| /dports/biology/seqan1/seqan-1.3.1/apps/rabema/ |
| H A D | verification.h | 48 size_t contigId; member
84 TContigIdType contigId, in verifyMatchestoErrorFunctionResults_FindReads()
123 TContigIdType contigId, in verifyMatchestoErrorFunctionResults_FindReads()
154 TContigIdType contigId, in verifyMatchestoErrorFunctionResults_FindReads()
183 TContigIdType contigId, in verifyMatchestoErrorFunctionResults_FindReads()
213 TContigIdType contigId, in verifyMatchestoErrorFunctionResults_FindReads()
273 for (TContigId contigId = 0; contigId < length(contigs); ++contigId) { in verifyMatchesToErrorFunctionResults() local
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| H A D | witio.h | 41 size_t contigId; member
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| H A D | evaluation.h | 168 TContigId contigId = alignedRead.contigId; in bestScoreForAligned() local
234 size_t const & contigId, in compareAlignedReadsToReferenceOnContigForOneRead()
477 size_t const & contigId, in compareAlignedReadsToReferenceOnContig()
557 size_t contigId = _min(alignedReadsBegin->contigId, witRecordsBegin->contigId); in compareAlignedReadsToReference() local
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/rep_sep/ |
| H A D | rgraph_construction.h | 32 TId const contigId) in construct()
127 const TId contigId) in add_mate_pairs()
149 TId const contigId, in scoreGraph_()
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| H A D | column_scanner.h | 52 TId const contigId, in isCandidate()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/razers3/ |
| H A D | razers_window.h | 45 …unsigned contigId, // ... and its sequence nu… in _mapSingleReadsToContigWindow()
77 …unsigned contigId, // ... and its sequence nu… in _mapSingleReadsToContigWindow()
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| H A D | simulate_reads.cpp | 39 unsigned contigId = distContig(rng[id]); in simulateReads() local
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| /dports/biology/seqan1/seqan-1.3.1/apps/rep_sep/ |
| H A D | rgraph_construction.h | 32 TId const contigId) in construct()
127 const TId contigId) in add_mate_pairs()
149 TId const contigId, in scoreGraph_()
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| H A D | column_scanner.h | 52 TId const contigId, in isCandidate()
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| /dports/biology/pbbam/pbbam-0.18.0/src/vcf/ |
| H A D | VcfSort.cpp | 25 const auto& contigId = contigDefs.at(i).Id(); in SortFile() local
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/tutorial/simple_rna_seq/ |
| H A D | genequant_solution2.cpp | 64 TId contigId = getAnnotation(it).contigId; in extractGeneIntervals() local
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| H A D | genequant_assignment3.cpp | 66 TId contigId = getAnnotation(it).contigId; in extractGeneIntervals() local
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| H A D | genequant_solution3.cpp | 64 TId contigId = getAnnotation(it).contigId; in extractGeneIntervals() local
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| H A D | genequant_assignment4.cpp | 69 TId contigId = getAnnotation(it).contigId; in extractGeneIntervals() local
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| H A D | genequant_solution4.cpp | 66 TId contigId = getAnnotation(it).contigId; in extractGeneIntervals() local
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/yara/ |
| H A D | bits_matches.h | 121 typename Member<Match, ContigId>::Type contigId : MemberBits<Match, ContigId>::VALUE; member
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| /dports/biology/seqan/seqan-library-2.4.0/include/seqan/consensus/ |
| H A D | consensus_base.h | 159 TId const contigId) in _loadContigReads()
203 TSize2 contigId, in convertAlignment()
318 TSize2 contigId, in convertAlignment()
344 TSize contigId) in getGappedConsensus()
380 TSize contigId) in assignGappedConsensus()
540 TContigId contigId) in updateContig()
1019 TContigId contigId, in consensusCalling()
1094 TContigId contigId, in consensusCalling()
1837 TId contigId = 0; in _writeCeleraCgb() local
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/consensus/ |
| H A D | consensus_base.h | 159 TId const contigId) in _loadContigReads()
203 TSize2 contigId, in convertAlignment()
318 TSize2 contigId, in convertAlignment()
344 TSize contigId) in getGappedConsensus()
380 TSize contigId) in assignGappedConsensus()
540 TContigId contigId) in updateContig()
1019 TContigId contigId, in consensusCalling()
1094 TContigId contigId, in consensusCalling()
1837 TId contigId = 0; in _writeCeleraCgb() local
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| /dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/consensus/ |
| H A D | consensus_base.h | 159 TId const contigId) in _loadContigReads()
203 TSize2 contigId, in convertAlignment()
318 TSize2 contigId, in convertAlignment()
344 TSize contigId) in getGappedConsensus()
378 TSize contigId) in assignGappedConsensus()
538 TContigId contigId) in updateContig()
1018 TContigId contigId, in consensusCalling()
1094 TContigId contigId, in consensusCalling()
1837 TId contigId = 0; in _writeCeleraCgb() local
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| /dports/biology/seqan1/seqan-1.3.1/apps/insegt/ |
| H A D | read_gff.h | 196 TId contigId; in readAnnotationsFromGFF() local
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| H A D | read_gtf.h | 198 TId contigId; in readAnnotationsFromGTF() local
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/dragstr/ |
| H A D | BufferedReferenceBases.java | 55 …c BufferedReferenceBases of(final ReferenceDataSource dataSource, final String contigId, final int… in of()
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| /dports/biology/seqan1/seqan-1.3.1/seqan/consensus/ |
| H A D | consensus_base.h | 165 TId const contigId) in _loadContigReads()
212 TSize2 contigId, in convertAlignment()
327 TSize2 contigId, in convertAlignment()
354 TSize contigId) in getGappedConsensus()
388 TSize contigId) in assignGappedConsensus()
506 TContigId contigId) in updateContig()
987 TContigId contigId, in consensusCalling()
1063 TContigId contigId, in consensusCalling()
1758 TId contigId = 0; in _writeCeleraCgb() local
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| /dports/biology/seqan1/seqan-1.3.1/seqan/store/ |
| H A D | store_annotation.h | 56 TId contigId; member
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/store/ |
| H A D | store_annotation.h | 145 TId contigId; member
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