp/njn_dynprogproblim.hpp:114:22: style: The function 'update' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:153:22: note: Virtual function in base class
diamond-2.1.11/src/lib/alp/njn_dynprogproblim.hpp:114:22: note: Function in derived class
diamond-2.1.11/src/lib/alp/njn_dynprogproblim.hpp:119:29: style: The function 'clear' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:135:22: note: Virtual function in base class
diamond-2.1.11/src/lib/alp/njn_dynprogproblim.hpp:119:29: note: Function in derived class
diamond-2.1.11/src/lib/alp/njn_dynprogproblim.hpp:130:29: style: The function 'clear' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:142:29: note: Virtual function in base class
diamond-2.1.11/src/lib/alp/njn_dynprogproblim.hpp:130:29: note: Function in derived class
diamond-2.1.11/src/lib/alp/njn_dynprogproblim.hpp:155:22: style: The function 'setValueBegin' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/lib/alp/njn_dynprogprob.hpp:223:22: note: Virtual function in base class
diamond-2.1.11/src/lib/alp/njn_dynprogproblim.hpp:155:22: note: Function in derived class
diamond-2.1.11/src/lib/alp/njn_dynprogproblim.cpp:104:28: style: Variable 'array' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/lib/alp/njn_dynprogproblim.cpp:134:28: style: Variable 'array' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/lib/alp/njn_ioutil.cpp:100:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/njn_ioutil.cpp:157:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_unialign.c:230:11: style: Condition 'unreachable' is always false [knownConditionTrueFalse]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_unialign.c:214:25: note: Assuming that condition 'unreachable' is not redundant
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_unialign.c:230:11: note: Condition 'unreachable' is always false
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_unialign.c:280:15: style:inconclusive: Function 'wavefront_unialign_print_status' argument 3 names different: declaration 'current_score' definition 'score'. [funcArgNamesDifferent]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_unialign.h:56:15: note: Function 'wavefront_unialign_print_status' argument 3 names different: declaration 'current_score' definition 'score'.
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_unialign.c:280:15: note: Function 'wavefront_unialign_print_status' argument 3 names different: declaration 'current_score' definition 'score'.
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_unialign.c:60:27: style: Variable 'alignment_form' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_unialign.c:109:29: style: Variable 'system' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_unialign.c:152:32: style: Variable 'sequences' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_unialign.c:185:28: style: Variable 'mwavefront' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_unialign.c:283:32: style: Variable 'sequences' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_unialign.c:126:22: style: Variable 'proposed_mem' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/lib/alp/njn_ioutil.cpp:114:21: style: Variable 'pbuf' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/lib/alp/njn_ioutil.cpp:153:58: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator]
diamond-2.1.11/src/lib/alp/njn_vector.hpp:204:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/njn_matrix.hpp:151:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/njn_matrix.hpp:294:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/njn_function.hpp:79:74: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LN_2 [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/njn_function.hpp:80:74: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LN_2 [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/njn_function.hpp:81:78: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LN_10 [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/njn_function.hpp:82:78: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LN_10 [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/njn_function.hpp:86:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LN_2 [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/njn_function.hpp:87:74: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LN_2 [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/njn_function.hpp:88:69: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LN_10 [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/njn_function.hpp:89:75: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LN_10 [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/njn_root.hpp:262:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/njn_root.hpp:350:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/njn_root.hpp:402:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/njn_localmaxstatutil.cpp:74:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REL_TOL [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/njn_localmaxstatutil.cpp:242:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REL_TOL [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/njn_localmaxstatutil.cpp:282:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REL_TOL [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/njn_localmaxstatutil.cpp:396:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REL_TOL [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/njn_localmaxstatutil.cpp:507:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable REL_TOL [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/njn_localmaxstat.hpp:135:28: performance:inconclusive: Technically the member function 'Njn::LocalMaxStat::out' can be static (but you may consider moving to unnamed namespace). [functionStatic]
diamond-2.1.11/src/lib/alp/njn_vector.hpp:59:27: style: Virtual function 'copy' is called from constructor 'Vector(const T*begin_,const T*end_)' at line 114. Dynamic binding is not used. [virtualCallInConstructor]
diamond-2.1.11/src/lib/alp/njn_vector.hpp:114:7: note: Calling copy
diamond-2.1.11/src/lib/alp/njn_vector.hpp:59:27: note: copy is a virtual function
diamond-2.1.11/src/lib/alp/njn_vector.hpp:60:27: style: Virtual function 'copy' is called from constructor 'Vector(long m_,const T&a_)' at line 123. Dynamic binding is not used. [virtualCallInConstructor]
diamond-2.1.11/src/lib/alp/njn_vector.hpp:123:7: note: Calling copy
diamond-2.1.11/src/lib/alp/njn_vector.hpp:60:27: note: copy is a virtual function
diamond-2.1.11/src/lib/alp/njn_vector.hpp:82:27: style: Virtual function 'free2' is called from destructor '~Vector()' at line 127. Dynamic binding is not used. [virtualCallInConstructor]
diamond-2.1.11/src/lib/alp/njn_vector.hpp:127:28: note: Calling free2
diamond-2.1.11/src/lib/alp/njn_vector.hpp:82:27: note: free2 is a virtual function
diamond-2.1.11/src/lib/alp/njn_matrix.hpp:74:29: style: Virtual function 'copy' is called from constructor 'Matrix(long m_,long n_,const T*vector_)' at line 237. Dynamic binding is not used. [virtualCallInConstructor]
diamond-2.1.11/src/lib/alp/njn_matrix.hpp:237:9: note: Calling copy
diamond-2.1.11/src/lib/alp/njn_matrix.hpp:74:29: note: copy is a virtual function
diamond-2.1.11/src/lib/alp/njn_matrix.hpp:75:29: style: Virtual function 'copy' is called from constructor 'Matrix(long m_,long n_,T a_=static_cast<T>(0)' at line 247. Dynamic binding is not used. [virtualCallInConstructor]
diamond-2.1.11/src/lib/alp/njn_matrix.hpp:247:9: note: Calling copy
diamond-2.1.11/src/lib/alp/njn_matrix.hpp:75:29: note: copy is a virtual function
diamond-2.1.11/src/lib/alp/njn_matrix.hpp:102:29: style: Virtual function 'free2' is called from destructor '~Matrix()' at line 251. Dynamic binding is not used. [virtualCallInConstructor]
diamond-2.1.11/src/lib/alp/njn_matrix.hpp:251:29: note: Calling free2
diamond-2.1.11/src/lib/alp/njn_matrix.hpp:102:29: note: free2 is a virtual function
diamond-2.1.11/src/lib/alp/njn_localmaxstat.hpp:66:14: style: Class 'LocalMaxStat' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/lib/alp/njn_localmaxstatmatrix.hpp:60:16: style: Class 'LocalMaxStatMatrix' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/lib/alp/njn_matrix.hpp:284:16: style: The scope of the variable 'j' can be reduced. [variableScope]
diamond-2.1.11/src/lib/alp/njn_vector.hpp:284:22: style: Local variable 'i' shadows outer variable [shadowVariable]
diamond-2.1.11/src/lib/alp/njn_vector.hpp:236:14: note: Shadowed declaration
diamond-2.1.11/src/lib/alp/njn_vector.hpp:284:22: note: Shadow variable
diamond-2.1.11/src/lib/alp/njn_vector.hpp:289:35: style: Local variable 'sstream' shadows outer variable [shadowVariable]
diamond-2.1.11/src/lib/alp/njn_vector.hpp:247:25: note: Shadowed declaration
diamond-2.1.11/src/lib/alp/njn_vector.hpp:289:35: note: Shadow variable
diamond-2.1.11/src/lib/alp/njn_matrix.hpp:267:17: style: Local variable 'matrix' shadows outer function [shadowFunction]
diamond-2.1.11/src/lib/alp/njn_matrix.hpp:55:35: note: Shadowed declaration
diamond-2.1.11/src/lib/alp/njn_matrix.hpp:267:17: note: Shadow variable
diamond-2.1.11/src/lib/alp/njn_matrix.hpp:296:37: style: Local variable 'j' shadows outer variable [shadowVariable]
diamond-2.1.11/src/lib/alp/njn_matrix.hpp:284:16: note: Shadowed declaration
diamond-2.1.11/src/lib/alp/njn_matrix.hpp:296:37: note: Shadow variable
diamond-2.1.11/src/lib/alp/njn_matrix.hpp:335:29: style: Local variable 'j' shadows outer variable [shadowVariable]
diamond-2.1.11/src/lib/alp/njn_matrix.hpp:284:16: note: Shadowed declaration
diamond-2.1.11/src/lib/alp/njn_matrix.hpp:335:29: note: Shadow variable
diamond-2.1.11/src/lib/alp/njn_matrix.hpp:409:29: style: Local variable 's' shadows outer variable [shadowVariable]
diamond-2.1.11/src/lib/alp/njn_matrix.hpp:364:21: note: Shadowed declaration
diamond-2.1.11/src/lib/alp/njn_matrix.hpp:409:29: note: Shadow variable
diamond-2.1.11/src/lib/alp/njn_matrix.hpp:410:35: style: Local variable 'sstream' shadows outer variable [shadowVariable]
diamond-2.1.11/src/lib/alp/njn_matrix.hpp:365:27: note: Shadowed declaration
diamond-2.1.11/src/lib/alp/njn_matrix.hpp:410:35: note: Shadow variable
diamond-2.1.11/src/lib/alp/njn_localmaxstatmatrix.cpp:128:14: performance: Function parameter 'localMaxStat_' should be passed by const reference. [passedByValue]
diamond-2.1.11/src/lib/alp/njn_vector.hpp:236:14: style: Variable 'i' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/lib/alp/njn_localmaxstatmatrix.cpp:92:14: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/lib/alp/sls_basic.hpp:62:47: performance: Variable 'st' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList]
diamond-2.1.11/src/lib/alp/njn_localmaxstat.cpp:105:8: style:inconclusive: Function 'copy' argument 15 names different: declaration 'meanDLE_' definition 'meanLength_'. [funcArgNamesDifferent]
diamond-2.1.11/src/lib/alp/njn_localmaxstat.hpp:132:14: note: Function 'copy' argument 15 names different: declaration 'meanDLE_' definition 'meanLength_'.
diamond-2.1.11/src/lib/alp/njn_localmaxstat.cpp:105:8: note: Function 'copy' argument 15 names different: declaration 'meanDLE_' definition 'meanLength_'.
diamond-2.1.11/src/lib/alp/sls_basic.hpp:62:21: performance: Function parameter 'st_' should be passed by const reference. [passedByValue]
diamond-2.1.11/src/lib/alp/sls_basic.hpp:172:39: style: Parameter 'pointer_' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/alp/njn_random.cpp:68:25: style:inconclusive: Function 'seed' argument 1 names different: declaration 'n' definition 'x'. [funcArgNamesDifferent]
diamond-2.1.11/src/lib/alp/njn_random.hpp:46:23: note: Function 'seed' argument 1 names different: declaration 'n' definition 'x'.
diamond-2.1.11/src/lib/alp/njn_random.cpp:68:25: note: Function 'seed' argument 1 names different: declaration 'n' definition 'x'.
diamond-2.1.11/src/lib/alp/njn_integer.hpp:75:28: style: Condition 'i>=0' is always false [knownConditionTrueFalse]
diamond-2.1.11/src/lib/alp/njn_integer.hpp:73:19: note: Assuming that condition 'i<0' is not redundant
diamond-2.1.11/src/lib/alp/njn_integer.hpp:75:28: note: Condition 'i>=0' is always false
diamond-2.1.11/src/lib/alp/njn_root.hpp:292:15: style: The scope of the variable 'fx' can be reduced. [variableScope]
diamond-2.1.11/src/lib/alp/njn_root.hpp:293:15: style: The scope of the variable 'dfx' can be reduced. [variableScope]
diamond-2.1.11/src/lib/alp/njn_root.hpp:369:17: style: The scope of the variable 'fx' can be reduced. [variableScope]
diamond-2.1.11/src/lib/alp/njn_root.hpp:418:17: style: The scope of the variable 'x' can be reduced. [variableScope]
diamond-2.1.11/src/lib/alp/njn_integer.hpp:91:17: style: The scope of the variable 'remainder' can be reduced. [variableScope]
diamond-2.1.11/src/lib/alp/njn_localmaxstatutil.cpp:127:8: style:inconclusive: Function 'lambda' argument 1 names different: declaration 'dimMatrix_' definition 'dimension_'. [funcArgNamesDifferent]
diamond-2.1.11/src/lib/alp/njn_localmaxstatutil.hpp:59:16: note: Function 'lambda' argument 1 names different: declaration 'dimMatrix_' definition 'dimension_'.
diamond-2.1.11/src/lib/alp/njn_localmaxstatutil.cpp:127:8: note: Function 'lambda' argument 1 names different: declaration 'dimMatrix_' definition 'dimension_'.
diamond-2.1.11/src/lib/alp/njn_root.hpp:369:20: style: Variable 'fx' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/lib/alp/njn_root.hpp:418:19: style: Variable 'x' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/lib/alp/njn_root.hpp:419:20: style: Variable 'fx' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/lib/alp/njn_localmaxstatutil.cpp:61:14: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/lib/alp/njn_localmaxstatutil.cpp:123:20: style: Variable 'p' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/lib/alp/njn_localmaxstatutil.cpp:132:14: style: Variable 'j' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/lib/alp/njn_integer.hpp:91:27: style: Variable 'remainder' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:263:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAND_MAX [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:473:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:513:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/sls_alp.hpp:195:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/sls_alp.hpp:212:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:720:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:757:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:778:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:807:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:854:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:916:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:116:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:426:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable struct_for_randomization [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:583:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable struct_for_randomization [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:701:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable struct_for_randomization [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:718:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:828:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:902:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_EPSILON [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:1031:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:1187:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MIN [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:1408:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable q_elem [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:1531:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/sls_alp.cpp:2025:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable state [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:1261:14: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:380:11: warning: Member variable 'alp_data::d_realizations_number2' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:380:11: warning: Member variable 'alp_data::d_time_before1' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:486:11: warning: Member variable 'alp_data::d_realizations_number2' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:486:11: warning: Member variable 'alp_data::d_time_before1' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:386:17: performance:inconclusive: Technically the member function 'Sls::alp_data::ran2' can be static (but you may consider moving to unnamed namespace). [functionStatic]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:710:16: style:inconclusive: Technically the member function 'Sls::alp_data::check_out_file' can be const. [functionConst]
diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:396:8: note: Technically the member function 'Sls::alp_data::check_out_file' can be const.
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:710:16: note: Technically the member function 'Sls::alp_data::check_out_file' can be const.
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:1297:3: warning: Class 'importance_sampling' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:1297:3: warning: Class 'importance_sampling' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:540:3: warning: Class 'alp_data' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:540:3: warning: Class 'alp_data' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:103:3: style: Class 'array_positive' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:169:3: style: Class 'array' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:596:15: style: Condition 'v2_minus<0' is always true [knownConditionTrueFalse]
diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:581:15: note: Assuming that condition 'v2_minus>=0' is not redundant
diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:589:21: note: Assuming condition is false
diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:596:15: note: Condition 'v2_minus<0' is always true
diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::lambda' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:863:3: style: Exception should be caught by reference. [catchExceptionByValue]
diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::lambda_error' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::C' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::C_error' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::K' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::K_error' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::a_I' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::a_I_error' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::a_J' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::a_J_error' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::sigma' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::sigma_error' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::alpha_I' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::alpha_I_error' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::alpha_J' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::alpha_J_error' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::a' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::a_error' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::alpha' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::alpha_error' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::gapless_a' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::gapless_a_error' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::gapless_alpha' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::gapless_alpha_error' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::G' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::G1' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::G2' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::m_CalcTime' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::vi_y_thr' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::vj_y_thr' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::c_y_thr' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_alignment_evaluer.hpp:60:3: warning: Member variable 'gapped_computation_parameters_struct::d_total_realizations_number_with_ALP' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_alignment_evaluer.hpp:60:3: warning: Member variable 'gapped_computation_parameters_struct::d_total_realizations_number_with_killing' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_alp.hpp:153:14: performance:inconclusive: Technically the member function 'Sls::alp::swap' can be static (but you may consider moving to unnamed namespace). [functionStatic]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:797:33: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:1242:49: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:1270:4: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/alp/sls_alp.hpp:94:2: style: Class 'alp' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/lib/alp/sls_alp_sim.hpp:78:3: style: Class 'alp_sim' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:169:3: style: Class 'array < long >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:103:3: style: Class 'array_positive < long >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:103:3: style: Class 'array_positive < double >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:103:3: style: Class 'array_positive < state * >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:103:3: style: Class 'array_positive < alp * >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:1355:27: style: Redundant assignment of 'd_elements_values[ind]' to itself. [selfAssignment]
diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:501:13: style: The scope of the variable 'i' can be reduced. [variableScope]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:998:13: style: Local variable 'i' shadows outer variable [shadowVariable]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:958:12: note: Shadowed declaration
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:998:13: note: Shadow variable
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:50:8: performance: Function parameter 'randout_' should be passed by const reference. [passedByValue]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:51:8: performance: Function parameter 'smatr_file_name_' should be passed by const reference. [passedByValue]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:52:8: performance: Function parameter 'RR1_file_name_' should be passed by const reference. [passedByValue]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:53:8: performance: Function parameter 'RR2_file_name_' should be passed by const reference. [passedByValue]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:217:8: performance: Function parameter 'randout_' should be passed by const reference. [passedByValue]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:382:8: performance: Function parameter 'randout_' should be passed by const reference. [passedByValue]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:392:8: performance: Function parameter 'smatr_file_name_' should be passed by const reference. [passedByValue]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:393:8: performance: Function parameter 'RR1_file_name_' should be passed by const reference. [passedByValue]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:394:8: performance: Function parameter 'RR2_file_name_' should be passed by const reference. [passedByValue]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:711:9: performance: Function parameter 'out_file_name_' should be passed by const reference. [passedByValue]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:818:8: performance: Function parameter 'smatr_file_name_' should be passed by const reference. [passedByValue]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:868:8: performance: Function parameter 'RR_file_name_' should be passed by const reference. [passedByValue]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:890:8: performance: Function parameter 'RR_file_name_' should be passed by const reference. [passedByValue]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:1019:8: performance: Function parameter 'RR_file_name_' should be passed by const reference. [passedByValue]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:1522:8: performance: Function parameter 'str_' should be passed by const reference. [passedByValue]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:61:10: style: Parameter 'letterFreqs1_' can be declared as pointer to const [constParameterReference]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:62:10: style: Parameter 'letterFreqs2_' can be declared as pointer to const [constParameterReference]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:488:27: style: Parameter 'randomization_parameters_' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:739:8: style: Variable 'str_for_test0' can be declared as const array [constVariable]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:740:9: style: Variable 'test_flag0' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:747:8: style: Variable 'str_for_test' can be declared as const array [constVariable]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:749:8: style: Variable 'test_flag' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:800:10: style: Variable 'd_RR1' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:801:10: style: Variable 'd_RR2' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:314:24: warning:inconclusive: Division of result of sizeof() on pointer type. [divideSizeof]
diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:694:23: warning:inconclusive: Division of result of sizeof() on pointer type. [divideSizeof]
diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:541:7: style: Variable 'v1' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/lib/alp/sls_alignment_evaluer.cpp:1106:9: style: Local variable 'area' shadows outer function [shadowFunction]
diamond-2.1.11/src/lib/alp/sls_alignment_evaluer.hpp:150:9: note: Shadowed declaration
diamond-2.1.11/src/lib/alp/sls_alignment_evaluer.cpp:1106:9: note: Shadow variable
diamond-2.1.11/src/lib/alp/sls_alignment_evaluer.cpp:100:14: performance: Function parameter 'function_name_' should be passed by const reference. [passedByValue]
diamond-2.1.11/src/lib/alp/sls_alp_regression.cpp:300:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MAX [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/sls_alp_regression.cpp:511:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MAX [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/sls_alp_regression.cpp:699:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/sls_alp_regression.cpp:366:9: style: Parameter 'values_' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/alp/sls_alp_regression.cpp:367:9: style: Parameter 'errors_' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/alp/sls_alp_regression.cpp:568:9: style: Parameter 'values_' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/alp/sls_alp_regression.cpp:569:9: style: Parameter 'errors_' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/alp/sls_alp_regression.cpp:635:9: style: Parameter 'array_' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/alp/sls_alp_regression.cpp:164:6: style: Variable 'y2' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/lib/alp/sls_basic.cpp:136:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable pi [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/sls_basic.cpp:172:9: style: Parameter 'p_' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/gsl/gsl.h:51:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/gsl/gsl.h:59:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:1059:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MAX [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:1198:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:551:13: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:751:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:1077:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MAX [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2017:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable alp [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2148:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable alp [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2241:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable alp [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2337:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable alp [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:560:17: performance:inconclusive: Technically the member function 'Sls::pvalues::log_area' can be static (but you may consider moving to unnamed namespace). [functionStatic]
diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:212:10: note: Technically the member function 'Sls::pvalues::log_area' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:560:17: note: Technically the member function 'Sls::pvalues::log_area' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:977:15: style:inconclusive: Technically the member function 'Sls::pvalues::calculate_P_values' can be const. [functionConst]
diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:250:8: note: Technically the member function 'Sls::pvalues::calculate_P_values' can be const.
diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:977:15: note: Technically the member function 'Sls::pvalues::calculate_P_values' can be const.
diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:114:5: style: Condition 'blast_' is always false [knownConditionTrueFalse]
diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:68:9: note: Assignment 'blast_=false', assigned value is 0
diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:114:5: note: Condition 'blast_' is always false
diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:154:21: style: Condition 'blast_' is always false [knownConditionTrueFalse]
diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:68:9: note: Assignment 'blast_=false', assigned value is 0
diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:154:21: note: Condition 'blast_' is always false
diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:412:5: style: Condition 'blast_' is always false [knownConditionTrueFalse]
diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:384:9: note: Assignment 'blast_=false', assigned value is 0
diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:412:5: note: Condition 'blast_' is always false
diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:439:21: style: Condition 'blast_' is always false [knownConditionTrueFalse]
diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:384:9: note: Assignment 'blast_=false', assigned value is 0
diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:439:21: note: Condition 'blast_' is always false
diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:597:6: style: Condition 'blast_' is always false [knownConditionTrueFalse]
diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:569:11: note: Assignment 'blast_=false', assigned value is 0
diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:597:6: note: Condition 'blast_' is always false
diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:624:26: style: Condition 'blast_' is always false [knownConditionTrueFalse]
diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:569:11: note: Assignment 'blast_=false', assigned value is 0
diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:624:26: note: Condition 'blast_' is always false
diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:1022:10: style: The scope of the variable 'P_tmp' can be reduced. [variableScope]
diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:1022:16: style: The scope of the variable 'E_tmp' can be reduced. [variableScope]
diamond-2.1.11/src/lib/alp/sls_alp.cpp:1998:8: warning: Member variable 'state::d_HS_ij_next' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_alp.cpp:1998:8: warning: Member variable 'state::d_HI_ij_next' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_alp.cpp:1998:8: warning: Member variable 'state::d_HD_ij_next' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_alp.cpp:1998:8: warning: Member variable 'state::d_H_ij_next' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_alp.cpp:1998:8: warning: Member variable 'state::d_H_matr_len' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_alp.cpp:1998:8: warning: Member variable 'state::d_M' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/gsl/gsl.h:255:19: style: Variable 'P' can be declared as const array [constVariable]
diamond-2.1.11/src/lib/alp/sls_alp.cpp:1998:8: warning: Member variable 'state::d_sentinel_i_next' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/gsl/gsl.h:263:19: style: Variable 'Q' can be declared as const array [constVariable]
diamond-2.1.11/src/lib/alp/sls_alp.cpp:1998:8: warning: Member variable 'state::d_sentinel_j_next' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_alp.cpp:44:6: warning: Member variable 'alp::d_nalp_killing' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_alp.cpp:44:6: warning: Member variable 'alp::d_diff_opt' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_alp.cpp:44:6: warning: Member variable 'alp::d_sentinels_flag' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_alp.cpp:44:6: warning: Member variable 'alp::d_IS_state' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_alp.cpp:127:3: warning: Class 'alp' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
diamond-2.1.11/src/lib/alp/sls_alp.cpp:127:3: warning: Class 'alp' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:571:17: style: Variable 'lambda_' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:572:12: style: Variable 'k_' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:571:9: style: Variable 'lambda_' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:572:9: style: Variable 'k_' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/lib/alp/sls_alp.cpp:269:11: style: The scope of the variable 'i' can be reduced. [variableScope]
diamond-2.1.11/src/lib/alp/sls_alp.cpp:386:11: style: The scope of the variable 'i' can be reduced. [variableScope]
diamond-2.1.11/src/lib/alp/sls_alp.cpp:1203:12: style: The scope of the variable 'i' can be reduced. [variableScope]
diamond-2.1.11/src/lib/alp/sls_alp.cpp:1389:12: style: The scope of the variable 'i' can be reduced. [variableScope]
diamond-2.1.11/src/lib/alp/sls_alp.cpp:1673:12: style: The scope of the variable 'i' can be reduced. [variableScope]
diamond-2.1.11/src/lib/alp/sls_alp.cpp:1906:12: style: The scope of the variable 'i' can be reduced. [variableScope]
diamond-2.1.11/src/lib/alp/sls_alp.cpp:1203:12: style: Local variable 'i' shadows outer variable [shadowVariable]
diamond-2.1.11/src/lib/alp/sls_alp.cpp:1143:11: note: Shadowed declaration
diamond-2.1.11/src/lib/alp/sls_alp.cpp:1203:12: note: Shadow variable
diamond-2.1.11/src/lib/alp/sls_alp.cpp:1389:12: style: Local variable 'i' shadows outer variable [shadowVariable]
diamond-2.1.11/src/lib/alp/sls_alp.cpp:1322:11: note: Shadowed declaration
diamond-2.1.11/src/lib/alp/sls_alp.cpp:1389:12: note: Shadow variable
diamond-2.1.11/src/lib/alp/sls_alp.cpp:1648:12: style: Local variable 'i' shadows outer variable [shadowVariable]
diamond-2.1.11/src/lib/alp/sls_alp.cpp:1580:11: note: Shadowed declaration
diamond-2.1.11/src/lib/alp/sls_alp.cpp:1648:12: note: Shadow variable
diamond-2.1.11/src/lib/alp/sls_alp.cpp:1673:12: style: Local variable 'i' shadows outer variable [shadowVariable]
diamond-2.1.11/src/lib/alp/sls_alp.cpp:1580:11: note: Shadowed declaration
diamond-2.1.11/src/lib/alp/sls_alp.cpp:1673:12: note: Shadow variable
diamond-2.1.11/src/lib/alp/sls_alp.cpp:1881:12: style: Local variable 'i' shadows outer variable [shadowVariable]
diamond-2.1.11/src/lib/alp/sls_alp.cpp:1813:11: note: Shadowed declaration
diamond-2.1.11/src/lib/alp/sls_alp.cpp:1881:12: note: Shadow variable
diamond-2.1.11/src/lib/alp/sls_alp.cpp:1906:12: style: Local variable 'i' shadows outer variable [shadowVariable]
diamond-2.1.11/src/lib/alp/sls_alp.cpp:1813:11: note: Shadowed declaration
diamond-2.1.11/src/lib/alp/sls_alp.cpp:1906:12: note: Shadow variable
diamond-2.1.11/src/lib/alp/sls_alp.cpp:2108:11: style: Parameter 'M_upper_level_' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/alp/sls_alp.cpp:2208:24: style: Variable 'd_is_tmp' can be declared as pointer to const [constVariableReference]
diamond-2.1.11/src/lib/alp/sls_alp.cpp:2252:4: style: Variable 'UI' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/lib/alp/sls_alp.cpp:2255:4: style: Variable 'VD' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/lib/blast/blast_filter.cpp:58:7: warning: If memory allocation fails, then there is a possible null pointer dereference: loc->ssr [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_filter.cpp:57:34: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_filter.cpp:57:15: note: Assignment 'loc->ssr=(struct SSeqRange*)calloc(1,sizeof(struct SSeqRange))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_filter.cpp:58:7: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_filter.cpp:205:5: warning: If memory allocation fails, then there is a possible null pointer dereference: retval [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_filter.cpp:204:51: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_filter.cpp:204:28: note: Assignment 'retval=(struct BlastMaskLoc*)calloc(1,sizeof(struct BlastMaskLoc))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_filter.cpp:205:5: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_filter.cpp:207:9: warning: If memory allocation fails, then there is a possible null pointer dereference: retval [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_filter.cpp:204:51: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_filter.cpp:204:28: note: Assignment 'retval=(struct BlastMaskLoc*)calloc(1,sizeof(struct BlastMaskLoc))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_filter.cpp:207:9: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_filter.cpp:53:24: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_filter.cpp:57:16: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_filter.cpp:112:17: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_filter.cpp:135:15: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_filter.cpp:136:17: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_filter.cpp:166:5: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_filter.cpp:174:5: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_filter.cpp:175:5: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_filter.cpp:204:29: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_filter.cpp:207:33: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_filter.cpp:243:4: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_filter.cpp:244:4: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_filter.cpp:251:25: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_filter.cpp:252:25: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_filter.cpp:253:23: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_filter.cpp:254:23: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_filter.cpp:306:5: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_filter.cpp:169:47: style:inconclusive: Function 'BlastSeqLocNodeFree' argument 1 names different: declaration 'node' definition 'loc'. [funcArgNamesDifferent]
diamond-2.1.11/src/lib/blast/blast_filter.h:87:47: note: Function 'BlastSeqLocNodeFree' argument 1 names different: declaration 'node' definition 'loc'.
diamond-2.1.11/src/lib/blast/blast_filter.cpp:169:47: note: Function 'BlastSeqLocNodeFree' argument 1 names different: declaration 'node' definition 'loc'.
diamond-2.1.11/src/lib/blast/blast_filter.cpp:253:15: style: Variable 'loc1' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/blast/blast_filter.cpp:254:15: style: Variable 'loc2' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/blast/blast_message.cpp:73:9: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_message.cpp:74:9: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_message.cpp:91:7: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_message.cpp:94:7: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_message.cpp:110:14: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_message.cpp:136:34: style: Parameter 'blast_msg' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/blast/blast_message.cpp:83:29: style: Variable 'next' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1582:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:2298:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HUGE_VAL [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2055:21: style: Condition 'status<0' is always false [knownConditionTrueFalse]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1961:21: note: Assignment 'status=0', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2053:25: note: Calling function 's_Trim' returns 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2053:25: note: Assignment 'status=s_Trim(temp_seq,&leftend,&rightend,sparamsp)', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2055:21: note: Condition 'status<0' is always false
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1516:21: warning: If memory allocation fails, then there is a possible null pointer dereference: win [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1555:32: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1555:13: note: Assignment 'win=(struct SSequence*)calloc(1,sizeof(struct SSequence))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1575:12: note: Calling function 's_StateOn', 1st argument 'win' value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1516:21: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1518:6: warning: If memory allocation fails, then there is a possible null pointer dereference: win [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1555:32: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1555:13: note: Assignment 'win=(struct SSequence*)calloc(1,sizeof(struct SSequence))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1575:12: note: Calling function 's_StateOn', 1st argument 'win' value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1518:6: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1521:2: warning: If memory allocation fails, then there is a possible null pointer dereference: win [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1555:32: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1555:13: note: Assignment 'win=(struct SSequence*)calloc(1,sizeof(struct SSequence))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1575:12: note: Calling function 's_StateOn', 1st argument 'win' value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1521:2: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1524:12: warning: If memory allocation fails, then there is a possible null pointer dereference: win [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1555:32: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1555:13: note: Assignment 'win=(struct SSequence*)calloc(1,sizeof(struct SSequence))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1575:12: note: Calling function 's_StateOn', 1st argument 'win' value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1524:12: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1526:3: warning: If memory allocation fails, then there is a possible null pointer dereference: win [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1555:32: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1555:13: note: Assignment 'win=(struct SSequence*)calloc(1,sizeof(struct SSequence))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1575:12: note: Calling function 's_StateOn', 1st argument 'win' value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1524:38: note: Assuming condition is false
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1526:3: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1559:7: warning: If memory allocation fails, then there is a possible null pointer dereference: win [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1555:32: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1555:13: note: Assignment 'win=(struct SSequence*)calloc(1,sizeof(struct SSequence))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1559:7: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1560:7: warning: If memory allocation fails, then there is a possible null pointer dereference: win [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1555:32: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1555:13: note: Assignment 'win=(struct SSequence*)calloc(1,sizeof(struct SSequence))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1560:7: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1564:7: warning: If memory allocation fails, then there is a possible null pointer dereference: win [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1555:32: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1555:13: note: Assignment 'win=(struct SSequence*)calloc(1,sizeof(struct SSequence))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1564:7: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1565:7: warning: If memory allocation fails, then there is a possible null pointer dereference: win [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1555:32: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1555:13: note: Assignment 'win=(struct SSequence*)calloc(1,sizeof(struct SSequence))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1565:7: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1566:2: warning: If memory allocation fails, then there is a possible null pointer dereference: win [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1555:32: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1555:13: note: Assignment 'win=(struct SSequence*)calloc(1,sizeof(struct SSequence))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1566:2: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1568:9: warning: If memory allocation fails, then there is a possible null pointer dereference: win [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1555:32: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1555:13: note: Assignment 'win=(struct SSequence*)calloc(1,sizeof(struct SSequence))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1568:9: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1569:2: warning: If memory allocation fails, then there is a possible null pointer dereference: win [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1555:32: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1555:13: note: Assignment 'win=(struct SSequence*)calloc(1,sizeof(struct SSequence))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1569:2: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1571:2: warning: If memory allocation fails, then there is a possible null pointer dereference: win [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1555:32: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1555:13: note: Assignment 'win=(struct SSequence*)calloc(1,sizeof(struct SSequence))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1571:2: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1572:2: warning: If memory allocation fails, then there is a possible null pointer dereference: win [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1555:32: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1555:13: note: Assignment 'win=(struct SSequence*)calloc(1,sizeof(struct SSequence))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1572:2: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1573:2: warning: If memory allocation fails, then there is a possible null pointer dereference: win [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1555:32: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1555:13: note: Assignment 'win=(struct SSequence*)calloc(1,sizeof(struct SSequence))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1573:2: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1751:7: warning: If memory allocation fails, then there is a possible null pointer dereference: H [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1747:24: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1747:8: note: Assignment 'H=(double*)calloc(seq->length,sizeof(double))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1751:7: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2082:10: warning: If memory allocation fails, then there is a possible null pointer dereference: seg [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2081:30: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2081:16: note: Assignment 'seg=(struct SSeg*)calloc(1,sizeof(struct SSeg))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2082:10: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2083:10: warning: If memory allocation fails, then there is a possible null pointer dereference: seg [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2081:30: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2081:16: note: Assignment 'seg=(struct SSeg*)calloc(1,sizeof(struct SSeg))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2083:10: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2084:10: warning: If memory allocation fails, then there is a possible null pointer dereference: seg [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2081:30: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2081:16: note: Assignment 'seg=(struct SSeg*)calloc(1,sizeof(struct SSeg))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2084:10: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2145:7: warning: If memory allocation fails, then there is a possible null pointer dereference: loc [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2144:47: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2144:26: note: Assignment 'loc=(struct BlastSeqLoc*)calloc(1,sizeof(struct BlastSeqLoc))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2145:7: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2146:7: warning: If memory allocation fails, then there is a possible null pointer dereference: loc [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2144:47: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2144:26: note: Assignment 'loc=(struct BlastSeqLoc*)calloc(1,sizeof(struct BlastSeqLoc))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2146:7: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2146:10: warning: If memory allocation fails, then there is a possible null pointer dereference: loc->ssr [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2145:37: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2145:18: note: Assignment 'loc->ssr=(struct SSeqRange*)calloc(1,sizeof(struct SSeqRange))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2146:10: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2147:7: warning: If memory allocation fails, then there is a possible null pointer dereference: loc [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2144:47: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2144:26: note: Assignment 'loc=(struct BlastSeqLoc*)calloc(1,sizeof(struct BlastSeqLoc))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2147:7: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2148:7: warning: If memory allocation fails, then there is a possible null pointer dereference: loc [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2144:47: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2144:26: note: Assignment 'loc=(struct BlastSeqLoc*)calloc(1,sizeof(struct BlastSeqLoc))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2148:7: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2176:4: warning: If memory allocation fails, then there is a possible null pointer dereference: palpha [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2174:28: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2174:13: note: Assignment 'palpha=(struct Alpha*)calloc(1,sizeof(struct Alpha))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2176:4: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2177:4: warning: If memory allocation fails, then there is a possible null pointer dereference: palpha [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2174:28: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2174:13: note: Assignment 'palpha=(struct Alpha*)calloc(1,sizeof(struct Alpha))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2177:4: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2178:4: warning: If memory allocation fails, then there is a possible null pointer dereference: palpha [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2174:28: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2174:13: note: Assignment 'palpha=(struct Alpha*)calloc(1,sizeof(struct Alpha))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2178:4: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2195:4: warning: If memory allocation fails, then there is a possible null pointer dereference: palpha [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2174:28: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2174:13: note: Assignment 'palpha=(struct Alpha*)calloc(1,sizeof(struct Alpha))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2195:4: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2196:4: warning: If memory allocation fails, then there is a possible null pointer dereference: palpha [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2174:28: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2174:13: note: Assignment 'palpha=(struct Alpha*)calloc(1,sizeof(struct Alpha))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2196:4: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2208:4: warning: If memory allocation fails, then there is a possible null pointer dereference: sparamsp [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2206:38: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2206:15: note: Assignment 'sparamsp=(struct SegParameters*)calloc(1,sizeof(struct SegParameters))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2208:4: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2209:4: warning: If memory allocation fails, then there is a possible null pointer dereference: sparamsp [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2206:38: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2206:15: note: Assignment 'sparamsp=(struct SegParameters*)calloc(1,sizeof(struct SegParameters))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2209:4: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2210:4: warning: If memory allocation fails, then there is a possible null pointer dereference: sparamsp [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2206:38: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2206:15: note: Assignment 'sparamsp=(struct SegParameters*)calloc(1,sizeof(struct SegParameters))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2210:4: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2211:4: warning: If memory allocation fails, then there is a possible null pointer dereference: sparamsp [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2206:38: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2206:15: note: Assignment 'sparamsp=(struct SegParameters*)calloc(1,sizeof(struct SegParameters))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2211:4: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2212:4: warning: If memory allocation fails, then there is a possible null pointer dereference: sparamsp [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2206:38: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2206:15: note: Assignment 'sparamsp=(struct SegParameters*)calloc(1,sizeof(struct SegParameters))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2212:4: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2213:4: warning: If memory allocation fails, then there is a possible null pointer dereference: sparamsp [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2206:38: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2206:15: note: Assignment 'sparamsp=(struct SegParameters*)calloc(1,sizeof(struct SegParameters))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2213:4: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2214:4: warning: If memory allocation fails, then there is a possible null pointer dereference: sparamsp [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2206:38: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2206:15: note: Assignment 'sparamsp=(struct SegParameters*)calloc(1,sizeof(struct SegParameters))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2214:4: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2215:4: warning: If memory allocation fails, then there is a possible null pointer dereference: sparamsp [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2206:38: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2206:15: note: Assignment 'sparamsp=(struct SegParameters*)calloc(1,sizeof(struct SegParameters))', assigned value is 0
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2215:4: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1359:11: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1388:4: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1389:4: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1390:4: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1405:4: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1407:4: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1408:4: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1409:4: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1426:7: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1462:8: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1463:8: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1489:17: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1521:15: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1555:14: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1702:32: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1703:32: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1705:4: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1747:8: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2081:17: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2090:4: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2121:10: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2144:27: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2145:19: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2174:14: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2180:17: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2181:16: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2206:16: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2253:4: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2280:18: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1478:10: style: The scope of the variable 'letter' can be reduced. [variableScope]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1513:23: style: The scope of the variable 'c' can be reduced. [variableScope]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1442:14: style: Variable 'seqmax' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1460:7: style: Variable 'np1' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1460:13: style: Variable 'np2' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1479:14: style: Variable 'seqmax' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1480:18: style: Variable 'alphaindex' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1481:24: style: Variable 'alphaflag' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1587:20: style: Parameter 'sv' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1661:18: style: Variable 'alphaindex' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1662:24: style: Variable 'alphaflag' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1792:74: style: Parameter 'H' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:1815:75: style: Parameter 'H' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/blast/blast_seg.cpp:2101:24: style: Parameter 'seq' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:359:21: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:371:25: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:388:26: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:391:19: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:430:18: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:543:29: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:553:33: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:565:33: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:578:25: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:581:29: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:596:25: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:603:29: portability: Non reentrant function 'strtok' called. For threadsafe applications it is recommended to use the reentrant replacement function 'strtok_r'. [prohibitedstrtokCalled]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1553:16: style: Expression 'exp(x) - 1' can be replaced by 'expm1(x)' to avoid loss of precision. [unpreciseMathCall]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:2020:12: warning: Identical condition and return expression 'status', return value is always 0 [identicalConditionAfterEarlyExit]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:2016:9: note: If condition 'status' is true, the function will return/exit
diamond-2.1.11/src/lib/blast/blastn_score.cpp:2020:12: note: Returning identical expression 'status'
diamond-2.1.11/src/lib/blast/blastn_score.cpp:979:62: style: Condition '(status=BlastScoreBlkNuclMatrixCreate(sbp))!=0' is always false [knownConditionTrueFalse]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:979:55: note: Calling function 'BlastScoreBlkNuclMatrixCreate' returns 0
diamond-2.1.11/src/lib/blast/blastn_score.cpp:979:62: note: Condition '(status=BlastScoreBlkNuclMatrixCreate(sbp))!=0' is always false
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1040:49: style: Condition '(status=BlastScoreBlkMaxScoreSet(sbp))!=0' is always false [knownConditionTrueFalse]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1040:42: note: Calling function 'BlastScoreBlkMaxScoreSet' returns 0
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1040:49: note: Condition '(status=BlastScoreBlkMaxScoreSet(sbp))!=0' is always false
diamond-2.1.11/src/lib/blast/blastn_score.cpp:2091:13: warning: If memory allocation fails, then there is a possible null pointer dereference: ambig_buffer [nullPointerOutOfMemory]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:2088:40: note: Assuming allocation function fails
diamond-2.1.11/src/lib/blast/blastn_score.cpp:2088:24: note: Assignment 'ambig_buffer=(Uint1*)calloc(sbp->ambig_size,sizeof(Uint1))', assigned value is 0
diamond-2.1.11/src/lib/blast/blastn_score.cpp:2091:13: note: Null pointer dereference
diamond-2.1.11/src/lib/blast/blastn_score.cpp:182:9: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:184:5: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:246:24: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:246:53: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:254:9: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:256:5: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:266:5: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:267:5: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:268:5: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:296:14: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:302:21: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:359:14: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:371:18: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:388:19: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:531:14: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:538:38: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:543:22: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:553:26: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:565:26: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:578:18: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:581:22: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:596:18: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:603:22: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:935:55: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1052:15: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1057:20: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1065:21: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1080:8: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1116:13: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1118:17: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1120:21: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1122:17: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1124:21: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1132:5: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1140:5: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1153:31: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1153:63: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1160:5: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1172:9: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1173:5: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1200:5: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1203:5: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1204:5: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1205:5: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1206:5: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1210:9: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1213:5: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1214:5: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1224:12: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1238:12: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1244:18: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1349:9: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1351:5: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1448:13: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1529:9: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1859:9: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1860:9: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1917:17: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1918:17: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1924:5: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1925:5: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:2028:9: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:2088:24: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:2093:9: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:2121:13: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:2313:12: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:2318:18: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:778:27: style: The scope of the variable 'degen' can be reduced. [variableScope]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1374:21: style: The scope of the variable 'first' can be reduced. [variableScope]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1374:28: style: The scope of the variable 'last' can be reduced. [variableScope]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1381:21: style: The scope of the variable 'score_avg' can be reduced. [variableScope]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:2025:11: style: The scope of the variable 'i' can be reduced. [variableScope]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:2079:10: style: The scope of the variable 'index' can be reduced. [variableScope]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:2339:24: style: The scope of the variable 'p' can be reduced. [variableScope]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:2039:44: style:inconclusive: Function 'BLAST_FillScoringOptions' argument 2 names different: declaration 'program' definition 'program_number'. [funcArgNamesDifferent]
diamond-2.1.11/src/lib/blast/blast_options.h:851:74: note: Function 'BLAST_FillScoringOptions' argument 2 names different: declaration 'program' definition 'program_number'.
diamond-2.1.11/src/lib/blast/blastn_score.cpp:2039:44: note: Function 'BLAST_FillScoringOptions' argument 2 names different: declaration 'program' definition 'program_number'.
diamond-2.1.11/src/lib/blast/blastn_score.cpp:2119:42: style:inconclusive: Function 'BlastScoringOptionsNew' argument 1 names different: declaration 'program' definition 'program_number'. [funcArgNamesDifferent]
diamond-2.1.11/src/lib/blast/blast_options.h:837:47: note: Function 'BlastScoringOptionsNew' argument 1 names different: declaration 'program' definition 'program_number'.
diamond-2.1.11/src/lib/blast/blastn_score.cpp:2119:42: note: Function 'BlastScoringOptionsNew' argument 1 names different: declaration 'program' definition 'program_number'.
diamond-2.1.11/src/lib/blast/blastn_score.cpp:215:42: style: Parameter 'kbp' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:317:18: style: Variable 'lp' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:504:20: style: Variable 'lp' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:848:68: style: Parameter 'kbp_from' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1078:7: style: Variable 'use_old_fsc' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1393:28: style: Variable 'ptr1' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1393:35: style: Variable 'ptr2' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1393:42: style: Variable 'ptr1e' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1808:13: style: Variable 'probs' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:2156:27: style: Parameter 'probs' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:34:14: style: struct member 'MatrixInfo::name' is never used. [unusedStructMember]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:35:18: style: struct member 'MatrixInfo::values' is never used. [unusedStructMember]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:36:15: style: struct member 'MatrixInfo::prefs' is never used. [unusedStructMember]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:37:14: style: struct member 'MatrixInfo::max_number_values' is never used. [unusedStructMember]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:161:11: style: struct member 'BLAST_LetterProb::ch' is never used. [unusedStructMember]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1337:12: style: Variable 'stdrfp' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1338:9: style: Variable 'sfp' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1454:66: style: Variable 'oldsum2' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/lib/blast/blastn_score.cpp:1489:17: style: Variable 'oldsum2' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/lib/blast/ncbi_std.cpp:59:16: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/ncbi_std.cpp:155:9: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/ncbi_std.cpp:175:9: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/ncbi_std.cpp:177:9: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/nlm_linear_algebra.cpp:44:11: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/nlm_linear_algebra.cpp:46:18: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/nlm_linear_algebra.cpp:71:12: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/nlm_linear_algebra.cpp:73:16: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/nlm_linear_algebra.cpp:105:11: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/nlm_linear_algebra.cpp:107:18: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/blast/nlm_linear_algebra.cpp:65:9: style: The scope of the variable 'i' can be reduced. [variableScope]
diamond-2.1.11/src/lib/blast/nlm_linear_algebra.cpp:102:9: style: The scope of the variable 'i' can be reduced. [variableScope]
diamond-2.1.11/src/lib/blast/nlm_linear_algebra.cpp:164:12: style: The scope of the variable 'temp' can be reduced. [variableScope]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:45:10: warning: Member variable 'alp_sim::m_GaplessAlpha' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:45:10: warning: Member variable 'alp_sim::m_GaplessAlphaError' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:45:10: warning: Member variable 'alp_sim::m_GaplessA' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:45:10: warning: Member variable 'alp_sim::m_GaplessAError' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:45:10: warning: Member variable 'alp_sim::m_G' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:45:10: warning: Member variable 'alp_sim::m_G1' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:45:10: warning: Member variable 'alp_sim::m_G2' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2593:15: performance:inconclusive: Technically the member function 'Sls::alp_sim::memory_release_for_get_minimal_simulation' can be static (but you may consider moving to unnamed namespace). [functionStatic]
diamond-2.1.11/src/lib/alp/sls_alp_sim.hpp:102:8: note: Technically the member function 'Sls::alp_sim::memory_release_for_get_minimal_simulation' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2593:15: note: Technically the member function 'Sls::alp_sim::memory_release_for_get_minimal_simulation' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3534:15: performance:inconclusive: Technically the member function 'Sls::alp_sim::calculate_C' can be static (but you may consider moving to unnamed namespace). [functionStatic]
diamond-2.1.11/src/lib/alp/sls_alp_sim.hpp:136:8: note: Technically the member function 'Sls::alp_sim::calculate_C' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3534:15: note: Technically the member function 'Sls::alp_sim::calculate_C' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2773:15: performance:inconclusive: Technically the member function 'Sls::alp_sim::memory_release_for_calculate_FSC' can be static (but you may consider moving to unnamed namespace). [functionStatic]
diamond-2.1.11/src/lib/alp/sls_alp_sim.hpp:148:8: note: Technically the member function 'Sls::alp_sim::memory_release_for_calculate_FSC' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2773:15: note: Technically the member function 'Sls::alp_sim::memory_release_for_calculate_FSC' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3493:15: performance:inconclusive: Technically the member function 'Sls::alp_sim::sigma_calculation' can be static (but you may consider moving to unnamed namespace). [functionStatic]
diamond-2.1.11/src/lib/alp/sls_alp_sim.hpp:206:8: note: Technically the member function 'Sls::alp_sim::sigma_calculation' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3493:15: note: Technically the member function 'Sls::alp_sim::sigma_calculation' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:1104:15: style:inconclusive: Technically the member function 'Sls::alp_sim::memory_release_for_calculate_main_parameters2m' can be const. [functionConst]
diamond-2.1.11/src/lib/alp/sls_alp_sim.hpp:354:8: note: Technically the member function 'Sls::alp_sim::memory_release_for_calculate_main_parameters2m' can be const.
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:1104:15: note: Technically the member function 'Sls::alp_sim::memory_release_for_calculate_main_parameters2m' can be const.
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:72:3: warning: Class 'alp_sim' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:72:3: warning: Class 'alp_sim' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:372:9: style: Condition '!loop_break_flag' is always true [knownConditionTrueFalse]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:329:7: note: Assuming that condition 'loop_break_flag' is not redundant
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:372:9: note: Condition '!loop_break_flag' is always true
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:475:9: style: Condition '!loop_break_flag' is always true [knownConditionTrueFalse]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:432:7: note: Assuming that condition 'loop_break_flag' is not redundant
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:475:9: note: Condition '!loop_break_flag' is always true
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:660:5: style: Exception should be caught by reference. [catchExceptionByValue]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2908:32: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3585:33: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3586:40: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3686:33: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3687:40: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3951:5: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3952:5: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3957:32: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3958:39: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:4410:45: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:4430:33: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:4431:40: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:570:6: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:575:6: note: Found duplicate branches for 'if' and 'else'.
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:570:6: note: Found duplicate branches for 'if' and 'else'.
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:4314:35: style: Variable 'tmp_struct.d_calculate_alp_number' is reassigned a value before the old one has been used. [redundantAssignment]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:4311:35: note: tmp_struct.d_calculate_alp_number is assigned
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:4314:35: note: tmp_struct.d_calculate_alp_number is overwritten
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:277:12: style: The scope of the variable 'number_of_realizations_with_ALP_pred' can be reduced. [variableScope]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:383:12: style: The scope of the variable 'number_of_realizations_with_killing_pred' can be reduced. [variableScope]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:590:10: style: The scope of the variable 'sucess_flag' can be reduced. [variableScope]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2006:11: style: The scope of the variable 'i' can be reduced. [variableScope]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2302:12: style: The scope of the variable 'alp_number' can be reduced. [variableScope]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:4354:9: style: The scope of the variable 'sum2_error' can be reduced. [variableScope]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:1469:13: style: Local variable 'j' shadows outer variable [shadowVariable]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:1336:12: note: Shadowed declaration
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:1469:13: note: Shadow variable
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:1487:11: style: Local variable 'test_difference' shadows outer argument [shadowArgument]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:1250:9: note: Shadowed declaration
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:1487:11: note: Shadow variable
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:1488:11: style: Local variable 'test_difference_error' shadows outer argument [shadowArgument]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:1251:9: note: Shadowed declaration
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:1488:11: note: Shadow variable
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2062:12: style: Local variable 'i' shadows outer variable [shadowVariable]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2049:11: note: Shadowed declaration
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2062:12: note: Shadow variable
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2066:9: style: Local variable 'flag' shadows outer variable [shadowVariable]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2043:7: note: Shadowed declaration
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2066:9: note: Shadow variable
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2090:11: style: Local variable 'flag' shadows outer variable [shadowVariable]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2066:9: note: Shadowed declaration
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2090:11: note: Shadow variable
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2363:13: style: Local variable 'i' shadows outer variable [shadowVariable]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2326:12: note: Shadowed declaration
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2363:13: note: Shadow variable
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2477:14: style: Local variable 'i' shadows outer variable [shadowVariable]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2363:13: note: Shadowed declaration
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2477:14: note: Shadow variable
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2918:11: style: Local variable 'tmp' shadows outer variable [shadowVariable]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2908:27: note: Shadowed declaration
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2918:11: note: Shadow variable
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3028:13: style: Local variable 'j' shadows outer variable [shadowVariable]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2988:12: note: Shadowed declaration
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3028:13: note: Shadow variable
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3731:13: style: Local variable 'number_of_elements' shadows outer variable [shadowVariable]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3620:12: note: Shadowed declaration
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3731:13: note: Shadow variable
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3733:9: style: Local variable 'cut_left_tail' shadows outer variable [shadowVariable]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3622:8: note: Shadowed declaration
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3733:9: note: Shadow variable
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3734:9: style: Local variable 'cut_right_tail' shadows outer variable [shadowVariable]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3623:8: note: Shadowed declaration
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3734:9: note: Shadow variable
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3738:11: style: Local variable 'beta1' shadows outer variable [shadowVariable]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3617:10: note: Shadowed declaration
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3738:11: note: Shadow variable
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3740:11: style: Local variable 'beta1_error' shadows outer variable [shadowVariable]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3618:10: note: Shadowed declaration
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3740:11: note: Shadow variable
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3742:9: style: Local variable 'res_was_calculated' shadows outer variable [shadowVariable]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3634:8: note: Shadowed declaration
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3742:9: note: Shadow variable
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:4460:13: style: Local variable 'k' shadows outer variable [shadowVariable]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:4427:12: note: Shadowed declaration
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:4460:13: note: Shadow variable
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2762:11: style: Parameter 'i_' can be declared as reference to const [constParameterReference]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3947:14: style: Variable 'alp_tmp' can be declared as reference to const [constVariableReference]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3948:12: style: Variable 'weight_tmp' can be declared as reference to const [constVariableReference]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:4042:14: style: Variable 'alp_tmp' can be declared as reference to const [constVariableReference]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:4043:12: style: Variable 'weight_tmp' can be declared as reference to const [constVariableReference]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:4146:14: style: Variable 'alp_tmp' can be declared as reference to const [constVariableReference]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:4147:12: style: Variable 'weight_tmp' can be declared as reference to const [constVariableReference]
diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2763:10: style: Parameter 'exp_array_' can be declared as pointer to const [constParameterReference]
diamond-2.1.11/src/lib/mio/detail/mmap.ipp:124:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable invalid_argument [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/mio/detail/mmap.ipp:208:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable read [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/mio/detail/mmap.ipp:252:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable invalid_handle [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/mio/detail/mmap.ipp:266:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data_ [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/mio/detail/mmap.ipp:296:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable file_handle_ [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/mio/detail/mmap.ipp:308:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable invalid_argument [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/mio/detail/mmap.ipp:330:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable invalid_handle [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/mio/detail/mmap.ipp:378:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bad_file_descriptor [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/mio/detail/mmap.ipp:415:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data_ [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/mio/detail/mmap.ipp:456:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable data_ [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/mio/detail/mmap.ipp:225:5: error: Memory leak: mapping_start [memleak]
diamond-2.1.11/src/lib/mio/detail/mmap.ipp:219:30: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
diamond-2.1.11/src/lib/mio/detail/mmap.ipp:205:52: note: Assuming allocation function fails
diamond-2.1.11/src/lib/mio/detail/mmap.ipp:205:45: note: Assignment 'mapping_start=static_cast<char*>(::mmap(0,length_to_map,mode==access_mode::read?PROT_READ:PROT_WRITE,MAP_SHARED,file_handle,aligned_offset))', assigned value is 0
diamond-2.1.11/src/lib/mio/detail/mmap.ipp:219:30: note: Null pointer addition
diamond-2.1.11/src/lib/murmurhash/MurmurHash3.cpp:109:27: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/murmurhash/MurmurHash3.cpp:120:30: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/murmurhash/MurmurHash3.cpp:138:27: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/murmurhash/MurmurHash3.cpp:157:4: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/murmurhash/MurmurHash3.cpp:165:27: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/murmurhash/MurmurHash3.cpp:181:30: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/murmurhash/MurmurHash3.cpp:210:27: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/murmurhash/MurmurHash3.cpp:259:4: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/murmurhash/MurmurHash3.cpp:260:4: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/murmurhash/MurmurHash3.cpp:261:4: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/murmurhash/MurmurHash3.cpp:262:4: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/murmurhash/MurmurHash3.cpp:272:27: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/murmurhash/MurmurHash3.cpp:275:18: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/murmurhash/MurmurHash3.cpp:276:18: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/murmurhash/MurmurHash3.cpp:284:30: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/murmurhash/MurmurHash3.cpp:303:27: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/murmurhash/MurmurHash3.cpp:344:4: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/murmurhash/MurmurHash3.cpp:345:4: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/lib/tantan/LambdaCalculator.cc:54:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MAX [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/tantan/LambdaCalculator.cc:198:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MAX [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/lib/tantan/LambdaCalculator.cc:271:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAND_MAX [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/masking/masking.cpp:91:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MASK_LETTER [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/masking/masking.cpp:96:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable block_id [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/masking/masking.cpp:108:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable block_id [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/masking/masking.cpp:129:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable max_motif_len [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/masking/masking.cpp:137:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable alphabet_size [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/masking/masking.cpp:167:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TANTAN [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/masking/masking.cpp:198:115: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable tantan_minMaskProb [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/masking/masking.cpp:205:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable mask_char [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/masking/masking.cpp:221:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/masking/masking.cpp:233:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NONE [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/masking/masking.cpp:68:15: warning:inconclusive: Member variable 'MaskingTable::mtx_' is not assigned in the copy constructor. Should it be copied? [missingMemberCopy]
diamond-2.1.11/src/masking/masking.cpp:201:15: performance:inconclusive: Technically the member function 'Masking::bit_to_hard_mask' can be static (but you may consider moving to unnamed namespace). [functionStatic]
diamond-2.1.11/src/masking/masking.h:44:7: note: Technically the member function 'Masking::bit_to_hard_mask' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/masking/masking.cpp:201:15: note: Technically the member function 'Masking::bit_to_hard_mask' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/masking/masking.cpp:210:15: performance:inconclusive: Technically the member function 'Masking::remove_bit_mask' can be static (but you may consider moving to unnamed namespace). [functionStatic]
diamond-2.1.11/src/masking/masking.h:45:7: note: Technically the member function 'Masking::remove_bit_mask' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/masking/masking.cpp:210:15: note: Technically the member function 'Masking::remove_bit_mask' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/masking/masking.h:40:2: style: Struct 'Masking' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/masking/masking.cpp:168:55: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/masking/masking.cpp:177:16: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/masking/masking.cpp:198:37: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/masking/masking.cpp:178:12: style: The scope of the variable 'nMasked' can be reduced. [variableScope]
diamond-2.1.11/src/masking/masking.cpp:181:17: style: Variable 'l' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/masking/masking.cpp:142:21: style: Variable 'int_matrix[i][j]' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/lib/tantan/LambdaCalculator.cc:196:24: performance:inconclusive: Technically the member function 'cbrc::LambdaCalculator::find_ub' can be static (but you may consider moving to unnamed namespace). [functionStatic]
diamond-2.1.11/src/lib/tantan/LambdaCalculator.hh:50:8: note: Technically the member function 'cbrc::LambdaCalculator::find_ub' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/lib/tantan/LambdaCalculator.cc:196:24: note: Technically the member function 'cbrc::LambdaCalculator::find_ub' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/lib/tantan/LambdaCalculator.cc:84:7: style: The scope of the variable 'v' can be reduced. [variableScope]
diamond-2.1.11/src/lib/tantan/LambdaCalculator.cc:200:10: style: The scope of the variable 'r_max' can be reduced. [variableScope]
diamond-2.1.11/src/lib/tantan/LambdaCalculator.cc:201:10: style: The scope of the variable 'c_max' can be reduced. [variableScope]
diamond-2.1.11/src/lib/tantan/LambdaCalculator.cc:203:10: style: The scope of the variable 'r_min' can be reduced. [variableScope]
diamond-2.1.11/src/lib/tantan/LambdaCalculator.cc:204:10: style: The scope of the variable 'c_min' can be reduced. [variableScope]
diamond-2.1.11/src/lib/tantan/LambdaCalculator.cc:112:51: style: Parameter 'b' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/output/output_format.h:171:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable salltitles [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/output_format.h:191:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable salltitles [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/blast_pairwise_format.cpp:28:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable command [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/output_format.h:116:2: style: Struct 'TabularFormat' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/output/output_format.h:91:24: style: The function 'clone' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/output/output_format.h:70:24: note: Virtual function in base class
diamond-2.1.11/src/output/output_format.h:91:24: note: Function in derived class
diamond-2.1.11/src/output/output_format.h:100:24: style: The function 'clone' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/output/output_format.h:70:24: note: Virtual function in base class
diamond-2.1.11/src/output/output_format.h:100:24: note: Function in derived class
diamond-2.1.11/src/output/output_format.h:122:14: style: The destructor '~TabularFormat' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/output/output_format.h:71:11: note: Virtual destructor in base class
diamond-2.1.11/src/output/output_format.h:122:14: note: Destructor in derived class
diamond-2.1.11/src/output/output_format.h:142:11: style: The destructor '~PAF_format' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/output/output_format.h:71:11: note: Virtual destructor in base class
diamond-2.1.11/src/output/output_format.h:142:11: note: Destructor in derived class
diamond-2.1.11/src/output/output_format.h:158:11: style: The destructor '~Sam_format' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/output/output_format.h:71:11: note: Virtual destructor in base class
diamond-2.1.11/src/output/output_format.h:158:11: note: Destructor in derived class
diamond-2.1.11/src/output/output_format.h:178:11: style: The destructor '~XML_format' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/output/output_format.h:71:11: note: Virtual destructor in base class
diamond-2.1.11/src/output/output_format.h:178:11: note: Destructor in derived class
diamond-2.1.11/src/output/output_format.h:198:11: style: The destructor '~Pairwise_format' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/output/output_format.h:71:11: note: Virtual destructor in base class
diamond-2.1.11/src/output/output_format.h:198:11: note: Destructor in derived class
diamond-2.1.11/src/output/output_format.h:211:11: style: The destructor '~TaxonFormat' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/output/output_format.h:71:11: note: Virtual destructor in base class
diamond-2.1.11/src/output/output_format.h:211:11: note: Destructor in derived class
diamond-2.1.11/src/output/output_format.h:234:11: style: The destructor '~Edge' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/output/output_format.h:71:11: note: Virtual destructor in base class
diamond-2.1.11/src/output/output_format.h:234:11: note: Destructor in derived class
diamond-2.1.11/src/output/output_format.h:197:15: style: The function 'print_footer' overrides a function in a base class but is identical to the overridden function [uselessOverride]
diamond-2.1.11/src/output/output_format.h:68:15: note: Virtual function in base class
diamond-2.1.11/src/output/output_format.h:197:15: note: Function in derived class
diamond-2.1.11/src/output/blast_pairwise_format.cpp:78:46: style:inconclusive: Function 'print_footer' argument 1 names different: declaration 'f' definition 'out'. [funcArgNamesDifferent]
diamond-2.1.11/src/output/output_format.h:197:38: note: Function 'print_footer' argument 1 names different: declaration 'f' definition 'out'.
diamond-2.1.11/src/output/blast_pairwise_format.cpp:78:46: note: Function 'print_footer' argument 1 names different: declaration 'f' definition 'out'.
diamond-2.1.11/src/output/blast_pairwise_format.cpp:83:56: style:inconclusive: Function 'print_query_epilog' argument 1 names different: declaration 'infos' definition 'info'. [funcArgNamesDifferent]
diamond-2.1.11/src/output/output_format.h:196:48: note: Function 'print_query_epilog' argument 1 names different: declaration 'infos' definition 'info'.
diamond-2.1.11/src/output/blast_pairwise_format.cpp:83:56: note: Function 'print_query_epilog' argument 1 names different: declaration 'infos' definition 'info'.
diamond-2.1.11/src/masking/tantan.cpp:92:16: style: Local variable 's' shadows outer variable [shadowVariable]
diamond-2.1.11/src/masking/tantan.cpp:82:15: note: Shadowed declaration
diamond-2.1.11/src/masking/tantan.cpp:92:16: note: Shadow variable
diamond-2.1.11/src/output/daa/daa_file.h:100:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable magic_number [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/daa/daa_record.h:119:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable query_translated [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/daa/daa_record.cpp:36:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable blastp [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/daa/daa_record.cpp:63:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable score [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/daa/daa_file.h:41:2: warning: Member variable 'DAA_header2::db_seqs' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/output/daa/daa_file.h:41:2: warning: Member variable 'DAA_header2::db_seqs_used' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/output/daa/daa_file.h:41:2: warning: Member variable 'DAA_header2::db_letters' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/output/daa/daa_file.h:41:2: warning: Member variable 'DAA_header2::flags' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/output/daa/daa_file.h:41:2: warning: Member variable 'DAA_header2::query_records' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/output/daa/daa_file.h:41:2: warning: Member variable 'DAA_header2::mode' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/output/daa/daa_file.h:41:2: warning: Member variable 'DAA_header2::gap_open' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/output/daa/daa_file.h:41:2: warning: Member variable 'DAA_header2::gap_extend' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/output/daa/daa_file.h:41:2: warning: Member variable 'DAA_header2::reward' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/output/daa/daa_file.h:41:2: warning: Member variable 'DAA_header2::penalty' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/output/daa/daa_file.h:41:2: warning: Member variable 'DAA_header2::reserved1' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/output/daa/daa_file.h:41:2: warning: Member variable 'DAA_header2::reserved2' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/output/daa/daa_file.h:41:2: warning: Member variable 'DAA_header2::reserved3' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/output/daa/daa_file.h:41:2: warning: Member variable 'DAA_header2::k' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/output/daa/daa_file.h:41:2: warning: Member variable 'DAA_header2::lambda' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/output/daa/daa_file.h:41:2: warning: Member variable 'DAA_header2::evalue' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/output/daa/daa_file.h:41:2: warning: Member variable 'DAA_header2::reserved5' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/output/daa/daa_file.h:41:2: warning: Member variable 'DAA_header2::score_matrix' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/output/daa/daa_record.h:38:3: warning: Member variable 'Match::hsp_num' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/output/daa/daa_record.h:38:3: warning: Member variable 'Match::subject_len' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/output/daa/daa_file.h:82:2: style: Struct 'DAA_header2' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/output/daa/daa_file.h:95:2: style: Struct 'DAAFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/output/daa/daa_record.h:38:3: style: Struct 'Match' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/output/daa/daa_record.cpp:80:3: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/output/daa/daa_record.cpp:31:11: style: Local variable 'query_len' shadows outer function [shadowFunction]
diamond-2.1.11/src/output/daa/daa_record.h:117:9: note: Shadowed declaration
diamond-2.1.11/src/output/daa/daa_record.cpp:31:11: note: Shadow variable
diamond-2.1.11/src/output/blast_tab_format.cpp:134:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cluster [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/blast_tab_format.cpp:154:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable output_format [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/blast_tab_format.cpp:250:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable id_delimiters [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/blast_tab_format.cpp:564:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable report_unaligned [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/blast_tab_format.cpp:641:101: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable key [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/blast_tab_format.cpp:652:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable blastp [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/output.h:53:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable begin_ [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/output.h:62:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable begin_ [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/output.h:78:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRANSCRIPT [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/daa/daa_write.cpp:24:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable id_delimiters [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/daa/daa_write.cpp:51:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable begin_ [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/daa/daa_write.cpp:67:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable matrix [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/output.h:94:2: style: Struct 'OutputWriter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/output/daa/daa_write.cpp:34:3: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/output/daa/daa_write.cpp:97:41: style:inconclusive: Function 'DAA_header2' argument 1 names different: declaration 'f' definition 'daa_in'. [funcArgNamesDifferent]
diamond-2.1.11/src/output/daa/daa_file.h:82:29: note: Function 'DAA_header2' argument 1 names different: declaration 'f' definition 'daa_in'.
diamond-2.1.11/src/output/daa/daa_write.cpp:97:41: note: Function 'DAA_header2' argument 1 names different: declaration 'f' definition 'daa_in'.
diamond-2.1.11/src/output/output.h:91:37: performance: Function parameter 'tmp_file_names' should be passed by const reference. [passedByValue]
diamond-2.1.11/src/output/daa/daa_write.cpp:126:41: style: Parameter 'daa_in' can be declared as reference to const [constParameterReference]
diamond-2.1.11/src/output/daa/daa_write.cpp:144:41: style: Parameter 'daa_in' can be declared as reference to const [constParameterReference]
diamond-2.1.11/src/output/blast_tab_format.cpp:563:14: style: The scope of the variable 'out' can be reduced. [variableScope]
diamond-2.1.11/src/output/blast_tab_format.cpp:328:30: style: Local variable 'i' shadows outer variable [shadowVariable]
diamond-2.1.11/src/output/blast_tab_format.cpp:240:12: note: Shadowed declaration
diamond-2.1.11/src/output/blast_tab_format.cpp:328:30: note: Shadow variable
diamond-2.1.11/src/output/blast_tab_format.cpp:420:30: style: Local variable 'i' shadows outer variable [shadowVariable]
diamond-2.1.11/src/output/blast_tab_format.cpp:240:12: note: Shadowed declaration
diamond-2.1.11/src/output/blast_tab_format.cpp:420:30: note: Shadow variable
diamond-2.1.11/src/output/blast_tab_format.cpp:424:30: style: Local variable 'i' shadows outer variable [shadowVariable]
diamond-2.1.11/src/output/blast_tab_format.cpp:240:12: note: Shadowed declaration
diamond-2.1.11/src/output/blast_tab_format.cpp:424:30: note: Shadow variable
diamond-2.1.11/src/output/blast_tab_format.cpp:414:35: style: Clarify calculation precedence for '<<' and '?'. [clarifyCalculation]
diamond-2.1.11/src/output/blast_tab_format.cpp:623:36: style: Clarify calculation precedence for '<<' and '?'. [clarifyCalculation]
diamond-2.1.11/src/lib/ksw2/ksw2_extz.c:6:126: style:inconclusive: Function 'ksw_extz' argument 8 names different: declaration 'q' definition 'gapo'. [funcArgNamesDifferent]
diamond-2.1.11/src/lib/ksw2/ksw2.h:62:13: note: Function 'ksw_extz' argument 8 names different: declaration 'q' definition 'gapo'.
diamond-2.1.11/src/lib/ksw2/ksw2_extz.c:6:126: note: Function 'ksw_extz' argument 8 names different: declaration 'q' definition 'gapo'.
diamond-2.1.11/src/lib/ksw2/ksw2_extz.c:6:139: style:inconclusive: Function 'ksw_extz' argument 9 names different: declaration 'e' definition 'gape'. [funcArgNamesDifferent]
diamond-2.1.11/src/lib/ksw2/ksw2.h:62:23: note: Function 'ksw_extz' argument 9 names different: declaration 'e' definition 'gape'.
diamond-2.1.11/src/lib/ksw2/ksw2_extz.c:6:139: note: Function 'ksw_extz' argument 9 names different: declaration 'e' definition 'gape'.
diamond-2.1.11/src/lib/ksw2/ksw2_extz.c:40:11: style: Variable 'q' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/output/daa/merge.cpp:34:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable file_name [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/daa/merge.cpp:83:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable input_ref_file [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/daa/merge.cpp:50:16: style: Variable 'size' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/output/daa/merge.cpp:50:11: style: Variable 'size' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/output/daa/view.cpp:101:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable forwardonly [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/daa/view.cpp:141:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable daa_file [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/target_culling.h:51:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INCLUDE [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/target_culling.h:70:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable INCLUDE [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/target_culling.h:93:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable taxon_k [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/target_culling.h:102:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable taxon_k [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/target_culling.h:127:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable toppercent [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/target_culling.h:142:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable toppercent [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/join_blocks.cpp:55:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NO_AUTODETECT [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/join_blocks.cpp:228:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable target_dict_id [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/join_blocks.cpp:292:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ALIGNED [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/join_blocks.cpp:343:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable multiprocessing [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/daa/view.cpp:65:2: warning: Member variable 'ViewFetcher::n' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/output/daa/view.cpp:65:2: warning: Member variable 'ViewFetcher::query_num' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/output/output_format.cpp:57:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NONE [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/output_format.cpp:78:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable blastx [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/output_format.cpp:113:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NONE [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/output_format.cpp:149:108: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable FASTA_HEADER_SEP [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/output_format.cpp:177:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable output_format [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/output_format.cpp:217:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable command [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/daa/view.cpp:65:2: style: Struct 'ViewFetcher' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/output/daa/view.cpp:87:69: style: Parameter 'format' can be declared as reference to const [constParameterReference]
diamond-2.1.11/src/output/output_format.cpp:101:3: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/output/output_format.cpp:167:21: style: Parameter 'hsp' can be declared as reference to const [constParameterReference]
diamond-2.1.11/src/output/output_sink.cpp:44:4: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable verbose_stream [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/output_sink.cpp:38:56: style: Variable 't0' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/output/paf_format.cpp:25:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable id_delimiters [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/paf_format.cpp:32:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable id_delimiters [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/sam_format.cpp:45:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable alphabet [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/sam_format.cpp:86:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable id_delimiters [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/sam_format.cpp:94:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable id_delimiters [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/sam_format.cpp:137:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable version_string [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/target_culling.cpp:23:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable query_range_culling [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/taxon_format.cpp:47:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable include_lineage [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/taxon_format.cpp:61:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/taxon_format.cpp:68:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable id_delimiters [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/target_culling.h:43:2: style: Struct 'GlobalCulling' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/output/target_culling.h:116:2: style: Struct 'RangeCulling' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/output/target_culling.h:48:33: style: The function 'cull' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/output/target_culling.h:32:33: note: Virtual function in base class
diamond-2.1.11/src/output/target_culling.h:48:33: note: Function in derived class
diamond-2.1.11/src/output/target_culling.h:67:14: style: The function 'cull' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/output/target_culling.h:33:14: note: Virtual function in base class
diamond-2.1.11/src/output/target_culling.h:67:14: note: Function in derived class
diamond-2.1.11/src/output/target_culling.h:88:15: style: The function 'add' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/output/target_culling.h:34:15: note: Virtual function in base class
diamond-2.1.11/src/output/target_culling.h:88:15: note: Function in derived class
diamond-2.1.11/src/output/target_culling.h:97:15: style: The function 'add' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/output/target_culling.h:35:15: note: Virtual function in base class
diamond-2.1.11/src/output/target_culling.h:97:15: note: Function in derived class
diamond-2.1.11/src/output/target_culling.h:106:11: style: The destructor '~GlobalCulling' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/output/target_culling.h:36:11: note: Virtual destructor in base class
diamond-2.1.11/src/output/target_culling.h:106:11: note: Destructor in derived class
diamond-2.1.11/src/output/target_culling.h:119:33: style: The function 'cull' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/output/target_culling.h:32:33: note: Virtual function in base class
diamond-2.1.11/src/output/target_culling.h:119:33: note: Function in derived class
diamond-2.1.11/src/output/target_culling.h:135:14: style: The function 'cull' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/output/target_culling.h:33:14: note: Virtual function in base class
diamond-2.1.11/src/output/target_culling.h:135:14: note: Function in derived class
diamond-2.1.11/src/output/target_culling.h:149:15: style: The function 'add' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/output/target_culling.h:34:15: note: Virtual function in base class
diamond-2.1.11/src/output/target_culling.h:149:15: note: Function in derived class
diamond-2.1.11/src/output/target_culling.h:154:15: style: The function 'add' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/output/target_culling.h:35:15: note: Virtual function in base class
diamond-2.1.11/src/output/target_culling.h:154:15: note: Function in derived class
diamond-2.1.11/src/output/target_culling.h:159:11: style: The destructor '~RangeCulling' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/output/target_culling.h:36:11: note: Virtual destructor in base class
diamond-2.1.11/src/output/target_culling.h:159:11: note: Destructor in derived class
diamond-2.1.11/src/output/join_blocks.cpp:85:2: warning: Member variable 'JoinFetcher::query_id' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/output/join_blocks.cpp:85:2: warning: Member variable 'JoinFetcher::unaligned_from' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/output/join_blocks.cpp:85:2: style: Struct 'JoinFetcher' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/output/join_blocks.cpp:113:2: style: Struct 'JoinWriter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/output/join_blocks.cpp:129:28: style: Redundant condition: !rhs.same_subject_. 'A || (!A && B)' is equivalent to 'A || B' [redundantCondition]
diamond-2.1.11/src/output/join_blocks.cpp:134:28: style: Redundant condition: !rhs.same_subject_. 'A || (!A && B)' is equivalent to 'A || B' [redundantCondition]
diamond-2.1.11/src/run/config.cpp:43:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable multiprocessing [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/xml_format.cpp:21:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable xml_blord_format [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/xml_format.cpp:83:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/xml_format.cpp:116:77: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable XML [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/output/xml_format.cpp:146:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/run/config.cpp:27:9: warning: Member variable 'Config::extension_mode' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/run/config.cpp:27:9: warning: Member variable 'Config::seed_complexity_cut' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/run/config.cpp:27:9: warning: Member variable 'Config::freq_sd' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/run/config.cpp:27:9: warning: Member variable 'Config::hamming_filter_id' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/run/config.cpp:27:9: warning: Member variable 'Config::ungapped_evalue' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/run/config.cpp:27:9: warning: Member variable 'Config::ungapped_evalue_short' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/run/config.cpp:27:9: warning: Member variable 'Config::gapped_filter_evalue' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/run/config.cpp:27:9: warning: Member variable 'Config::index_chunks' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/run/config.cpp:27:9: warning: Member variable 'Config::seedp_bits' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/run/config.cpp:27:9: warning: Member variable 'Config::query_bins' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/run/config.cpp:27:9: warning: Member variable 'Config::current_query_block' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/run/config.cpp:27:9: warning: Member variable 'Config::current_ref_block' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/run/config.cpp:27:9: warning: Member variable 'Config::blocked_processing' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/run/config.cpp:27:9: warning: Member variable 'Config::db_seqs' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/run/config.cpp:27:9: warning: Member variable 'Config::db_letters' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/run/config.cpp:27:9: warning: Member variable 'Config::ref_blocks' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/run/config.cpp:153:14: performance:inconclusive: Technically the member function 'Search::Config::free' can be static (but you may consider moving to unnamed namespace). [functionStatic]
diamond-2.1.11/src/run/config.h:87:7: note: Technically the member function 'Search::Config::free' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/run/config.cpp:153:14: note: Technically the member function 'Search::Config::free' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/run/config.h:62:2: style: Struct 'Round' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/run/config.cpp:69:26: style: Redundant condition: !sensitivity.empty(). 'A || (!A && B)' is equivalent to 'A || B' [redundantCondition]
diamond-2.1.11/src/run/config.cpp:57:16: style: Local variable 'target' shadows outer variable [shadowVariable]
diamond-2.1.11/src/run/config.h:120:52: note: Shadowed declaration
diamond-2.1.11/src/run/config.cpp:57:16: note: Shadow variable
diamond-2.1.11/src/run/main.cpp:95:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable config [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/search/kmer_ranking.cpp:28:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/run/tools.cpp:50:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable database [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/run/tools.cpp:57:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable database [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/run/tools.cpp:96:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/run/tools.cpp:126:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable input_value_traits [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/run/tools.cpp:155:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/run/tools.cpp:184:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable op_substitution [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/run/tools.cpp:198:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable input_value_traits [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/run/tools.cpp:212:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable input_value_traits [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/run/tools.cpp:227:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable input_value_traits [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/search/kmer_ranking.h:15:6: style:inconclusive: Technically the member function 'Search::KmerRanking::highest_ranking' can be const. [functionConst]
diamond-2.1.11/src/search/kmer_ranking.h:13:2: style: Struct 'KmerRanking' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/search/kmer_ranking.cpp:17:105: style: Parameter 'query_seed_hits' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/search/kmer_ranking.cpp:17:146: style: Parameter 'ref_seed_hits' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/search/seed_complexity.cpp:44:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE_AA [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/search/seed_complexity.cpp:60:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE_AA [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/search/seed_complexity.cpp:81:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SPACED_FACTOR [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/search/seed_complexity.cpp:104:15: style: Local variable 'p' shadows outer variable [shadowVariable]
diamond-2.1.11/src/search/seed_complexity.cpp:92:17: note: Shadowed declaration
diamond-2.1.11/src/search/seed_complexity.cpp:104:15: note: Shadow variable
diamond-2.1.11/src/run/double_indexed.cpp:87:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable parallel_tmpdir [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/run/double_indexed.cpp:92:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable parallel_tmpdir [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/run/double_indexed.cpp:98:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable target_indexed [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/run/double_indexed.cpp:116:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable threads_ [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/run/double_indexed.cpp:258:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable query_aligned [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/run/double_indexed.cpp:449:60: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SELF_ALN_SCORES [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/run/double_indexed.cpp:552:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable multiprocessing [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/run/double_indexed.cpp:744:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable align_mode [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/run/tools.cpp:127:20: style: Variable 'max' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/run/tools.cpp:127:16: style: Variable 'max' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/search/hit.h:77:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable query_contexts [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/search/hit.h:81:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable query_contexts [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/search/hit.h:84:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable query_contexts [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/search/hit.h:93:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable d [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/search/setup.cpp:305:114: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SeedOffset [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/search/setup.cpp:313:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sensitivity [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/search/setup.cpp:324:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable global_ranking_targets [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/search/setup.cpp:330:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable swipe_all [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/search/setup.cpp:347:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable sensitivity [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/search/stage0.cpp:62:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable memory_order_relaxed [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/search/stage0.cpp:76:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable global_ranking_targets [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/search/stage0.cpp:95:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable query_seqs [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/search/hit.h:50:2: warning: Member variable 'Hit::score_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/search/finger_print.h:135:2: style: Struct 'Byte_finger_print_48' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/search/hit.h:192:21: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/search/hit.h:227:13: style: Local variable 'x' shadows outer variable [shadowVariable]
diamond-2.1.11/src/search/hit.h:219:12: note: Shadowed declaration
diamond-2.1.11/src/search/hit.h:227:13: note: Shadow variable
diamond-2.1.11/src/run/double_indexed.cpp:441:8: style: The scope of the variable 'db_file' can be reduced. [variableScope]
diamond-2.1.11/src/run/double_indexed.cpp:617:13: style: Local variable 'timer' shadows outer variable [shadowVariable]
diamond-2.1.11/src/run/double_indexed.cpp:599:12: note: Shadowed declaration
diamond-2.1.11/src/run/double_indexed.cpp:617:13: note: Shadow variable
diamond-2.1.11/src/run/double_indexed.cpp:322:21: style: Variable 'mp_last_chunk' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/run/double_indexed.cpp:322:7: style: Variable 'mp_last_chunk' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/stats/score_matrix.h:131:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable lambda [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/stats/score_matrix.h:136:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable K [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/stats/cbs.cpp:73:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE_AA [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/stats/cbs.cpp:79:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable comp_based_stats [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/stats/cbs.cpp:94:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable comp_based_stats [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/stats/score_matrix.h:211:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable alphabet_size [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/stats/score_matrix.h:226:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/search/sse_dist.h:189:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SEED_MASK [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/search/left_most.h:34:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable shapes [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/search/stage2.h:47:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable short_query_max_len [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/search/stage2.h:57:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable query_translated [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/search/stage2.h:78:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CHANNELS [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/search/stage2.h:151:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TENTATIVE_MATCHES1 [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/search/stage1.h:56:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable block_id [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/search/stage1.h:85:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable block_id [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/search/stage1.h:115:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable vs [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/search/stage1.h:137:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable vs [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/search/stage1.h:158:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable vs [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/search/stage1.h:181:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable vs [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/search/stage1.h:206:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable tile_size [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/search/stage1.h:247:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable vs [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/search/stage1.h:286:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable vs [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/search/stage1.h:322:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable vs [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/search/stage1.h:343:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable lin_stage1 [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/search/stage1.h:359:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable lin_stage1 [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/stats/comp_based_stats.cpp:394:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable MASK_LETTER [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/stats/comp_based_stats.cpp:437:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE_AA [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/stats/comp_based_stats.cpp:465:87: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE_AA [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/stats/comp_based_stats.cpp:501:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AMINO_ACID_COUNT [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/stats/comp_based_stats.cpp:542:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE_AA [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/stats/cbs.h:36:5: warning:inconclusive: Member variable 'TargetMatrix::score_min' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/stats/cbs.h:36:5: warning:inconclusive: Member variable 'TargetMatrix::score_max' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/stats/score_matrix.h:39:2: warning: Member variable 'ScoreMatrix::standard_matrix_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/stats/score_matrix.h:39:2: warning: Member variable 'ScoreMatrix::score_array_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/stats/score_matrix.h:39:2: warning: Member variable 'ScoreMatrix::gap_open_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/stats/score_matrix.h:39:2: warning: Member variable 'ScoreMatrix::gap_extend_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/stats/score_matrix.h:39:2: warning: Member variable 'ScoreMatrix::frame_shift_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/stats/score_matrix.h:39:2: warning: Member variable 'ScoreMatrix::db_letters_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/stats/score_matrix.h:39:2: warning: Member variable 'ScoreMatrix::scale_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/stats/score_matrix.h:39:2: warning: Member variable 'ScoreMatrix::bias_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/stats/score_matrix.h:39:2: warning: Member variable 'ScoreMatrix::ideal_lambda_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/stats/score_matrix.h:39:2: warning: Member variable 'ScoreMatrix::background_scores_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/stats/score_matrix.h:208:3: warning:inconclusive: Member variable 'Scores < int8_t >::data' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/stats/score_matrix.h:208:3: warning:inconclusive: Member variable 'Scores < int >::data' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/stats/score_matrix.h:208:3: warning:inconclusive: Member variable 'Scores < uint8_t >::data' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/stats/score_matrix.h:208:3: warning:inconclusive: Member variable 'Scores < int16_t >::data' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/stats/score_matrix.h:124:9: performance:inconclusive: Technically the member function 'ScoreMatrix::bitscore_norm' can be static (but you may consider moving to unnamed namespace). [functionStatic]
diamond-2.1.11/src/stats/score_matrix.h:209:3: style: Struct 'Scores < int8_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/stats/score_matrix.h:209:3: style: Struct 'Scores < int >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/stats/score_matrix.h:209:3: style: Struct 'Scores < uint8_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/stats/score_matrix.h:209:3: style: Struct 'Scores < int16_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/stats/score_matrix.h:196:14: performance: Function 'name()' should return member 'name_' by const reference. [returnByReference]
diamond-2.1.11/src/stats/hauser_correction.cpp:59:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cbs_window [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/stats/hauser_correction.cpp:153:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE_AA [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/stats/hauser_correction.h:32:2: style: Struct 'HauserCorrection' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/search/stage1.h:273:14: style: Local variable 'qlen' shadows outer variable [shadowVariable]
diamond-2.1.11/src/search/stage1.h:256:13: note: Shadowed declaration
diamond-2.1.11/src/search/stage1.h:273:14: note: Shadow variable
diamond-2.1.11/src/search/stage1.h:310:14: style: Local variable 'tlen' shadows outer variable [shadowVariable]
diamond-2.1.11/src/search/stage1.h:295:13: note: Shadowed declaration
diamond-2.1.11/src/search/stage1.h:310:14: note: Shadow variable
diamond-2.1.11/src/search/sse_dist.h:137:11: portability: Shifting signed 32-bit value by 31 bits is implementation-defined behaviour. See condition at line 136. [shiftTooManyBitsSigned]
diamond-2.1.11/src/search/sse_dist.h:136:10: note: Assuming that condition 'len<32' is not redundant
diamond-2.1.11/src/search/sse_dist.h:137:11: note: Shift
diamond-2.1.11/src/stats/comp_based_stats.cpp:87:11: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/stats/comp_based_stats.cpp:89:18: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/stats/comp_based_stats.cpp:309:18: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/stats/comp_based_stats.cpp:84:9: style: The scope of the variable 'i' can be reduced. [variableScope]
diamond-2.1.11/src/stats/comp_based_stats.cpp:131:27: style: Parameter 'probs' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/stats/comp_based_stats.cpp:359:24: style: Parameter 'M' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/stats/comp_based_stats.cpp:552:97: warning: Uninitialized variable: bg [uninitvar]
diamond-2.1.11/src/stats/comp_based_stats.cpp:544:26: note: Assuming condition is false
diamond-2.1.11/src/stats/comp_based_stats.cpp:552:97: note: Uninitialized variable: bg
diamond-2.1.11/src/stats/comp_based_stats.cpp:389:20: style: Variable 'cols' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/stats/comp_based_stats.cpp:389:15: style: Variable 'cols' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/stats/matrix_adjust_eigen.cpp:53:1: debug: Failed to parse 'typedef decltype ( Matrix < float , 2 * N , 1 > ( ) . head < 2 * N - 1 > ( ) ) Block2N ;'. The checking continues anyway. [simplifyTypedef]
diamond-2.1.11/src/stats/matrix_adjust_eigen.cpp:320:45: style: Parameter 'scores' can be declared as reference to const [constParameterReference]
diamond-2.1.11/src/stats/matrix_adjust_eigen.cpp:208:7: style: Variable 'n' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/stats/stats.cpp:46:0: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm]
diamond-2.1.11/src/stats/matrix_adjust.cpp:914:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE_AA [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/stats/matrix_adjust.cpp:1021:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE_AA [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/stats/matrix_adjust.cpp:1085:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/stats/matrix_adjust.cpp:1271:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AMINO_ACID_COUNT [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/stats/score_matrix.h:181:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Lambda [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/stats/score_matrix.cpp:40:99: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable u [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/stats/score_matrix.cpp:66:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable K [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/stats/score_matrix.cpp:73:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable alphabet_size [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/stats/score_matrix.cpp:82:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable alphabet_size [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/stats/score_matrix.cpp:108:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AMINO_ACID_COUNT [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/stats/score_matrix.cpp:169:16: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE_AA [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/stats/score_matrix.cpp:226:77: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable K [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/stats/score_matrix.cpp:230:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable min_bit_score [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/stats/score_matrix.cpp:241:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable background_freqs [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/stats/score_matrix.cpp:190:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable alphabet_size [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/test/test.cpp:53:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable config [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/test/test.cpp:96:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bootstrap [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/tools/benchmark.cpp:58:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WIDTH [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/tools/benchmark.cpp:112:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable message_stream [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/tools/benchmark.cpp:339:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable message_stream [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/tools/benchmark.cpp:436:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable message_stream [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/tools/benchmark.cpp:448:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE_AA [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/tools/benchmark.cpp:479:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable type [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/tools/benchmark.cpp:450:31: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/tools/benchmark.cpp:105:16: style: Variable 'score' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/tools/benchmark_io.cpp:63:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable message_stream [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/tools/benchmark_io.cpp:94:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chunk_size [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/tools/benchmark_io.cpp:119:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GIGABYTES [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/tools/benchmark_io.cpp:134:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GIGABYTES [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/tools/benchmark_io.cpp:156:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable database [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/tools/benchmark_io.cpp:221:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable GIGABYTES [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/tools/benchmark_io.cpp:235:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable type [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/stats/matrix_adjust.cpp:469:22: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/stats/matrix_adjust.cpp:481:13: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/stats/matrix_adjust.cpp:485:13: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/stats/matrix_adjust.cpp:779:16: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/stats/matrix_adjust.cpp:781:16: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/stats/matrix_adjust.cpp:784:9: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/stats/matrix_adjust.cpp:786:18: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/stats/matrix_adjust.cpp:788:17: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/stats/matrix_adjust.cpp:680:12: style: The scope of the variable 'temp' can be reduced. [variableScope]
diamond-2.1.11/src/stats/matrix_adjust.cpp:1172:12: style: The scope of the variable 'temp' can be reduced. [variableScope]
diamond-2.1.11/src/tools/find_shapes.cpp:111:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/tools/find_shapes.cpp:130:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/stats/matrix_adjust.cpp:609:13: style: Variable 'Dinv' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/stats/matrix_adjust.cpp:610:13: style: Variable 'grad_re' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/stats/score_matrix.cpp:45:83: style:inconclusive: Function 'ScoreMatrix' argument 4 names different: declaration 'frame_shift' definition 'frameshift'. [funcArgNamesDifferent]
diamond-2.1.11/src/stats/score_matrix.h:40:75: note: Function 'ScoreMatrix' argument 4 names different: declaration 'frame_shift' definition 'frameshift'.
diamond-2.1.11/src/stats/score_matrix.cpp:45:83: note: Function 'ScoreMatrix' argument 4 names different: declaration 'frame_shift' definition 'frameshift'.
diamond-2.1.11/src/stats/matrix_adjust.cpp:1216:24: style: Variable 'corr_factor' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/stats/matrix_adjust.cpp:1231:21: style: Variable 'corr_factor' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/stats/score_matrix.cpp:109:12: style: Unused variable: s [unusedVariable]
diamond-2.1.11/src/tools/find_shapes.cpp:69:5: style: Consider using std::any_of algorithm instead of a raw loop. [useStlAlgorithm]
diamond-2.1.11/src/tools/find_shapes.cpp:81:6: style: Consider using std::count_if algorithm instead of a raw loop. [useStlAlgorithm]
diamond-2.1.11/src/tools/greedy_vertex_cover.cpp:53:93: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DEFAULT_MEMBER_COVER [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/tools/rocid.cpp:64:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable message_stream [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/tools/rocid.cpp:87:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable family_map [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/tools/roc.cpp:77:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cut_bar [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/tools/roc.cpp:120:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable log_evalue_scale [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/tools/roc.cpp:137:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable query_count [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/tools/roc.cpp:156:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable output_hits [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/tools/roc.cpp:198:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable check_multi_target [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/tools/roc.cpp:299:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable output_hits [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/tools/roc.cpp:353:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable family_map [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/tools/rocid.cpp:85:9: style: Variable 'n' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/tools/tools.cpp:40:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chunk_size [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/tools/tools.cpp:71:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/tools/tools.cpp:93:65: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable database [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/tools/tools.cpp:124:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STRING [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/tools/tools.cpp:90:8: performance:inconclusive: Technically the member function 'list_seeds::Callback::finish' can be static (but you may consider moving to unnamed namespace). [functionStatic]
diamond-2.1.11/src/tools/roc.cpp:117:6: style:inconclusive: Technically the member function 'Histogram::bin' can be const. [functionConst]
diamond-2.1.11/src/tools/roc.cpp:65:2: style: Struct 'FamilyMapping' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/tools/tools.cpp:116:9: style: The scope of the variable 's' can be reduced. [variableScope]
diamond-2.1.11/src/tools/roc.cpp:319:10: style: The scope of the variable 'buf' can be reduced. [variableScope]
diamond-2.1.11/src/tools/roc.cpp:177:13: style: Local variable 'i' shadows outer variable [shadowVariable]
diamond-2.1.11/src/tools/roc.cpp:168:9: note: Shadowed declaration
diamond-2.1.11/src/tools/roc.cpp:177:13: note: Shadow variable
diamond-2.1.11/src/tools/roc.cpp:326:33: style: Local variable 'lock' shadows outer variable [shadowVariable]
diamond-2.1.11/src/tools/roc.cpp:323:33: note: Shadowed declaration
diamond-2.1.11/src/tools/roc.cpp:326:33: note: Shadow variable
diamond-2.1.11/src/tools/tsv.cpp:10:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable tsv_read_size [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/tools/tsv.cpp:24:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable tsv_read_size [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/tools/roc.cpp:379:38: style: Variable 'buf_size' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/tools/roc.cpp:379:29: style: Variable 'buf_size' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/util/io/exceptions.h:32:2: style: Struct 'FileOpenException' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/io/exceptions.h:39:2: style: Struct 'FileReadException' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/io/exceptions.h:46:2: style: Struct 'FileWriteException' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/io/stream_entity.h:26:2: style: Struct 'StreamEntity' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/io/stream_entity.h:30:2: style: Struct 'StreamEntity' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/io/input_stream_buffer.h:30:2: style: Struct 'InputStreamBuffer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/io/compressed_stream.h:27:2: style: Struct 'ZlibSource' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/io/compressed_stream.h:41:2: style: Struct 'ZlibSink' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/io/compressed_stream.h:28:17: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/util/io/stream_entity.h:46:17: note: Virtual function in base class
diamond-2.1.11/src/util/io/compressed_stream.h:28:17: note: Function in derived class
diamond-2.1.11/src/util/io/compressed_stream.h:29:15: style: The function 'close' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/util/io/stream_entity.h:53:15: note: Virtual function in base class
diamond-2.1.11/src/util/io/compressed_stream.h:29:15: note: Function in derived class
diamond-2.1.11/src/util/io/compressed_stream.h:30:15: style: The function 'rewind' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/util/io/stream_entity.h:34:15: note: Virtual function in base class
diamond-2.1.11/src/util/io/compressed_stream.h:30:15: note: Function in derived class
diamond-2.1.11/src/util/io/compressed_stream.h:42:15: style: The function 'close' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/util/io/stream_entity.h:53:15: note: Virtual function in base class
diamond-2.1.11/src/util/io/compressed_stream.h:42:15: note: Function in derived class
diamond-2.1.11/src/util/io/compressed_stream.h:43:15: style: The function 'write' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/util/io/stream_entity.h:61:15: note: Virtual function in base class
diamond-2.1.11/src/util/io/compressed_stream.h:43:15: note: Function in derived class
diamond-2.1.11/src/util/io/compressed_stream.cpp:47:18: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/util/io/compressed_stream.cpp:58:19: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/util/io/compressed_stream.cpp:104:17: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/util/io/compressed_stream.cpp:109:19: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/util/io/compressed_stream.cpp:101:64: style:inconclusive: Function 'deflate_loop' argument 3 names different: declaration 'code' definition 'flush'. [funcArgNamesDifferent]
diamond-2.1.11/src/util/io/compressed_stream.h:45:55: note: Function 'deflate_loop' argument 3 names different: declaration 'code' definition 'flush'.
diamond-2.1.11/src/util/io/compressed_stream.cpp:101:64: note: Function 'deflate_loop' argument 3 names different: declaration 'code' definition 'flush'.
diamond-2.1.11/src/util/io/compressed_stream.cpp:64:8: style: Local variable 'ret' shadows outer variable [shadowVariable]
diamond-2.1.11/src/util/io/compressed_stream.cpp:62:7: note: Shadowed declaration
diamond-2.1.11/src/util/io/compressed_stream.cpp:64:8: note: Shadow variable
diamond-2.1.11/src/util/io/compressed_stream.cpp:107:16: style: Local variable 'chunk_size' shadows outer variable [shadowVariable]
diamond-2.1.11/src/util/io/compressed_stream.h:46:22: note: Shadowed declaration
diamond-2.1.11/src/util/io/compressed_stream.cpp:107:16: note: Shadow variable
diamond-2.1.11/src/util/command_line_parser.cpp:114:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/command_line_parser.cpp:131:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/io/deserializer.h:104:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/io/deserializer.h:119:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/io/deserializer.h:33:2: style: Struct 'Deserializer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/io/deserializer.cpp:87:13: style: Condition 'avail()<n' is always true [knownConditionTrueFalse]
diamond-2.1.11/src/util/io/deserializer.cpp:83:14: note: Assuming that condition 'avail()>=n' is not redundant
diamond-2.1.11/src/util/io/deserializer.cpp:87:13: note: Condition 'avail()<n' is always true
diamond-2.1.11/src/util/io/deserializer.h:108:10: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/util/io/deserializer.h:112:21: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/util/io/deserializer.h:119:19: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/util/io/deserializer.h:132:21: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/util/io/deserializer.h:132:40: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/util/io/deserializer.h:152:21: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/util/io/deserializer.h:152:40: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/util/io/deserializer.cpp:103:20: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/util/io/deserializer.cpp:103:39: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/util/util.h:95:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable n [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/util.h:101:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable n [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/log_stream.h:40:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/log_stream.h:102:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/log_stream.h:129:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable flush [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/algo/greedy_vertex_cover.cpp:130:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/options/option.h:62:2: warning: Member variable 'Option < double >::value_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/util/options/option.h:62:2: warning: Member variable 'Option < double >::base_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/util/options/option.h:105:2: warning: Member variable 'Option < int64_t >::value_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/util/options/option.h:105:2: warning: Member variable 'Option < int64_t >::base_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/util/options/option.h:30:2: warning: Member variable 'Option < std :: string >::base_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/util/options/option.h:30:2: warning: Member variable 'Option < std :: vector < std :: string > >::base_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/util/command_line_parser.cpp:111:25: style:inconclusive: Technically the member function 'CommandLineParser::print_help' can be const. [functionConst]
diamond-2.1.11/src/util/command_line_parser.h:248:7: note: Technically the member function 'CommandLineParser::print_help' can be const.
diamond-2.1.11/src/util/command_line_parser.cpp:111:25: note: Technically the member function 'CommandLineParser::print_help' can be const.
diamond-2.1.11/src/util/command_line_parser.cpp:128:25: style:inconclusive: Technically the member function 'CommandLineParser::print_documentation' can be const. [functionConst]
diamond-2.1.11/src/util/command_line_parser.h:249:10: note: Technically the member function 'CommandLineParser::print_documentation' can be const.
diamond-2.1.11/src/util/command_line_parser.cpp:128:25: note: Technically the member function 'CommandLineParser::print_documentation' can be const.
diamond-2.1.11/src/util/command_line_parser.h:209:3: style: Struct 'AddFunc' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/command_line_parser.h:178:15: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/util/options/option.h:17:15: note: Virtual function in base class
diamond-2.1.11/src/util/command_line_parser.h:178:15: note: Function in derived class
diamond-2.1.11/src/util/command_line_parser.h:184:15: style: The function 'present' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/util/options/option.h:18:15: note: Virtual function in base class
diamond-2.1.11/src/util/command_line_parser.h:184:15: note: Function in derived class
diamond-2.1.11/src/util/command_line_parser.h:187:15: style: The function 'set_default' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/util/options/option.h:19:15: note: Virtual function in base class
diamond-2.1.11/src/util/command_line_parser.h:187:15: note: Function in derived class
diamond-2.1.11/src/util/command_line_parser.h:191:11: style: The destructor '~OptionDesc' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/util/options/option.h:20:11: note: Virtual destructor in base class
diamond-2.1.11/src/util/command_line_parser.h:191:11: note: Destructor in derived class
diamond-2.1.11/src/util/command_line_parser.cpp:135:22: style: Local variable 'i' shadows outer variable [shadowVariable]
diamond-2.1.11/src/util/command_line_parser.cpp:133:15: note: Shadowed declaration
diamond-2.1.11/src/util/command_line_parser.cpp:135:22: note: Shadow variable
diamond-2.1.11/src/util/io/file_sink.cpp:42:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_WRONLY [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/io/file_sink.cpp:58:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable S_IRUSR [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/io/file_sink.cpp:92:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/io/file_sink.cpp:76:2: warning: Struct 'FileSink' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
diamond-2.1.11/src/util/io/file_sink.cpp:76:2: warning: Struct 'FileSink' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
diamond-2.1.11/src/util/io/file_sink.cpp:76:2: warning: Struct 'FileSink' does not have a destructor which is recommended since it has dynamic memory/resource allocation(s). [noDestructor]
diamond-2.1.11/src/util/io/file_sink.h:29:2: style: Struct 'FileSink' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/io/file_sink.h:47:8: style: Class 'FileSink' is unsafe, 'FileSink::f_' can leak by wrong usage. [unsafeClassCanLeak]
diamond-2.1.11/src/util/io/file_sink.cpp:105:19: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/util/io/file_sink.cpp:105:9: style: Variable 'n' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/util/io/file_source.cpp:52:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_RDONLY [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/io/file_source.cpp:57:2: warning: Struct 'FileSource' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
diamond-2.1.11/src/util/io/file_source.cpp:57:2: warning: Struct 'FileSource' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
diamond-2.1.11/src/util/io/file_source.h:24:2: style: Struct 'FileSource' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/io/file_source.h:42:3: style: The destructor '~FileSource' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/util/io/stream_entity.h:89:11: note: Virtual destructor in base class
diamond-2.1.11/src/util/io/file_source.h:42:3: note: Destructor in derived class
diamond-2.1.11/src/util/io/file_source.cpp:81:31: style:inconclusive: Function 'seek' argument 1 names different: declaration 'p' definition 'pos'. [funcArgNamesDifferent]
diamond-2.1.11/src/util/io/file_source.h:27:28: note: Function 'seek' argument 1 names different: declaration 'p' definition 'pos'.
diamond-2.1.11/src/util/io/file_source.cpp:81:31: note: Function 'seek' argument 1 names different: declaration 'p' definition 'pos'.
diamond-2.1.11/src/util/io/serializer.h:80:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/io/serializer.h:95:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/io/input_file.cpp:114:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/io/input_stream_buffer.cpp:29:20: warning: Member variable 'InputStreamBuffer::file_offset_' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/util/io/input_stream_buffer.cpp:49:38: style:inconclusive: Function 'seek' argument 1 names different: declaration 'p' definition 'pos'. [funcArgNamesDifferent]
diamond-2.1.11/src/util/io/input_stream_buffer.h:32:28: note: Function 'seek' argument 1 names different: declaration 'p' definition 'pos'.
diamond-2.1.11/src/util/io/input_stream_buffer.cpp:49:38: note: Function 'seek' argument 1 names different: declaration 'p' definition 'pos'.
diamond-2.1.11/src/util/io/output_file.h:34:14: warning: The struct 'OutputFile' defines member function with name 'file_name' also defined in its parent struct 'Serializer'. [duplInheritedMember]
diamond-2.1.11/src/util/io/serializer.h:103:14: note: Parent function 'Serializer::file_name'
diamond-2.1.11/src/util/io/output_file.h:34:14: note: Derived function 'OutputFile::file_name'
diamond-2.1.11/src/util/io/serializer.h:28:2: style: Struct 'Serializer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/io/output_file.h:27:2: style: Struct 'OutputFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/io/temp_file.h:34:2: style: Struct 'TempFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/io/temp_file.h:35:2: style: Struct 'TempFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/io/input_file.h:38:2: style: Struct 'InputFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/io/input_file.h:39:2: style: Struct 'InputFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/io/input_file.h:40:2: style: Struct 'InputFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/io/serializer.h:107:3: style: The destructor '~Serializer' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/util/io/consumer.h:6:11: note: Virtual destructor in base class
diamond-2.1.11/src/util/io/serializer.h:107:3: note: Destructor in derived class
diamond-2.1.11/src/util/io/output_file.h:34:14: performance: Function 'file_name()' should return member 'file_name_' by const reference. [returnByReference]
diamond-2.1.11/src/util/io/serializer.h:84:5: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/util/io/serializer.h:95:14: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/util/algo/algo.h:13:2: warning:inconclusive: Member variable 'Edge < int32_t >::node1' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/util/algo/algo.h:13:2: warning:inconclusive: Member variable 'Edge < int32_t >::node2' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/util/algo/algo.h:13:2: warning:inconclusive: Member variable 'Edge < int32_t >::weight' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/util/algo/algo.h:13:2: warning:inconclusive: Member variable 'Edge < int64_t >::node1' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/util/algo/algo.h:13:2: warning:inconclusive: Member variable 'Edge < int64_t >::node2' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/util/algo/algo.h:13:2: warning:inconclusive: Member variable 'Edge < int64_t >::weight' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/util/log_stream.h:132:17: performance:inconclusive: Technically the member function 'TaskTimer::get_stream' can be static (but you may consider moving to unnamed namespace). [functionStatic]
diamond-2.1.11/src/util/data_structures/flat_array.h:205:4: performance:inconclusive: Technically the member function 'FlatArray < Edge < int32_t > , int64_t >::sum' can be static (but you may consider moving to unnamed namespace). [functionStatic]
diamond-2.1.11/src/util/data_structures/flat_array.h:205:4: performance:inconclusive: Technically the member function 'FlatArray < Edge < int64_t > , int64_t >::sum' can be static (but you may consider moving to unnamed namespace). [functionStatic]
diamond-2.1.11/src/util/util.h:53:2: style: Struct 'Sd' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/util.h:133:2: style: Struct 'IndexIterator' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/log_stream.h:33:2: style: Struct 'MessageStream' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/log_stream.h:60:2: style: Struct 'TaskTimer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/log_stream.h:67:2: style: Struct 'TaskTimer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/log_stream.h:77:2: style: Struct 'TaskTimer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/data_structures/flat_array.h:40:2: style: Struct 'FlatArray < Edge < int32_t > , int64_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/data_structures/flat_array.h:40:2: style: Struct 'FlatArray < Edge < int64_t > , int64_t >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/io/output_file.cpp:69:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/data_structures/flat_array.h:256:2: style: Label 'std' is not used. [unusedLabel]
diamond-2.1.11/src/util/data_structures/flat_array.h:209:12: style: Local variable 'size' shadows outer function [shadowFunction]
diamond-2.1.11/src/util/data_structures/flat_array.h:81:4: note: Shadowed declaration
diamond-2.1.11/src/util/data_structures/flat_array.h:209:12: note: Shadow variable
diamond-2.1.11/src/util/algo/transform_iterator.h:30:48: performance:inconclusive: Function parameter 'd' should be passed by const reference. [passedByValue]
diamond-2.1.11/src/util/io/output_stream_buffer.h:26:2: style: Struct 'OutputStreamBuffer' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/util.h:182:5: style: Consider using std::transform algorithm instead of a raw loop. [useStlAlgorithm]
diamond-2.1.11/src/util/io/zstd_stream.h:8:2: style: Struct 'ZstdSink' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/io/zstd_stream.h:17:2: style: Struct 'ZstdSource' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/io/zstd_stream.h:9:15: style: The function 'close' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/util/io/stream_entity.h:53:15: note: Virtual function in base class
diamond-2.1.11/src/util/io/zstd_stream.h:9:15: note: Function in derived class
diamond-2.1.11/src/util/io/zstd_stream.h:10:15: style: The function 'write' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/util/io/stream_entity.h:61:15: note: Virtual function in base class
diamond-2.1.11/src/util/io/zstd_stream.h:10:15: note: Function in derived class
diamond-2.1.11/src/util/io/zstd_stream.h:18:17: style: The function 'read' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/util/io/stream_entity.h:46:17: note: Virtual function in base class
diamond-2.1.11/src/util/io/zstd_stream.h:18:17: note: Function in derived class
diamond-2.1.11/src/util/io/zstd_stream.h:19:15: style: The function 'close' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/util/io/stream_entity.h:53:15: note: Virtual function in base class
diamond-2.1.11/src/util/io/zstd_stream.h:19:15: note: Function in derived class
diamond-2.1.11/src/util/io/zstd_stream.h:20:15: style: The function 'rewind' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride]
diamond-2.1.11/src/util/io/stream_entity.h:34:15: note: Virtual function in base class
diamond-2.1.11/src/util/io/zstd_stream.h:20:15: note: Function in derived class
diamond-2.1.11/src/util/io/temp_file.cpp:74:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable tmpdir [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/io/text_input_file.cpp:48:21: warning: The struct 'TextInputFile' defines member function with name 'rewind' also defined in its parent struct 'Deserializer'. [duplInheritedMember]
diamond-2.1.11/src/util/io/deserializer.h:34:7: note: Parent function 'Deserializer::rewind'
diamond-2.1.11/src/util/io/text_input_file.cpp:48:21: note: Derived function 'TextInputFile::rewind'
diamond-2.1.11/src/util/io/text_input_file.h:25:2: style: Struct 'TextInputFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/io/text_input_file.h:26:2: style: Struct 'TextInputFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/io/temp_file.cpp:104:11: warning: Member variable 'TempFile::unlinked' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/util/io/text_input_file.h:27:2: style: Struct 'TextInputFile' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/io/temp_file.cpp:113:11: warning: Member variable 'TempFile::unlinked' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/util/io/temp_file.cpp:51:23: style:inconclusive: Technically the member function 'TempFileHandler::init' can be const. [functionConst]
diamond-2.1.11/src/util/io/temp_file.h:24:7: note: Technically the member function 'TempFileHandler::init' can be const.
diamond-2.1.11/src/util/io/temp_file.cpp:51:23: note: Technically the member function 'TempFileHandler::init' can be const.
diamond-2.1.11/src/util/parallel/multiprocessing.h:65:86: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value_type [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/parallel/multiprocessing.h:81:93: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value_type [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/parallel/filestack.cpp:54:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/parallel/filestack.cpp:63:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_RDWR [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/parallel/filestack.cpp:86:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable F_WRLCK [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/parallel/filestack.cpp:110:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable F_UNLCK [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/parallel/filestack.cpp:144:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/parallel/filestack.cpp:383:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/parallel/multiprocessing.cpp:70:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable binary [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/search/seed_table.cpp:26:82: style: Parameter 'out' can be declared as reference to const [constParameterReference]
diamond-2.1.11/src/util/parallel/parallelizer.cpp:72:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/parallel/parallelizer.cpp:249:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/parallel/parallelizer.cpp:260:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/parallel/parallelizer.cpp:59:15: warning: Member variable 'Parallelizer::rank' is not initialized in the constructor. [uninitMemberVar]
diamond-2.1.11/src/util/parallel/parallelizer.cpp:108:20: performance:inconclusive: Technically the member function 'Parallelizer::clear' can be static (but you may consider moving to unnamed namespace). [functionStatic]
diamond-2.1.11/src/util/parallel/parallelizer.h:37:14: note: Technically the member function 'Parallelizer::clear' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/util/parallel/parallelizer.cpp:108:20: note: Technically the member function 'Parallelizer::clear' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/util/parallel/parallelizer.cpp:124:19: style:inconclusive: Technically the member function 'Parallelizer::get_rank' can be const. [functionConst]
diamond-2.1.11/src/util/parallel/parallelizer.h:39:13: note: Technically the member function 'Parallelizer::get_rank' can be const.
diamond-2.1.11/src/util/parallel/parallelizer.cpp:124:19: note: Technically the member function 'Parallelizer::get_rank' can be const.
diamond-2.1.11/src/util/parallel/parallelizer.cpp:120:22: style:inconclusive: Technically the member function 'Parallelizer::get_id' can be const. [functionConst]
diamond-2.1.11/src/util/parallel/parallelizer.h:40:21: note: Technically the member function 'Parallelizer::get_id' can be const.
diamond-2.1.11/src/util/parallel/parallelizer.cpp:120:22: note: Technically the member function 'Parallelizer::get_id' can be const.
diamond-2.1.11/src/util/parallel/parallelizer.cpp:128:22: style:inconclusive: Technically the member function 'Parallelizer::get_work_directory' can be const. [functionConst]
diamond-2.1.11/src/util/parallel/parallelizer.h:41:21: note: Technically the member function 'Parallelizer::get_work_directory' can be const.
diamond-2.1.11/src/util/parallel/parallelizer.cpp:128:22: note: Technically the member function 'Parallelizer::get_work_directory' can be const.
diamond-2.1.11/src/util/parallel/parallelizer.cpp:132:19: style:inconclusive: Technically the member function 'Parallelizer::get_n_registered' can be const. [functionConst]
diamond-2.1.11/src/util/parallel/parallelizer.h:42:13: note: Technically the member function 'Parallelizer::get_n_registered' can be const.
diamond-2.1.11/src/util/parallel/parallelizer.cpp:132:19: note: Technically the member function 'Parallelizer::get_n_registered' can be const.
diamond-2.1.11/src/util/parallel/parallelizer.cpp:136:20: style:inconclusive: Technically the member function 'Parallelizer::is_master' can be const. [functionConst]
diamond-2.1.11/src/util/parallel/parallelizer.h:44:14: note: Technically the member function 'Parallelizer::is_master' can be const.
diamond-2.1.11/src/util/parallel/parallelizer.cpp:136:20: note: Technically the member function 'Parallelizer::is_master' can be const.
diamond-2.1.11/src/util/parallel/parallelizer.cpp:140:22: style:inconclusive: Technically the member function 'Parallelizer::get_barrier_file_name' can be const. [functionConst]
diamond-2.1.11/src/util/parallel/parallelizer.h:82:21: note: Technically the member function 'Parallelizer::get_barrier_file_name' can be const.
diamond-2.1.11/src/util/parallel/parallelizer.cpp:140:22: note: Technically the member function 'Parallelizer::get_barrier_file_name' can be const.
diamond-2.1.11/src/util/parallel/filestack.h:38:9: style: Class 'FileStack' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/parallel/parallelizer.h:40:21: performance: Function 'get_id()' should return member 'id' by const reference. [returnByReference]
diamond-2.1.11/src/util/parallel/parallelizer.h:41:21: performance: Function 'get_work_directory()' should return member 'work_directory' by const reference. [returnByReference]
diamond-2.1.11/src/util/parallel/parallelizer.cpp:232:9: style: Redundant checking of STL container element existence before removing it. [redundantIfRemove]
diamond-2.1.11/src/util/parallel/filestack.cpp:426:16: style:inconclusive: Technically the member function 'FileStack::get_max_line_length' can be const. [functionConst]
diamond-2.1.11/src/util/parallel/filestack.h:59:13: note: Technically the member function 'FileStack::get_max_line_length' can be const.
diamond-2.1.11/src/util/parallel/filestack.cpp:426:16: note: Technically the member function 'FileStack::get_max_line_length' can be const.
diamond-2.1.11/src/util/parallel/filestack.cpp:154:23: style: Condition 'line_size>0' is always true [knownConditionTrueFalse]
diamond-2.1.11/src/util/parallel/filestack.cpp:153:46: note: Assignment 'line_size=end-begin+1', assigned value is greater than 0
diamond-2.1.11/src/util/parallel/filestack.cpp:154:23: note: Condition 'line_size>0' is always true
diamond-2.1.11/src/util/parallel/filestack.cpp:396:5: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
diamond-2.1.11/src/util/parallel/filestack.cpp:411:5: style: Consecutive return, break, continue, goto or throw statements are unnecessary. [duplicateBreak]
diamond-2.1.11/src/util/parallel/filestack.cpp:129:17: style: Local variable 'size' shadows outer function [shadowFunction]
diamond-2.1.11/src/util/parallel/filestack.h:42:16: note: Shadowed declaration
diamond-2.1.11/src/util/parallel/filestack.cpp:129:17: note: Shadow variable
diamond-2.1.11/src/util/parallel/filestack.cpp:248:17: style: Local variable 'size' shadows outer function [shadowFunction]
diamond-2.1.11/src/util/parallel/filestack.h:42:16: note: Shadowed declaration
diamond-2.1.11/src/util/parallel/filestack.cpp:248:17: note: Shadow variable
diamond-2.1.11/src/util/parallel/filestack.cpp:263:14: style: Variable 'stat' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/util/parallel/filestack.cpp:266:18: style: Variable 'n' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/util/parallel/filestack.cpp:263:9: style: Variable 'stat' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/util/parallel/filestack.cpp:266:16: style: Variable 'n' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/util/parallel/filestack.cpp:401:12: style: Unused variable: buf [unusedVariable]
diamond-2.1.11/src/util/string/string.h:12:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/string/string.h:19:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/string/string.cpp:31:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fixed [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/string/string.cpp:40:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/string/string.cpp:49:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable fixed [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/string/string.cpp:124:112: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable int64_t [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/system/getRSS.cpp:29:0: error: #error "Cannot define getPeakRSS( ) or getCurrentRSS( ) for an unknown OS." [preprocessorErrorDirective]
diamond-2.1.11/src/util/system/getRSS.cpp:29:2: error: #error "Cannot define getPeakRSS( ) or getCurrentRSS( ) for an unknown OS." [preprocessorErrorDirective]
diamond-2.1.11/src/util/sequence/sequence.h:36:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DELIMITER [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/sequence/translate.h:101:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STOP_LETTER [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/table.h:67:76: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/sequence/sequence.cpp:88:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/sequence/sequence.cpp:172:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable TRUE_AA [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/sequence/sequence.cpp:188:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable STOP_LETTER [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/string/tokenizer.h:135:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ignore [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/string/string.cpp:31:97: warning: Either the condition 'div<(sizeof(SIZES)/sizeof(*SIZES))' is redundant or the array 'SIZES[6]' is accessed at index 6, which is out of bounds. [arrayIndexOutOfBoundsCond]
diamond-2.1.11/src/util/string/string.cpp:24:29: note: Assuming that condition 'div<(sizeof(SIZES)/sizeof(*SIZES))' is not redundant
diamond-2.1.11/src/util/string/string.cpp:31:97: note: Array index out of bounds
diamond-2.1.11/src/util/system/system.cpp:164:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable O_RDONLY [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/system/system.cpp:169:3: error: Resource leak: fd [resourceLeak]
diamond-2.1.11/src/util/system/system.cpp:175:3: error: Resource leak: fd [resourceLeak]
diamond-2.1.11/src/util/system/system.cpp:177:40: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/util/system/system.cpp:184:9: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/util/system/system.cpp:181:23: style: Parameter 'ptr' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/util/string/tokenizer.h:35:2: style: Struct 'TokenizerException' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/string/tokenizer.h:43:2: style: Struct 'CharDelimiter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/string/tokenizer.h:63:2: style: Struct 'StringDelimiter' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/sequence/sequence.h:36:8: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/util/sequence/sequence.cpp:81:36: style:inconclusive: Function 'get_accession' argument 1 names different: declaration 't' definition 'title'. [funcArgNamesDifferent]
diamond-2.1.11/src/util/sequence/sequence.h:61:46: note: Function 'get_accession' argument 1 names different: declaration 't' definition 'title'.
diamond-2.1.11/src/util/sequence/sequence.cpp:81:36: note: Function 'get_accession' argument 1 names different: declaration 't' definition 'title'.
diamond-2.1.11/src/util/sequence/sequence.cpp:150:14: style: Local variable 'i' shadows outer variable [shadowVariable]
diamond-2.1.11/src/util/sequence/sequence.cpp:139:9: note: Shadowed declaration
diamond-2.1.11/src/util/sequence/sequence.cpp:150:14: note: Shadow variable
diamond-2.1.11/src/util/sequence/translate.h:99:48: style: Variable 'end' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/util/sequence/sequence.cpp:44:17: style: Variable 'l' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/util/sequence/sequence.cpp:44:15: style: Variable 'l' is assigned a value that is never used. [unreadVariable]
diamond-2.1.11/src/util/text_buffer.h:82:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/text_buffer.h:273:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/enum.h:56:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable from_string [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/tsv/file.cpp:156:75: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _1 [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/tsv/merge.cpp:24:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/tsv/file.cpp:112:12: style:inconclusive: Technically the member function 'Util::Tsv::File::eof' can be const. [functionConst]
diamond-2.1.11/src/util/tsv/file.h:56:7: note: Technically the member function 'Util::Tsv::File::eof' can be const.
diamond-2.1.11/src/util/tsv/file.cpp:112:12: note: Technically the member function 'Util::Tsv::File::eof' can be const.
diamond-2.1.11/src/util/tsv/file.h:69:7: performance:inconclusive: Technically the member function 'Util::Tsv::File::read' can be static (but you may consider moving to unnamed namespace). [functionStatic]
diamond-2.1.11/src/util/tsv/file.h:95:7: style:inconclusive: Technically the member function 'Util::Tsv::File::write_record' can be const. [functionConst]
diamond-2.1.11/src/util/io/text_input_file.h:28:7: warning: The struct 'TextInputFile' defines member function with name 'rewind' also defined in its parent struct 'Deserializer'. [duplInheritedMember]
diamond-2.1.11/src/util/io/deserializer.h:34:7: note: Parent function 'Deserializer::rewind'
diamond-2.1.11/src/util/io/text_input_file.h:28:7: note: Derived function 'TextInputFile::rewind'
diamond-2.1.11/src/util/tsv/table.h:15:2: style: Struct 'Table' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/enum.h:28:2: style: Struct 'FieldValue' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/tsv/file.h:42:2: style: Struct 'Config' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/tsv/build_helper.h:10:2: style: Struct 'BuildHelper' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/tsv/file.h:86:9: performance: Function 'schema()' should return member 'schema_' by const reference. [returnByReference]
diamond-2.1.11/src/util/tsv/file.h:115:14: performance: Function 'file_name()' should return member 'file_name' by const reference. [returnByReference]
diamond-2.1.11/src/util/algo/varint.h:31:4: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/util/algo/varint.h:35:4: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/util/algo/varint.h:39:4: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/util/algo/varint.h:40:4: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/util/algo/varint.h:44:4: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/util/algo/varint.h:48:4: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/util/algo/varint.h:49:4: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/util/algo/varint.h:67:9: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/util/algo/varint.h:72:9: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/util/algo/varint.h:76:9: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/util/text_buffer.h:62:11: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/util/tsv/file.cpp:75:35: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/util/tsv/build_helper.h:36:14: style: Local variable 'it' shadows outer variable [shadowVariable]
diamond-2.1.11/src/util/tsv/build_helper.h:27:35: note: Shadowed declaration
diamond-2.1.11/src/util/tsv/build_helper.h:36:14: note: Shadow variable
diamond-2.1.11/src/util/data_structures/reorder_queue.h:60:11: style: Local variable 'size' shadows outer function [shadowFunction]
diamond-2.1.11/src/util/data_structures/reorder_queue.h:15:9: note: Shadowed declaration
diamond-2.1.11/src/util/data_structures/reorder_queue.h:60:11: note: Shadow variable
diamond-2.1.11/src/util/tsv/file.cpp:213:42: style: Parameter 'buf' can be declared as pointer to const [constParameterPointer]
diamond-2.1.11/src/util/text_buffer.h:138:9: style: Variable 'end' can be declared as pointer to const [constVariablePointer]
diamond-2.1.11/src/util/data_structures/reorder_queue.h:78:2: debug: Wrong data detected by condition !var.valueType() [DacaWrongData]
diamond-2.1.11/src/util/tsv/join.cpp:17:115: style: Parameter 'out' can be declared as reference to const [constParameterReference]
diamond-2.1.11/src/util/tsv/construct.h:32:41: debug: simplifyOperatorName: found unsimplified operator name [debug]
diamond-2.1.11/src/util/tsv/file_read.h:37:49: debug: simplifyOperatorName: found unsimplified operator name [debug]
diamond-2.1.11/src/util/tsv/construct.h:32:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/tsv/file_read.h:32:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Targs [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/tsv/record.cpp:21:21: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/util/tsv/record.cpp:33:16: style: C-style pointer casting [cstyleCast]
diamond-2.1.11/src/util/tsv/merge_mt.cpp:6:1: error: Found an exit path from function with non-void return type that has missing return statement [missingReturn]
diamond-2.1.11/src/util/tsv/construct.h:39:4: style:inconclusive: Technically the member function 'Util::Tsv::Construct < void >::operator()' can be const. [functionConst]
diamond-2.1.11/src/util/tsv/table.cpp:51:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable value_type [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/tsv/table.cpp:157:110: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable _1 [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/profiler.h:24:85: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/util.cpp:45:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/util.cpp:54:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable k [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/util.cpp:89:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/util.cpp:109:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/util.cpp:115:7: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar]
diamond-2.1.11/src/util/profiler.h:7:2: style: Struct 'Profiler' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
diamond-2.1.11/src/util/tsv/table.cpp:135:13: performance:inconclusive: Technically the member function 'Util::Tsv::Table::write_record' can be static (but you may consider moving to unnamed namespace). [functionStatic]
diamond-2.1.11/src/util/tsv/table.h:71:7: note: Technically the member function 'Util::Tsv::Table::write_record' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/util/tsv/table.cpp:135:13: note: Technically the member function 'Util::Tsv::Table::write_record' can be static (but you may consider moving to unnamed namespace).
diamond-2.1.11/src/util/tsv/table.cpp:155:67: style: Parameter 'f' can be declared as reference to const [constParameterReference]
diff:
head diamond-2.1.11/src/align/legacy/query_mapper.cpp:197:17: style: Variable 'query_len' is assigned a value that is never used. [unreadVariable]
2.17.0 diamond-2.1.11/src/chaining/aligner.h:13:6: style:inconclusive: Technically the member function 'Chaining::Aligner::get_approximate_link' can be const. [functionConst]
     diamond-2.1.11/src/chaining/greedy_align.cpp:222:15: note: Technically the member function 'Chaining::Aligner::get_approximate_link' can be const.
     diamond-2.1.11/src/chaining/aligner.h:13:6: note: Technically the member function 'Chaining::Aligner::get_approximate_link' can be const.
head diamond-2.1.11/src/chaining/greedy_align.cpp:222:15: style:inconclusive: Technically the member function 'Chaining::Aligner::get_approximate_link' can be const. [functionConst]
     diamond-2.1.11/src/chaining/aligner.h:13:6: note: Technically the member function 'Chaining::Aligner::get_approximate_link' can be const.
     diamond-2.1.11/src/chaining/greedy_align.cpp:222:15: note: Technically the member function 'Chaining::Aligner::get_approximate_link' can be const.
head diamond-2.1.11/src/cluster/cascaded/cascaded.cpp:92:86: style: C-style pointer casting [cstyleCast]
head diamond-2.1.11/src/cluster/helpers.cpp:78:16: style: Variable 'lines' is assigned a value that is never used. [unreadVariable]
head diamond-2.1.11/src/contrib/mcl/mcl.cpp:212:33: performance:inconclusive: Technically the member function 'Workflow::Cluster::MCL::get_sparse_matrix_and_clear' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     diamond-2.1.11/src/contrib/mcl/mcl.h:85:29: note: Technically the member function 'Workflow::Cluster::MCL::get_sparse_matrix_and_clear' can be static (but you may consider moving to unnamed namespace).
     diamond-2.1.11/src/contrib/mcl/mcl.cpp:212:33: note: Technically the member function 'Workflow::Cluster::MCL::get_sparse_matrix_and_clear' can be static (but you may consider moving to unnamed namespace).
head diamond-2.1.11/src/contrib/mcl/mcl.cpp:227:22: performance:inconclusive: Technically the member function 'Workflow::Cluster::MCL::get_dense_matrix_and_clear' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     diamond-2.1.11/src/contrib/mcl/mcl.h:86:18: note: Technically the member function 'Workflow::Cluster::MCL::get_dense_matrix_and_clear' can be static (but you may consider moving to unnamed namespace).
     diamond-2.1.11/src/contrib/mcl/mcl.cpp:227:22: note: Technically the member function 'Workflow::Cluster::MCL::get_dense_matrix_and_clear' can be static (but you may consider moving to unnamed namespace).
head diamond-2.1.11/src/contrib/mcl/mcl.cpp:64:11: performance:inconclusive: Technically the member function 'Workflow::Cluster::MCL::print_stats' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     diamond-2.1.11/src/contrib/mcl/mcl.h:78:7: note: Technically the member function 'Workflow::Cluster::MCL::print_stats' can be static (but you may consider moving to unnamed namespace).
     diamond-2.1.11/src/contrib/mcl/mcl.cpp:64:11: note: Technically the member function 'Workflow::Cluster::MCL::print_stats' can be static (but you may consider moving to unnamed namespace).
2.17.0 diamond-2.1.11/src/contrib/mcl/mcl.h:75:32: performance:inconclusive: Technically the member function 'Workflow::Cluster::MCL::sparse_matrix_multiply' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     diamond-2.1.11/src/contrib/mcl/sparse.h:26:36: note: Technically the member function 'Workflow::Cluster::MCL::sparse_matrix_multiply' can be static (but you may consider moving to unnamed namespace).
     diamond-2.1.11/src/contrib/mcl/mcl.h:75:32: note: Technically the member function 'Workflow::Cluster::MCL::sparse_matrix_multiply' can be static (but you may consider moving to unnamed namespace).
2.17.0 diamond-2.1.11/src/contrib/mcl/mcl.h:76:32: performance:inconclusive: Technically the member function 'Workflow::Cluster::MCL::sparse_matrix_get_gamma' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     diamond-2.1.11/src/contrib/mcl/sparse.h:90:36: note: Technically the member function 'Workflow::Cluster::MCL::sparse_matrix_get_gamma' can be static (but you may consider moving to unnamed namespace).
     diamond-2.1.11/src/contrib/mcl/mcl.h:76:32: note: Technically the member function 'Workflow::Cluster::MCL::sparse_matrix_get_gamma' can be static (but you may consider moving to unnamed namespace).
2.17.0 diamond-2.1.11/src/contrib/mcl/mcl.h:77:8: performance:inconclusive: Technically the member function 'Workflow::Cluster::MCL::sparse_matrix_get_norm' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     diamond-2.1.11/src/contrib/mcl/sparse.h:109:12: note: Technically the member function 'Workflow::Cluster::MCL::sparse_matrix_get_norm' can be static (but you may consider moving to unnamed namespace).
     diamond-2.1.11/src/contrib/mcl/mcl.h:77:8: note: Technically the member function 'Workflow::Cluster::MCL::sparse_matrix_get_norm' can be static (but you may consider moving to unnamed namespace).
2.17.0 diamond-2.1.11/src/contrib/mcl/mcl.h:78:7: performance:inconclusive: Technically the member function 'Workflow::Cluster::MCL::print_stats' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     diamond-2.1.11/src/contrib/mcl/mcl.cpp:64:11: note: Technically the member function 'Workflow::Cluster::MCL::print_stats' can be static (but you may consider moving to unnamed namespace).
     diamond-2.1.11/src/contrib/mcl/mcl.h:78:7: note: Technically the member function 'Workflow::Cluster::MCL::print_stats' can be static (but you may consider moving to unnamed namespace).
2.17.0 diamond-2.1.11/src/contrib/mcl/mcl.h:85:29: performance:inconclusive: Technically the member function 'Workflow::Cluster::MCL::get_sparse_matrix_and_clear' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     diamond-2.1.11/src/contrib/mcl/mcl.cpp:212:33: note: Technically the member function 'Workflow::Cluster::MCL::get_sparse_matrix_and_clear' can be static (but you may consider moving to unnamed namespace).
     diamond-2.1.11/src/contrib/mcl/mcl.h:85:29: note: Technically the member function 'Workflow::Cluster::MCL::get_sparse_matrix_and_clear' can be static (but you may consider moving to unnamed namespace).
2.17.0 diamond-2.1.11/src/contrib/mcl/mcl.h:86:18: performance:inconclusive: Technically the member function 'Workflow::Cluster::MCL::get_dense_matrix_and_clear' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     diamond-2.1.11/src/contrib/mcl/mcl.cpp:227:22: note: Technically the member function 'Workflow::Cluster::MCL::get_dense_matrix_and_clear' can be static (but you may consider moving to unnamed namespace).
     diamond-2.1.11/src/contrib/mcl/mcl.h:86:18: note: Technically the member function 'Workflow::Cluster::MCL::get_dense_matrix_and_clear' can be static (but you may consider moving to unnamed namespace).
head diamond-2.1.11/src/contrib/mcl/sparse.h:109:12: performance:inconclusive: Technically the member function 'Workflow::Cluster::MCL::sparse_matrix_get_norm' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     diamond-2.1.11/src/contrib/mcl/mcl.h:77:8: note: Technically the member function 'Workflow::Cluster::MCL::sparse_matrix_get_norm' can be static (but you may consider moving to unnamed namespace).
     diamond-2.1.11/src/contrib/mcl/sparse.h:109:12: note: Technically the member function 'Workflow::Cluster::MCL::sparse_matrix_get_norm' can be static (but you may consider moving to unnamed namespace).
head diamond-2.1.11/src/contrib/mcl/sparse.h:26:36: performance:inconclusive: Technically the member function 'Workflow::Cluster::MCL::sparse_matrix_multiply' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     diamond-2.1.11/src/contrib/mcl/mcl.h:75:32: note: Technically the member function 'Workflow::Cluster::MCL::sparse_matrix_multiply' can be static (but you may consider moving to unnamed namespace).
     diamond-2.1.11/src/contrib/mcl/sparse.h:26:36: note: Technically the member function 'Workflow::Cluster::MCL::sparse_matrix_multiply' can be static (but you may consider moving to unnamed namespace).
head diamond-2.1.11/src/contrib/mcl/sparse.h:90:36: performance:inconclusive: Technically the member function 'Workflow::Cluster::MCL::sparse_matrix_get_gamma' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     diamond-2.1.11/src/contrib/mcl/mcl.h:76:32: note: Technically the member function 'Workflow::Cluster::MCL::sparse_matrix_get_gamma' can be static (but you may consider moving to unnamed namespace).
     diamond-2.1.11/src/contrib/mcl/sparse.h:90:36: note: Technically the member function 'Workflow::Cluster::MCL::sparse_matrix_get_gamma' can be static (but you may consider moving to unnamed namespace).
head diamond-2.1.11/src/data/enum_seeds.h:26:12: style: Variable 'ptr' is assigned a value that is never used. [unreadVariable]
head diamond-2.1.11/src/data/frequent_seeds.cpp:96:21: performance:inconclusive: Technically the member function 'FrequentSeeds::build' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     diamond-2.1.11/src/data/frequent_seeds.h:33:7: note: Technically the member function 'FrequentSeeds::build' can be static (but you may consider moving to unnamed namespace).
     diamond-2.1.11/src/data/frequent_seeds.cpp:96:21: note: Technically the member function 'FrequentSeeds::build' can be static (but you may consider moving to unnamed namespace).
2.17.0 diamond-2.1.11/src/data/frequent_seeds.h:33:7: performance:inconclusive: Technically the member function 'FrequentSeeds::build' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     diamond-2.1.11/src/data/frequent_seeds.cpp:96:21: note: Technically the member function 'FrequentSeeds::build' can be static (but you may consider moving to unnamed namespace).
     diamond-2.1.11/src/data/frequent_seeds.h:33:7: note: Technically the member function 'FrequentSeeds::build' can be static (but you may consider moving to unnamed namespace).
head diamond-2.1.11/src/data/seed_histogram.h:64:5: style: Consider using std::accumulate algorithm instead of a raw loop. [useStlAlgorithm]
head diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:67:30: warning: If memory allocation fails, then there is a possible null pointer dereference: cigar [nullPointerOutOfMemory]
     diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:64:32: note: Assuming allocation function fails
     diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:64:32: note: Assignment 'cigar=malloc(sizeof(struct cigar_t))', assigned value is 0
     diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:67:30: note: Null pointer dereference
2.17.0 diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:793:37: error: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:791:27: note: Assuming allocation function fails
     diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:791:27: note: Assignment 'mem=calloc(3*max_buffer_length,1)', assigned value is 0
     diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:792:27: note: pattern_alg is assigned 'mem' here.
     diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:793:37: note: Null pointer addition
head diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:793:37: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:791:27: note: Assuming allocation function fails
     diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:791:27: note: Assignment 'mem=calloc(3*max_buffer_length,1)', assigned value is 0
     diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:792:27: note: pattern_alg is assigned 'mem' here.
     diamond-2.1.11/src/lib/WFA2-lib.diamond/alignment/cigar.c:793:37: note: Null pointer addition
head diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.cpp:282:16: style:inconclusive: Technically the member function 'wfa::WFAligner::getAlignmentStatus' can be const. [functionConst]
     diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.hpp:178:7: note: Technically the member function 'wfa::WFAligner::getAlignmentStatus' can be const.
     diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.cpp:282:16: note: Technically the member function 'wfa::WFAligner::getAlignmentStatus' can be const.
head diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.cpp:285:16: style:inconclusive: Technically the member function 'wfa::WFAligner::getAlignmentScore' can be const. [functionConst]
     diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.hpp:179:7: note: Technically the member function 'wfa::WFAligner::getAlignmentScore' can be const.
     diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.cpp:285:16: note: Technically the member function 'wfa::WFAligner::getAlignmentScore' can be const.
head diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.cpp:288:17: style:inconclusive: Technically the member function 'wfa::WFAligner::getAlignment' can be const. [functionConst]
     diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.hpp:180:8: note: Technically the member function 'wfa::WFAligner::getAlignment' can be const.
     diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.cpp:288:17: note: Technically the member function 'wfa::WFAligner::getAlignment' can be const.
head diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.cpp:294:24: style:inconclusive: Technically the member function 'wfa::WFAligner::getAlignment' can be const. [functionConst]
     diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.hpp:183:15: note: Technically the member function 'wfa::WFAligner::getAlignment' can be const.
     diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.cpp:294:24: note: Technically the member function 'wfa::WFAligner::getAlignment' can be const.
head diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.cpp:335:18: performance:inconclusive: Technically the member function 'wfa::WFAligner::strStatus' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.hpp:198:9: note: Technically the member function 'wfa::WFAligner::strStatus' can be static (but you may consider moving to unnamed namespace).
     diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.cpp:335:18: note: Technically the member function 'wfa::WFAligner::strStatus' can be static (but you may consider moving to unnamed namespace).
2.17.0 diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.hpp:178:7: style:inconclusive: Technically the member function 'wfa::WFAligner::getAlignmentStatus' can be const. [functionConst]
     diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.cpp:282:16: note: Technically the member function 'wfa::WFAligner::getAlignmentStatus' can be const.
     diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.hpp:178:7: note: Technically the member function 'wfa::WFAligner::getAlignmentStatus' can be const.
2.17.0 diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.hpp:179:7: style:inconclusive: Technically the member function 'wfa::WFAligner::getAlignmentScore' can be const. [functionConst]
     diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.cpp:285:16: note: Technically the member function 'wfa::WFAligner::getAlignmentScore' can be const.
     diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.hpp:179:7: note: Technically the member function 'wfa::WFAligner::getAlignmentScore' can be const.
2.17.0 diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.hpp:180:8: style:inconclusive: Technically the member function 'wfa::WFAligner::getAlignment' can be const. [functionConst]
     diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.cpp:288:17: note: Technically the member function 'wfa::WFAligner::getAlignment' can be const.
     diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.hpp:180:8: note: Technically the member function 'wfa::WFAligner::getAlignment' can be const.
2.17.0 diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.hpp:183:15: style:inconclusive: Technically the member function 'wfa::WFAligner::getAlignment' can be const. [functionConst]
     diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.cpp:294:24: note: Technically the member function 'wfa::WFAligner::getAlignment' can be const.
     diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.hpp:183:15: note: Technically the member function 'wfa::WFAligner::getAlignment' can be const.
2.17.0 diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.hpp:198:9: performance:inconclusive: Technically the member function 'wfa::WFAligner::strStatus' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.cpp:335:18: note: Technically the member function 'wfa::WFAligner::strStatus' can be static (but you may consider moving to unnamed namespace).
     diamond-2.1.11/src/lib/WFA2-lib.diamond/bindings/cpp/WFAligner.hpp:198:9: note: Technically the member function 'wfa::WFAligner::strStatus' can be static (but you may consider moving to unnamed namespace).
2.17.0 diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:322:40: error: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:319:37: note: Assuming allocation function fails
     diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:319:37: note: Assignment 'memory_base=malloc(num_bytes_allocated)', assigned value is 0
     diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:322:40: note: Null pointer addition
head diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:322:40: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:319:37: note: Assuming allocation function fails
     diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:319:37: note: Assignment 'memory_base=malloc(num_bytes_allocated)', assigned value is 0
     diamond-2.1.11/src/lib/WFA2-lib.diamond/system/mm_allocator.c:322:40: note: Null pointer addition
2.17.0 diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:117:27: error: If memory allocation fail: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:362:31: note: Assuming allocation function fails
     diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:362:31: note: Assignment 'seqlong=malloc(seqlong_length+1)', assigned value is 0
     diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:372:41: note: Calling function 'sequence_extract', 1st argument 'seqlong' value is 0
     diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:117:27: note: Null pointer addition
head diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:117:27: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:362:31: note: Assuming allocation function fails
     diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:362:31: note: Assignment 'seqlong=malloc(seqlong_length+1)', assigned value is 0
     diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:372:41: note: Calling function 'sequence_extract', 1st argument 'seqlong' value is 0
     diamond-2.1.11/src/lib/WFA2-lib.diamond/tools/generate_dataset/generate_dataset.c:117:27: note: Null pointer addition
head diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:73:35: warning: If memory allocation fails, then there is a possible null pointer dereference: heatmap [nullPointerOutOfMemory]
     diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:52:48: note: Assuming allocation function fails
     diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:52:30: note: Assignment 'heatmap=(struct heatmap_t*)malloc(sizeof(struct heatmap_t))', assigned value is 0
     diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:73:35: note: Null pointer dereference
head diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:76:39: warning: If memory allocation fails, then there is a possible null pointer dereference: heatmap [nullPointerOutOfMemory]
     diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:52:48: note: Assuming allocation function fails
     diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:52:30: note: Assignment 'heatmap=(struct heatmap_t*)malloc(sizeof(struct heatmap_t))', assigned value is 0
     diamond-2.1.11/src/lib/WFA2-lib.diamond/utils/heatmap.c:76:39: note: Null pointer dereference
head diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:47:50: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_plot [nullPointerOutOfMemory]
     diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:62: note: Assuming allocation function fails
     diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:37: note: Assignment 'wf_plot=(struct wavefront_plot_t*)malloc(sizeof(struct wavefront_plot_t))', assigned value is 0
     diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:101:36: note: Calling function 'wavefront_plot_heatmaps_allocate', 1st argument 'wf_plot' value is 0
     diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:47:50: note: Null pointer dereference
head diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:48:65: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_plot [nullPointerOutOfMemory]
     diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:62: note: Assuming allocation function fails
     diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:37: note: Assignment 'wf_plot=(struct wavefront_plot_t*)malloc(sizeof(struct wavefront_plot_t))', assigned value is 0
     diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:101:36: note: Calling function 'wavefront_plot_heatmaps_allocate', 1st argument 'wf_plot' value is 0
     diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:48:65: note: Null pointer dereference
head diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:49:50: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_plot [nullPointerOutOfMemory]
     diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:62: note: Assuming allocation function fails
     diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:37: note: Assignment 'wf_plot=(struct wavefront_plot_t*)malloc(sizeof(struct wavefront_plot_t))', assigned value is 0
     diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:101:36: note: Calling function 'wavefront_plot_heatmaps_allocate', 1st argument 'wf_plot' value is 0
     diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:49:50: note: Null pointer dereference
head diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:50:62: warning: If memory allocation fails, then there is a possible null pointer dereference: wf_plot [nullPointerOutOfMemory]
     diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:62: note: Assuming allocation function fails
     diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:92:37: note: Assignment 'wf_plot=(struct wavefront_plot_t*)malloc(sizeof(struct wavefront_plot_t))', assigned value is 0
     diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:101:36: note: Calling function 'wavefront_plot_heatmaps_allocate', 1st argument 'wf_plot' value is 0
     diamond-2.1.11/src/lib/WFA2-lib.diamond/wavefront/wavefront_plot.c:50:62: note: Null pointer dereference
2.17.0 diamond-2.1.11/src/lib/alp/njn_uniform.hpp:51:32: error: syntax error [syntaxError]
head diamond-2.1.11/src/lib/alp/sls_alignment_evaluer.cpp:100:14: performance: Function parameter 'function_name_' should be passed by const reference. [passedByValue]
head diamond-2.1.11/src/lib/alp/sls_alignment_evaluer.cpp:1106:9: style: Local variable 'area' shadows outer function [shadowFunction]
     diamond-2.1.11/src/lib/alp/sls_alignment_evaluer.hpp:150:9: note: Shadowed declaration
     diamond-2.1.11/src/lib/alp/sls_alignment_evaluer.cpp:1106:9: note: Shadow variable
head diamond-2.1.11/src/lib/alp/sls_alignment_evaluer.hpp:60:3: warning: Member variable 'gapped_computation_parameters_struct::d_total_realizations_number_with_ALP' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_alignment_evaluer.hpp:60:3: warning: Member variable 'gapped_computation_parameters_struct::d_total_realizations_number_with_killing' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_alp.cpp:1203:12: style: Local variable 'i' shadows outer variable [shadowVariable]
     diamond-2.1.11/src/lib/alp/sls_alp.cpp:1143:11: note: Shadowed declaration
     diamond-2.1.11/src/lib/alp/sls_alp.cpp:1203:12: note: Shadow variable
head diamond-2.1.11/src/lib/alp/sls_alp.cpp:1203:12: style: The scope of the variable 'i' can be reduced. [variableScope]
head diamond-2.1.11/src/lib/alp/sls_alp.cpp:127:3: warning: Class 'alp' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
head diamond-2.1.11/src/lib/alp/sls_alp.cpp:127:3: warning: Class 'alp' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
head diamond-2.1.11/src/lib/alp/sls_alp.cpp:1389:12: style: Local variable 'i' shadows outer variable [shadowVariable]
     diamond-2.1.11/src/lib/alp/sls_alp.cpp:1322:11: note: Shadowed declaration
     diamond-2.1.11/src/lib/alp/sls_alp.cpp:1389:12: note: Shadow variable
head diamond-2.1.11/src/lib/alp/sls_alp.cpp:1389:12: style: The scope of the variable 'i' can be reduced. [variableScope]
head diamond-2.1.11/src/lib/alp/sls_alp.cpp:1648:12: style: Local variable 'i' shadows outer variable [shadowVariable]
     diamond-2.1.11/src/lib/alp/sls_alp.cpp:1580:11: note: Shadowed declaration
     diamond-2.1.11/src/lib/alp/sls_alp.cpp:1648:12: note: Shadow variable
head diamond-2.1.11/src/lib/alp/sls_alp.cpp:1673:12: style: Local variable 'i' shadows outer variable [shadowVariable]
     diamond-2.1.11/src/lib/alp/sls_alp.cpp:1580:11: note: Shadowed declaration
     diamond-2.1.11/src/lib/alp/sls_alp.cpp:1673:12: note: Shadow variable
head diamond-2.1.11/src/lib/alp/sls_alp.cpp:1673:12: style: The scope of the variable 'i' can be reduced. [variableScope]
head diamond-2.1.11/src/lib/alp/sls_alp.cpp:1881:12: style: Local variable 'i' shadows outer variable [shadowVariable]
     diamond-2.1.11/src/lib/alp/sls_alp.cpp:1813:11: note: Shadowed declaration
     diamond-2.1.11/src/lib/alp/sls_alp.cpp:1881:12: note: Shadow variable
head diamond-2.1.11/src/lib/alp/sls_alp.cpp:1906:12: style: Local variable 'i' shadows outer variable [shadowVariable]
     diamond-2.1.11/src/lib/alp/sls_alp.cpp:1813:11: note: Shadowed declaration
     diamond-2.1.11/src/lib/alp/sls_alp.cpp:1906:12: note: Shadow variable
head diamond-2.1.11/src/lib/alp/sls_alp.cpp:1906:12: style: The scope of the variable 'i' can be reduced. [variableScope]
head diamond-2.1.11/src/lib/alp/sls_alp.cpp:1998:8: warning: Member variable 'state::d_HD_ij_next' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_alp.cpp:1998:8: warning: Member variable 'state::d_HI_ij_next' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_alp.cpp:1998:8: warning: Member variable 'state::d_HS_ij_next' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_alp.cpp:1998:8: warning: Member variable 'state::d_H_ij_next' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_alp.cpp:1998:8: warning: Member variable 'state::d_H_matr_len' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_alp.cpp:1998:8: warning: Member variable 'state::d_M' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_alp.cpp:1998:8: warning: Member variable 'state::d_sentinel_i_next' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_alp.cpp:1998:8: warning: Member variable 'state::d_sentinel_j_next' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_alp.cpp:2025:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable state [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/lib/alp/sls_alp.cpp:2108:11: style: Parameter 'M_upper_level_' can be declared as pointer to const [constParameterPointer]
head diamond-2.1.11/src/lib/alp/sls_alp.cpp:2208:24: style: Variable 'd_is_tmp' can be declared as pointer to const [constVariableReference]
head diamond-2.1.11/src/lib/alp/sls_alp.cpp:2252:4: style: Variable 'UI' is assigned a value that is never used. [unreadVariable]
head diamond-2.1.11/src/lib/alp/sls_alp.cpp:2255:4: style: Variable 'VD' is assigned a value that is never used. [unreadVariable]
head diamond-2.1.11/src/lib/alp/sls_alp.cpp:269:11: style: The scope of the variable 'i' can be reduced. [variableScope]
head diamond-2.1.11/src/lib/alp/sls_alp.cpp:386:11: style: The scope of the variable 'i' can be reduced. [variableScope]
head diamond-2.1.11/src/lib/alp/sls_alp.cpp:44:6: warning: Member variable 'alp::d_IS_state' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_alp.cpp:44:6: warning: Member variable 'alp::d_diff_opt' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_alp.cpp:44:6: warning: Member variable 'alp::d_nalp_killing' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_alp.cpp:44:6: warning: Member variable 'alp::d_sentinels_flag' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_alp.hpp:153:14: performance:inconclusive: Technically the member function 'Sls::alp::swap' can be static (but you may consider moving to unnamed namespace). [functionStatic]
head diamond-2.1.11/src/lib/alp/sls_alp.hpp:195:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/lib/alp/sls_alp.hpp:212:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/lib/alp/sls_alp.hpp:94:2: style: Class 'alp' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:1019:8: performance: Function parameter 'RR_file_name_' should be passed by const reference. [passedByValue]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:1031:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:116:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:1187:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MIN [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:1242:49: style: C-style pointer casting [cstyleCast]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:1261:14: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:1270:4: style: C-style pointer casting [cstyleCast]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:1297:3: warning: Class 'importance_sampling' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:1297:3: warning: Class 'importance_sampling' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:1355:27: style: Redundant assignment of 'd_elements_values[ind]' to itself. [selfAssignment]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:1408:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable q_elem [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:1522:8: performance: Function parameter 'str_' should be passed by const reference. [passedByValue]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:1531:2: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:217:8: performance: Function parameter 'randout_' should be passed by const reference. [passedByValue]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:314:24: warning:inconclusive: Division of result of sizeof() on pointer type. [divideSizeof]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:380:11: warning: Member variable 'alp_data::d_realizations_number2' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:380:11: warning: Member variable 'alp_data::d_time_before1' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:382:8: performance: Function parameter 'randout_' should be passed by const reference. [passedByValue]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:392:8: performance: Function parameter 'smatr_file_name_' should be passed by const reference. [passedByValue]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:393:8: performance: Function parameter 'RR1_file_name_' should be passed by const reference. [passedByValue]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:394:8: performance: Function parameter 'RR2_file_name_' should be passed by const reference. [passedByValue]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:426:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable struct_for_randomization [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:486:11: warning: Member variable 'alp_data::d_realizations_number2' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:486:11: warning: Member variable 'alp_data::d_time_before1' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:488:27: style: Parameter 'randomization_parameters_' can be declared as pointer to const [constParameterPointer]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:50:8: performance: Function parameter 'randout_' should be passed by const reference. [passedByValue]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:51:8: performance: Function parameter 'smatr_file_name_' should be passed by const reference. [passedByValue]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:52:8: performance: Function parameter 'RR1_file_name_' should be passed by const reference. [passedByValue]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:53:8: performance: Function parameter 'RR2_file_name_' should be passed by const reference. [passedByValue]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:540:3: warning: Class 'alp_data' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:540:3: warning: Class 'alp_data' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:583:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable struct_for_randomization [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:61:10: style: Parameter 'letterFreqs1_' can be declared as pointer to const [constParameterReference]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:62:10: style: Parameter 'letterFreqs2_' can be declared as pointer to const [constParameterReference]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:694:23: warning:inconclusive: Division of result of sizeof() on pointer type. [divideSizeof]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:701:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable struct_for_randomization [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:710:16: style:inconclusive: Technically the member function 'Sls::alp_data::check_out_file' can be const. [functionConst]
     diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:396:8: note: Technically the member function 'Sls::alp_data::check_out_file' can be const.
     diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:710:16: note: Technically the member function 'Sls::alp_data::check_out_file' can be const.
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:711:9: performance: Function parameter 'out_file_name_' should be passed by const reference. [passedByValue]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:718:37: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:739:8: style: Variable 'str_for_test0' can be declared as const array [constVariable]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:740:9: style: Variable 'test_flag0' can be declared as pointer to const [constVariablePointer]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:747:8: style: Variable 'str_for_test' can be declared as const array [constVariable]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:749:8: style: Variable 'test_flag' can be declared as pointer to const [constVariablePointer]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:797:33: style: C-style pointer casting [cstyleCast]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:800:10: style: Variable 'd_RR1' can be declared as pointer to const [constVariablePointer]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:801:10: style: Variable 'd_RR2' can be declared as pointer to const [constVariablePointer]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:818:8: performance: Function parameter 'smatr_file_name_' should be passed by const reference. [passedByValue]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:828:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable in [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:868:8: performance: Function parameter 'RR_file_name_' should be passed by const reference. [passedByValue]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:890:8: performance: Function parameter 'RR_file_name_' should be passed by const reference. [passedByValue]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:902:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_EPSILON [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:998:13: style: Local variable 'i' shadows outer variable [shadowVariable]
     diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:958:12: note: Shadowed declaration
     diamond-2.1.11/src/lib/alp/sls_alp_data.cpp:998:13: note: Shadow variable
head diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:103:3: style: Class 'array_positive < alp * >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:103:3: style: Class 'array_positive < double >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:103:3: style: Class 'array_positive < long >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:103:3: style: Class 'array_positive < state * >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:103:3: style: Class 'array_positive' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:169:3: style: Class 'array < long >' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:169:3: style: Class 'array' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:386:17: performance:inconclusive: Technically the member function 'Sls::alp_data::ran2' can be static (but you may consider moving to unnamed namespace). [functionStatic]
head diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:473:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:501:13: style: The scope of the variable 'i' can be reduced. [variableScope]
head diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:513:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:541:7: style: Variable 'v1' is assigned a value that is never used. [unreadVariable]
head diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:596:15: style: Condition 'v2_minus<0' is always true [knownConditionTrueFalse]
     diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:581:15: note: Assuming that condition 'v2_minus>=0' is not redundant
     diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:589:21: note: Assuming condition is false
     diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:596:15: note: Condition 'v2_minus<0' is always true
head diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:720:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:757:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:778:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:807:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:854:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:863:3: style: Exception should be caught by reference. [catchExceptionByValue]
head diamond-2.1.11/src/lib/alp/sls_alp_data.hpp:916:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:1077:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MAX [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:1104:15: style:inconclusive: Technically the member function 'Sls::alp_sim::memory_release_for_calculate_main_parameters2m' can be const. [functionConst]
     diamond-2.1.11/src/lib/alp/sls_alp_sim.hpp:354:8: note: Technically the member function 'Sls::alp_sim::memory_release_for_calculate_main_parameters2m' can be const.
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:1104:15: note: Technically the member function 'Sls::alp_sim::memory_release_for_calculate_main_parameters2m' can be const.
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:1469:13: style: Local variable 'j' shadows outer variable [shadowVariable]
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:1336:12: note: Shadowed declaration
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:1469:13: note: Shadow variable
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:1487:11: style: Local variable 'test_difference' shadows outer argument [shadowArgument]
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:1250:9: note: Shadowed declaration
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:1487:11: note: Shadow variable
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:1488:11: style: Local variable 'test_difference_error' shadows outer argument [shadowArgument]
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:1251:9: note: Shadowed declaration
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:1488:11: note: Shadow variable
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2006:11: style: The scope of the variable 'i' can be reduced. [variableScope]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2017:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable alp [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2062:12: style: Local variable 'i' shadows outer variable [shadowVariable]
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2049:11: note: Shadowed declaration
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2062:12: note: Shadow variable
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2066:9: style: Local variable 'flag' shadows outer variable [shadowVariable]
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2043:7: note: Shadowed declaration
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2066:9: note: Shadow variable
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2090:11: style: Local variable 'flag' shadows outer variable [shadowVariable]
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2066:9: note: Shadowed declaration
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2090:11: note: Shadow variable
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2148:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable alp [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2241:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable alp [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2302:12: style: The scope of the variable 'alp_number' can be reduced. [variableScope]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2337:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable alp [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2363:13: style: Local variable 'i' shadows outer variable [shadowVariable]
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2326:12: note: Shadowed declaration
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2363:13: note: Shadow variable
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2477:14: style: Local variable 'i' shadows outer variable [shadowVariable]
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2363:13: note: Shadowed declaration
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2477:14: note: Shadow variable
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2593:15: performance:inconclusive: Technically the member function 'Sls::alp_sim::memory_release_for_get_minimal_simulation' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     diamond-2.1.11/src/lib/alp/sls_alp_sim.hpp:102:8: note: Technically the member function 'Sls::alp_sim::memory_release_for_get_minimal_simulation' can be static (but you may consider moving to unnamed namespace).
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2593:15: note: Technically the member function 'Sls::alp_sim::memory_release_for_get_minimal_simulation' can be static (but you may consider moving to unnamed namespace).
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2762:11: style: Parameter 'i_' can be declared as reference to const [constParameterReference]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2763:10: style: Parameter 'exp_array_' can be declared as pointer to const [constParameterReference]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2773:15: performance:inconclusive: Technically the member function 'Sls::alp_sim::memory_release_for_calculate_FSC' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     diamond-2.1.11/src/lib/alp/sls_alp_sim.hpp:148:8: note: Technically the member function 'Sls::alp_sim::memory_release_for_calculate_FSC' can be static (but you may consider moving to unnamed namespace).
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2773:15: note: Technically the member function 'Sls::alp_sim::memory_release_for_calculate_FSC' can be static (but you may consider moving to unnamed namespace).
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:277:12: style: The scope of the variable 'number_of_realizations_with_ALP_pred' can be reduced. [variableScope]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2908:32: style: C-style pointer casting [cstyleCast]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2918:11: style: Local variable 'tmp' shadows outer variable [shadowVariable]
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2908:27: note: Shadowed declaration
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2918:11: note: Shadow variable
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3028:13: style: Local variable 'j' shadows outer variable [shadowVariable]
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:2988:12: note: Shadowed declaration
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3028:13: note: Shadow variable
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3493:15: performance:inconclusive: Technically the member function 'Sls::alp_sim::sigma_calculation' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     diamond-2.1.11/src/lib/alp/sls_alp_sim.hpp:206:8: note: Technically the member function 'Sls::alp_sim::sigma_calculation' can be static (but you may consider moving to unnamed namespace).
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3493:15: note: Technically the member function 'Sls::alp_sim::sigma_calculation' can be static (but you may consider moving to unnamed namespace).
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3534:15: performance:inconclusive: Technically the member function 'Sls::alp_sim::calculate_C' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     diamond-2.1.11/src/lib/alp/sls_alp_sim.hpp:136:8: note: Technically the member function 'Sls::alp_sim::calculate_C' can be static (but you may consider moving to unnamed namespace).
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3534:15: note: Technically the member function 'Sls::alp_sim::calculate_C' can be static (but you may consider moving to unnamed namespace).
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3585:33: style: C-style pointer casting [cstyleCast]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3586:40: style: C-style pointer casting [cstyleCast]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3686:33: style: C-style pointer casting [cstyleCast]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3687:40: style: C-style pointer casting [cstyleCast]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:372:9: style: Condition '!loop_break_flag' is always true [knownConditionTrueFalse]
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:329:7: note: Assuming that condition 'loop_break_flag' is not redundant
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:372:9: note: Condition '!loop_break_flag' is always true
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3731:13: style: Local variable 'number_of_elements' shadows outer variable [shadowVariable]
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3620:12: note: Shadowed declaration
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3731:13: note: Shadow variable
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3733:9: style: Local variable 'cut_left_tail' shadows outer variable [shadowVariable]
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3622:8: note: Shadowed declaration
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3733:9: note: Shadow variable
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3734:9: style: Local variable 'cut_right_tail' shadows outer variable [shadowVariable]
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3623:8: note: Shadowed declaration
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3734:9: note: Shadow variable
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3738:11: style: Local variable 'beta1' shadows outer variable [shadowVariable]
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3617:10: note: Shadowed declaration
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3738:11: note: Shadow variable
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3740:11: style: Local variable 'beta1_error' shadows outer variable [shadowVariable]
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3618:10: note: Shadowed declaration
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3740:11: note: Shadow variable
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3742:9: style: Local variable 'res_was_calculated' shadows outer variable [shadowVariable]
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3634:8: note: Shadowed declaration
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3742:9: note: Shadow variable
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:383:12: style: The scope of the variable 'number_of_realizations_with_killing_pred' can be reduced. [variableScope]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3947:14: style: Variable 'alp_tmp' can be declared as reference to const [constVariableReference]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3948:12: style: Variable 'weight_tmp' can be declared as reference to const [constVariableReference]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3951:5: style: C-style pointer casting [cstyleCast]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3952:5: style: C-style pointer casting [cstyleCast]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3957:32: style: C-style pointer casting [cstyleCast]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:3958:39: style: C-style pointer casting [cstyleCast]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:4042:14: style: Variable 'alp_tmp' can be declared as reference to const [constVariableReference]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:4043:12: style: Variable 'weight_tmp' can be declared as reference to const [constVariableReference]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:4146:14: style: Variable 'alp_tmp' can be declared as reference to const [constVariableReference]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:4147:12: style: Variable 'weight_tmp' can be declared as reference to const [constVariableReference]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:4314:35: style: Variable 'tmp_struct.d_calculate_alp_number' is reassigned a value before the old one has been used. [redundantAssignment]
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:4311:35: note: tmp_struct.d_calculate_alp_number is assigned
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:4314:35: note: tmp_struct.d_calculate_alp_number is overwritten
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:4354:9: style: The scope of the variable 'sum2_error' can be reduced. [variableScope]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:4410:45: style: C-style pointer casting [cstyleCast]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:4430:33: style: C-style pointer casting [cstyleCast]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:4431:40: style: C-style pointer casting [cstyleCast]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:4460:13: style: Local variable 'k' shadows outer variable [shadowVariable]
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:4427:12: note: Shadowed declaration
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:4460:13: note: Shadow variable
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:45:10: warning: Member variable 'alp_sim::m_G' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:45:10: warning: Member variable 'alp_sim::m_G1' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:45:10: warning: Member variable 'alp_sim::m_G2' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:45:10: warning: Member variable 'alp_sim::m_GaplessA' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:45:10: warning: Member variable 'alp_sim::m_GaplessAError' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:45:10: warning: Member variable 'alp_sim::m_GaplessAlpha' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:45:10: warning: Member variable 'alp_sim::m_GaplessAlphaError' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:475:9: style: Condition '!loop_break_flag' is always true [knownConditionTrueFalse]
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:432:7: note: Assuming that condition 'loop_break_flag' is not redundant
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:475:9: note: Condition '!loop_break_flag' is always true
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:570:6: style:inconclusive: Found duplicate branches for 'if' and 'else'. [duplicateBranch]
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:575:6: note: Found duplicate branches for 'if' and 'else'.
     diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:570:6: note: Found duplicate branches for 'if' and 'else'.
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:590:10: style: The scope of the variable 'sucess_flag' can be reduced. [variableScope]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:660:5: style: Exception should be caught by reference. [catchExceptionByValue]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:72:3: warning: Class 'alp_sim' does not have a copy constructor which is recommended since it has dynamic memory/resource allocation(s). [noCopyConstructor]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:72:3: warning: Class 'alp_sim' does not have a operator= which is recommended since it has dynamic memory/resource allocation(s). [noOperatorEq]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.cpp:751:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable out [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/lib/alp/sls_alp_sim.hpp:78:3: style: Class 'alp_sim' has a constructor with 1 argument that is not explicit. [noExplicitConstructor]
head diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:1022:10: style: The scope of the variable 'P_tmp' can be reduced. [variableScope]
head diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:1022:16: style: The scope of the variable 'E_tmp' can be reduced. [variableScope]
head diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:1059:19: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable DBL_MAX [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:114:5: style: Condition 'blast_' is always false [knownConditionTrueFalse]
     diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:68:9: note: Assignment 'blast_=false', assigned value is 0
     diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:114:5: note: Condition 'blast_' is always false
head diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:1198:6: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:154:21: style: Condition 'blast_' is always false [knownConditionTrueFalse]
     diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:68:9: note: Assignment 'blast_=false', assigned value is 0
     diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:154:21: note: Condition 'blast_' is always false
head diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:412:5: style: Condition 'blast_' is always false [knownConditionTrueFalse]
     diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:384:9: note: Assignment 'blast_=false', assigned value is 0
     diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:412:5: note: Condition 'blast_' is always false
head diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:439:21: style: Condition 'blast_' is always false [knownConditionTrueFalse]
     diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:384:9: note: Assignment 'blast_=false', assigned value is 0
     diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:439:21: note: Condition 'blast_' is always false
head diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:551:13: style: Expression 'log(1 + x)' can be replaced by 'log1p(x)' to avoid loss of precision. [unpreciseMathCall]
head diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:560:17: performance:inconclusive: Technically the member function 'Sls::pvalues::log_area' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:212:10: note: Technically the member function 'Sls::pvalues::log_area' can be static (but you may consider moving to unnamed namespace).
     diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:560:17: note: Technically the member function 'Sls::pvalues::log_area' can be static (but you may consider moving to unnamed namespace).
head diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:571:17: style: Variable 'lambda_' is assigned a value that is never used. [unreadVariable]
head diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:571:9: style: Variable 'lambda_' is assigned a value that is never used. [unreadVariable]
head diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:572:12: style: Variable 'k_' is assigned a value that is never used. [unreadVariable]
head diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:572:9: style: Variable 'k_' is assigned a value that is never used. [unreadVariable]
head diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:597:6: style: Condition 'blast_' is always false [knownConditionTrueFalse]
     diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:569:11: note: Assignment 'blast_=false', assigned value is 0
     diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:597:6: note: Condition 'blast_' is always false
head diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:624:26: style: Condition 'blast_' is always false [knownConditionTrueFalse]
     diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:569:11: note: Assignment 'blast_=false', assigned value is 0
     diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:624:26: note: Condition 'blast_' is always false
head diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:977:15: style:inconclusive: Technically the member function 'Sls::pvalues::calculate_P_values' can be const. [functionConst]
     diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:250:8: note: Technically the member function 'Sls::pvalues::calculate_P_values' can be const.
     diamond-2.1.11/src/lib/alp/sls_pvalues.cpp:977:15: note: Technically the member function 'Sls::pvalues::calculate_P_values' can be const.
head diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:263:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable RAND_MAX [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::C' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::C_error' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::G' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::G1' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::G2' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::K' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::K_error' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::a' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::a_I' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::a_I_error' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::a_J' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::a_J_error' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::a_error' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::alpha' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::alpha_I' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::alpha_I_error' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::alpha_J' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::alpha_J_error' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::alpha_error' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::c_y_thr' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::gapless_a' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::gapless_a_error' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::gapless_alpha' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::gapless_alpha_error' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::lambda' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::lambda_error' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::m_CalcTime' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::sigma' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::sigma_error' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::vi_y_thr' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/alp/sls_pvalues.hpp:53:3: warning: Member variable 'ALP_set_of_parameters::vj_y_thr' is not initialized in the constructor. [uninitMemberVar]
head diamond-2.1.11/src/lib/blast/blastn_score.cpp:1153:63: style: C-style pointer casting [cstyleCast]
head diamond-2.1.11/src/lib/blast/blastn_score.cpp:246:53: style: C-style pointer casting [cstyleCast]
head diamond-2.1.11/src/lib/gsl/gsl.h:255:19: style: Variable 'P' can be declared as const array [constVariable]
head diamond-2.1.11/src/lib/gsl/gsl.h:263:19: style: Variable 'Q' can be declared as const array [constVariable]
head diamond-2.1.11/src/lib/gsl/gsl.h:51:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/lib/gsl/gsl.h:59:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stdout [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/lib/mio/detail/mmap.ipp:219:30: error: If memory allocation fails: pointer addition with NULL pointer. [nullPointerArithmeticOutOfMemory]
     diamond-2.1.11/src/lib/mio/detail/mmap.ipp:205:52: note: Assuming allocation function fails
     diamond-2.1.11/src/lib/mio/detail/mmap.ipp:205:45: note: Assignment 'mapping_start=static_cast<char*>(::mmap(0,length_to_map,mode==access_mode::read?PROT_READ:PROT_WRITE,MAP_SHARED,file_handle,aligned_offset))', assigned value is 0
     diamond-2.1.11/src/lib/mio/detail/mmap.ipp:219:30: note: Null pointer addition
head diamond-2.1.11/src/lib/tantan/LambdaCalculator.cc:196:24: performance:inconclusive: Technically the member function 'cbrc::LambdaCalculator::find_ub' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     diamond-2.1.11/src/lib/tantan/LambdaCalculator.hh:50:8: note: Technically the member function 'cbrc::LambdaCalculator::find_ub' can be static (but you may consider moving to unnamed namespace).
     diamond-2.1.11/src/lib/tantan/LambdaCalculator.cc:196:24: note: Technically the member function 'cbrc::LambdaCalculator::find_ub' can be static (but you may consider moving to unnamed namespace).
2.17.0 diamond-2.1.11/src/lib/tantan/LambdaCalculator.hh:50:8: performance:inconclusive: Technically the member function 'cbrc::LambdaCalculator::find_ub' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     diamond-2.1.11/src/lib/tantan/LambdaCalculator.cc:196:24: note: Technically the member function 'cbrc::LambdaCalculator::find_ub' can be static (but you may consider moving to unnamed namespace).
     diamond-2.1.11/src/lib/tantan/LambdaCalculator.hh:50:8: note: Technically the member function 'cbrc::LambdaCalculator::find_ub' can be static (but you may consider moving to unnamed namespace).
head diamond-2.1.11/src/masking/masking.cpp:201:15: performance:inconclusive: Technically the member function 'Masking::bit_to_hard_mask' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     diamond-2.1.11/src/masking/masking.h:44:7: note: Technically the member function 'Masking::bit_to_hard_mask' can be static (but you may consider moving to unnamed namespace).
     diamond-2.1.11/src/masking/masking.cpp:201:15: note: Technically the member function 'Masking::bit_to_hard_mask' can be static (but you may consider moving to unnamed namespace).
head diamond-2.1.11/src/masking/masking.cpp:210:15: performance:inconclusive: Technically the member function 'Masking::remove_bit_mask' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     diamond-2.1.11/src/masking/masking.h:45:7: note: Technically the member function 'Masking::remove_bit_mask' can be static (but you may consider moving to unnamed namespace).
     diamond-2.1.11/src/masking/masking.cpp:210:15: note: Technically the member function 'Masking::remove_bit_mask' can be static (but you may consider moving to unnamed namespace).
2.17.0 diamond-2.1.11/src/masking/masking.h:44:7: performance:inconclusive: Technically the member function 'Masking::bit_to_hard_mask' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     diamond-2.1.11/src/masking/masking.cpp:201:15: note: Technically the member function 'Masking::bit_to_hard_mask' can be static (but you may consider moving to unnamed namespace).
     diamond-2.1.11/src/masking/masking.h:44:7: note: Technically the member function 'Masking::bit_to_hard_mask' can be static (but you may consider moving to unnamed namespace).
2.17.0 diamond-2.1.11/src/masking/masking.h:45:7: performance:inconclusive: Technically the member function 'Masking::remove_bit_mask' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     diamond-2.1.11/src/masking/masking.cpp:210:15: note: Technically the member function 'Masking::remove_bit_mask' can be static (but you may consider moving to unnamed namespace).
     diamond-2.1.11/src/masking/masking.h:45:7: note: Technically the member function 'Masking::remove_bit_mask' can be static (but you may consider moving to unnamed namespace).
head diamond-2.1.11/src/output/daa/merge.cpp:50:11: style: Variable 'size' is assigned a value that is never used. [unreadVariable]
head diamond-2.1.11/src/run/config.cpp:153:14: performance:inconclusive: Technically the member function 'Search::Config::free' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     diamond-2.1.11/src/run/config.h:87:7: note: Technically the member function 'Search::Config::free' can be static (but you may consider moving to unnamed namespace).
     diamond-2.1.11/src/run/config.cpp:153:14: note: Technically the member function 'Search::Config::free' can be static (but you may consider moving to unnamed namespace).
2.17.0 diamond-2.1.11/src/run/config.h:87:7: performance:inconclusive: Technically the member function 'Search::Config::free' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     diamond-2.1.11/src/run/config.cpp:153:14: note: Technically the member function 'Search::Config::free' can be static (but you may consider moving to unnamed namespace).
     diamond-2.1.11/src/run/config.h:87:7: note: Technically the member function 'Search::Config::free' can be static (but you may consider moving to unnamed namespace).
head diamond-2.1.11/src/run/double_indexed.cpp:322:7: style: Variable 'mp_last_chunk' is assigned a value that is never used. [unreadVariable]
head diamond-2.1.11/src/run/tools.cpp:127:16: style: Variable 'max' is assigned a value that is never used. [unreadVariable]
head diamond-2.1.11/src/stats/comp_based_stats.cpp:389:15: style: Variable 'cols' is assigned a value that is never used. [unreadVariable]
head diamond-2.1.11/src/tools/roc.cpp:379:29: style: Variable 'buf_size' is assigned a value that is never used. [unreadVariable]
head diamond-2.1.11/src/util/command_line_parser.cpp:111:25: style:inconclusive: Technically the member function 'CommandLineParser::print_help' can be const. [functionConst]
     diamond-2.1.11/src/util/command_line_parser.h:248:7: note: Technically the member function 'CommandLineParser::print_help' can be const.
     diamond-2.1.11/src/util/command_line_parser.cpp:111:25: note: Technically the member function 'CommandLineParser::print_help' can be const.
head diamond-2.1.11/src/util/command_line_parser.cpp:128:25: style:inconclusive: Technically the member function 'CommandLineParser::print_documentation' can be const. [functionConst]
     diamond-2.1.11/src/util/command_line_parser.h:249:10: note: Technically the member function 'CommandLineParser::print_documentation' can be const.
     diamond-2.1.11/src/util/command_line_parser.cpp:128:25: note: Technically the member function 'CommandLineParser::print_documentation' can be const.
2.17.0 diamond-2.1.11/src/util/command_line_parser.h:215:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
2.17.0 diamond-2.1.11/src/util/command_line_parser.h:248:7: style:inconclusive: Technically the member function 'CommandLineParser::print_help' can be const. [functionConst]
     diamond-2.1.11/src/util/command_line_parser.cpp:111:25: note: Technically the member function 'CommandLineParser::print_help' can be const.
     diamond-2.1.11/src/util/command_line_parser.h:248:7: note: Technically the member function 'CommandLineParser::print_help' can be const.
2.17.0 diamond-2.1.11/src/util/command_line_parser.h:249:10: style:inconclusive: Technically the member function 'CommandLineParser::print_documentation' can be const. [functionConst]
     diamond-2.1.11/src/util/command_line_parser.cpp:128:25: note: Technically the member function 'CommandLineParser::print_documentation' can be const.
     diamond-2.1.11/src/util/command_line_parser.h:249:10: note: Technically the member function 'CommandLineParser::print_documentation' can be const.
2.17.0 diamond-2.1.11/src/util/enum.h:44:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
2.17.0 diamond-2.1.11/src/util/enum.h:52:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/util/enum.h:56:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable from_string [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/util/io/deserializer.cpp:103:39: style: C-style pointer casting [cstyleCast]
head diamond-2.1.11/src/util/io/deserializer.h:132:40: style: C-style pointer casting [cstyleCast]
head diamond-2.1.11/src/util/io/deserializer.h:152:40: style: C-style pointer casting [cstyleCast]
head diamond-2.1.11/src/util/io/temp_file.cpp:51:23: style:inconclusive: Technically the member function 'TempFileHandler::init' can be const. [functionConst]
     diamond-2.1.11/src/util/io/temp_file.h:24:7: note: Technically the member function 'TempFileHandler::init' can be const.
     diamond-2.1.11/src/util/io/temp_file.cpp:51:23: note: Technically the member function 'TempFileHandler::init' can be const.
2.17.0 diamond-2.1.11/src/util/io/temp_file.h:24:7: style:inconclusive: Technically the member function 'TempFileHandler::init' can be const. [functionConst]
     diamond-2.1.11/src/util/io/temp_file.cpp:51:23: note: Technically the member function 'TempFileHandler::init' can be const.
     diamond-2.1.11/src/util/io/temp_file.h:24:7: note: Technically the member function 'TempFileHandler::init' can be const.
head diamond-2.1.11/src/util/parallel/filestack.cpp:263:9: style: Variable 'stat' is assigned a value that is never used. [unreadVariable]
head diamond-2.1.11/src/util/parallel/filestack.cpp:266:16: style: Variable 'n' is assigned a value that is never used. [unreadVariable]
head diamond-2.1.11/src/util/parallel/filestack.cpp:426:16: style:inconclusive: Technically the member function 'FileStack::get_max_line_length' can be const. [functionConst]
     diamond-2.1.11/src/util/parallel/filestack.h:59:13: note: Technically the member function 'FileStack::get_max_line_length' can be const.
     diamond-2.1.11/src/util/parallel/filestack.cpp:426:16: note: Technically the member function 'FileStack::get_max_line_length' can be const.
2.17.0 diamond-2.1.11/src/util/parallel/filestack.h:59:13: style:inconclusive: Technically the member function 'FileStack::get_max_line_length' can be const. [functionConst]
     diamond-2.1.11/src/util/parallel/filestack.cpp:426:16: note: Technically the member function 'FileStack::get_max_line_length' can be const.
     diamond-2.1.11/src/util/parallel/filestack.h:59:13: note: Technically the member function 'FileStack::get_max_line_length' can be const.
head diamond-2.1.11/src/util/parallel/parallelizer.cpp:108:20: performance:inconclusive: Technically the member function 'Parallelizer::clear' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     diamond-2.1.11/src/util/parallel/parallelizer.h:37:14: note: Technically the member function 'Parallelizer::clear' can be static (but you may consider moving to unnamed namespace).
     diamond-2.1.11/src/util/parallel/parallelizer.cpp:108:20: note: Technically the member function 'Parallelizer::clear' can be static (but you may consider moving to unnamed namespace).
head diamond-2.1.11/src/util/parallel/parallelizer.cpp:120:22: style:inconclusive: Technically the member function 'Parallelizer::get_id' can be const. [functionConst]
     diamond-2.1.11/src/util/parallel/parallelizer.h:40:21: note: Technically the member function 'Parallelizer::get_id' can be const.
     diamond-2.1.11/src/util/parallel/parallelizer.cpp:120:22: note: Technically the member function 'Parallelizer::get_id' can be const.
head diamond-2.1.11/src/util/parallel/parallelizer.cpp:124:19: style:inconclusive: Technically the member function 'Parallelizer::get_rank' can be const. [functionConst]
     diamond-2.1.11/src/util/parallel/parallelizer.h:39:13: note: Technically the member function 'Parallelizer::get_rank' can be const.
     diamond-2.1.11/src/util/parallel/parallelizer.cpp:124:19: note: Technically the member function 'Parallelizer::get_rank' can be const.
head diamond-2.1.11/src/util/parallel/parallelizer.cpp:128:22: style:inconclusive: Technically the member function 'Parallelizer::get_work_directory' can be const. [functionConst]
     diamond-2.1.11/src/util/parallel/parallelizer.h:41:21: note: Technically the member function 'Parallelizer::get_work_directory' can be const.
     diamond-2.1.11/src/util/parallel/parallelizer.cpp:128:22: note: Technically the member function 'Parallelizer::get_work_directory' can be const.
head diamond-2.1.11/src/util/parallel/parallelizer.cpp:132:19: style:inconclusive: Technically the member function 'Parallelizer::get_n_registered' can be const. [functionConst]
     diamond-2.1.11/src/util/parallel/parallelizer.h:42:13: note: Technically the member function 'Parallelizer::get_n_registered' can be const.
     diamond-2.1.11/src/util/parallel/parallelizer.cpp:132:19: note: Technically the member function 'Parallelizer::get_n_registered' can be const.
head diamond-2.1.11/src/util/parallel/parallelizer.cpp:136:20: style:inconclusive: Technically the member function 'Parallelizer::is_master' can be const. [functionConst]
     diamond-2.1.11/src/util/parallel/parallelizer.h:44:14: note: Technically the member function 'Parallelizer::is_master' can be const.
     diamond-2.1.11/src/util/parallel/parallelizer.cpp:136:20: note: Technically the member function 'Parallelizer::is_master' can be const.
head diamond-2.1.11/src/util/parallel/parallelizer.cpp:140:22: style:inconclusive: Technically the member function 'Parallelizer::get_barrier_file_name' can be const. [functionConst]
     diamond-2.1.11/src/util/parallel/parallelizer.h:82:21: note: Technically the member function 'Parallelizer::get_barrier_file_name' can be const.
     diamond-2.1.11/src/util/parallel/parallelizer.cpp:140:22: note: Technically the member function 'Parallelizer::get_barrier_file_name' can be const.
2.17.0 diamond-2.1.11/src/util/parallel/parallelizer.h:37:14: performance:inconclusive: Technically the member function 'Parallelizer::clear' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     diamond-2.1.11/src/util/parallel/parallelizer.cpp:108:20: note: Technically the member function 'Parallelizer::clear' can be static (but you may consider moving to unnamed namespace).
     diamond-2.1.11/src/util/parallel/parallelizer.h:37:14: note: Technically the member function 'Parallelizer::clear' can be static (but you may consider moving to unnamed namespace).
2.17.0 diamond-2.1.11/src/util/parallel/parallelizer.h:39:13: style:inconclusive: Technically the member function 'Parallelizer::get_rank' can be const. [functionConst]
     diamond-2.1.11/src/util/parallel/parallelizer.cpp:124:19: note: Technically the member function 'Parallelizer::get_rank' can be const.
     diamond-2.1.11/src/util/parallel/parallelizer.h:39:13: note: Technically the member function 'Parallelizer::get_rank' can be const.
2.17.0 diamond-2.1.11/src/util/parallel/parallelizer.h:40:21: style:inconclusive: Technically the member function 'Parallelizer::get_id' can be const. [functionConst]
     diamond-2.1.11/src/util/parallel/parallelizer.cpp:120:22: note: Technically the member function 'Parallelizer::get_id' can be const.
     diamond-2.1.11/src/util/parallel/parallelizer.h:40:21: note: Technically the member function 'Parallelizer::get_id' can be const.
2.17.0 diamond-2.1.11/src/util/parallel/parallelizer.h:41:21: style:inconclusive: Technically the member function 'Parallelizer::get_work_directory' can be const. [functionConst]
     diamond-2.1.11/src/util/parallel/parallelizer.cpp:128:22: note: Technically the member function 'Parallelizer::get_work_directory' can be const.
     diamond-2.1.11/src/util/parallel/parallelizer.h:41:21: note: Technically the member function 'Parallelizer::get_work_directory' can be const.
2.17.0 diamond-2.1.11/src/util/parallel/parallelizer.h:42:13: style:inconclusive: Technically the member function 'Parallelizer::get_n_registered' can be const. [functionConst]
     diamond-2.1.11/src/util/parallel/parallelizer.cpp:132:19: note: Technically the member function 'Parallelizer::get_n_registered' can be const.
     diamond-2.1.11/src/util/parallel/parallelizer.h:42:13: note: Technically the member function 'Parallelizer::get_n_registered' can be const.
2.17.0 diamond-2.1.11/src/util/parallel/parallelizer.h:44:14: style:inconclusive: Technically the member function 'Parallelizer::is_master' can be const. [functionConst]
     diamond-2.1.11/src/util/parallel/parallelizer.cpp:136:20: note: Technically the member function 'Parallelizer::is_master' can be const.
     diamond-2.1.11/src/util/parallel/parallelizer.h:44:14: note: Technically the member function 'Parallelizer::is_master' can be const.
2.17.0 diamond-2.1.11/src/util/parallel/parallelizer.h:82:21: style:inconclusive: Technically the member function 'Parallelizer::get_barrier_file_name' can be const. [functionConst]
     diamond-2.1.11/src/util/parallel/parallelizer.cpp:140:22: note: Technically the member function 'Parallelizer::get_barrier_file_name' can be const.
     diamond-2.1.11/src/util/parallel/parallelizer.h:82:21: note: Technically the member function 'Parallelizer::get_barrier_file_name' can be const.
head diamond-2.1.11/src/util/sequence/sequence.cpp:44:15: style: Variable 'l' is assigned a value that is never used. [unreadVariable]
head diamond-2.1.11/src/util/system/getRSS.cpp:29:2: error: #error "Cannot define getPeakRSS( ) or getCurrentRSS( ) for an unknown OS." [preprocessorErrorDirective]
2.17.0 diamond-2.1.11/src/util/tsv/construct.h:32:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Targs [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/util/tsv/construct.h:32:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable T [valueFlowBailoutIncompleteVar]
head diamond-2.1.11/src/util/tsv/file.cpp:112:12: style:inconclusive: Technically the member function 'Util::Tsv::File::eof' can be const. [functionConst]
     diamond-2.1.11/src/util/tsv/file.h:56:7: note: Technically the member function 'Util::Tsv::File::eof' can be const.
     diamond-2.1.11/src/util/tsv/file.cpp:112:12: note: Technically the member function 'Util::Tsv::File::eof' can be const.
2.17.0 diamond-2.1.11/src/util/tsv/file.h:56:7: style:inconclusive: Technically the member function 'Util::Tsv::File::eof' can be const. [functionConst]
     diamond-2.1.11/src/util/tsv/file.cpp:112:12: note: Technically the member function 'Util::Tsv::File::eof' can be const.
     diamond-2.1.11/src/util/tsv/file.h:56:7: note: Technically the member function 'Util::Tsv::File::eof' can be const.
head diamond-2.1.11/src/util/tsv/table.cpp:135:13: performance:inconclusive: Technically the member function 'Util::Tsv::Table::write_record' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     diamond-2.1.11/src/util/tsv/table.h:71:7: note: Technically the member function 'Util::Tsv::Table::write_record' can be static (but you may consider moving to unnamed namespace).
     diamond-2.1.11/src/util/tsv/table.cpp:135:13: note: Technically the member function 'Util::Tsv::Table::write_record' can be static (but you may consider moving to unnamed namespace).
2.17.0 diamond-2.1.11/src/util/tsv/table.h:71:7: performance:inconclusive: Technically the member function 'Util::Tsv::Table::write_record' can be static (but you may consider moving to unnamed namespace). [functionStatic]
     diamond-2.1.11/src/util/tsv/table.cpp:135:13: note: Technically the member function 'Util::Tsv::Table::write_record' can be static (but you may consider moving to unnamed namespace).
     diamond-2.1.11/src/util/tsv/table.h:71:7: note: Technically the member function 'Util::Tsv::Table::write_record' can be static (but you may consider moving to unnamed namespace).


DONE