| /dports/biology/bamutil/bamUtil-1.0.15/libStatGen/bam/test/ |
| H A D | TestCigarHelper.cpp | 58 newCigar.getCigarString(newCigarString); in testSoftClipBeginByRefPos()
65 newCigar.getCigarString(newCigarString); in testSoftClipBeginByRefPos()
77 newCigar.getCigarString(newCigarString); in testSoftClipBeginByRefPos()
85 newCigar.getCigarString(newCigarString); in testSoftClipBeginByRefPos()
92 newCigar.getCigarString(newCigarString); in testSoftClipBeginByRefPos()
99 newCigar.getCigarString(newCigarString); in testSoftClipBeginByRefPos()
106 newCigar.getCigarString(newCigarString); in testSoftClipBeginByRefPos()
113 newCigar.getCigarString(newCigarString); in testSoftClipBeginByRefPos()
120 newCigar.getCigarString(newCigarString); in testSoftClipBeginByRefPos()
127 newCigar.getCigarString(newCigarString); in testSoftClipBeginByRefPos()
[all …]
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| /dports/biology/bamutil/bamUtil-1.0.15/libStatGen/general/ |
| H A D | Cigar.h | 334 void getCigarString(String& cigarString) const;
338 void getCigarString(std::string& cigarString) const;
373 getCigarString(cigarString); in Dump()
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| H A D | Cigar.cpp | 36 void Cigar::getCigarString(std::string& cigarString) const in getCigarString() function in Cigar
52 void Cigar::getCigarString(String& cigarString) const in getCigarString() function in Cigar
56 getCigarString(cigar); in getCigarString()
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| /dports/biology/seqan/seqan-library-2.4.0/include/seqan/bam_io/ |
| H A D | cigar.h | 267 getCigarString(
346 getCigarString(
351 return getCigarString(cigar, gaps1, gaps2, 20);
362 getCigarString(
506 getCigarString(cigar, contigGaps, readGaps);
561 getCigarString(cigar, contigGaps, readGaps);
571 getCigarString(cigar, contigGaps, readGaps);
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/bam_io/ |
| H A D | cigar.h | 267 getCigarString(
346 getCigarString(
351 return getCigarString(cigar, gaps1, gaps2, 20);
362 getCigarString(
506 getCigarString(cigar, contigGaps, readGaps);
561 getCigarString(cigar, contigGaps, readGaps);
571 getCigarString(cigar, contigGaps, readGaps);
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| /dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/bam_io/ |
| H A D | cigar.h | 266 getCigarString(
345 getCigarString(
350 return getCigarString(cigar, gaps1, gaps2, 20);
361 getCigarString(
505 getCigarString(cigar, contigGaps, readGaps);
560 getCigarString(cigar, contigGaps, readGaps);
570 getCigarString(cigar, contigGaps, readGaps);
|
| /dports/biology/ugene/ugene-40.1/src/corelibs/U2View/src/ov_assembly/ |
| H A D | AssemblyReadsAreaHint.cpp | 69 static QString getCigarString(const QString &ci) { in getCigarString() function
148 …text += QString("<tr><td><b>Cigar</b>: %1</td></tr>").arg(getCigarString(U2AssemblyUtils::cig… in formatReadInfo()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/evidence/ |
| H A D | BreakpointEvidence.java | 344 public String getCigarString() { return cigarString; } in getCigarString() method in BreakpointEvidence.ReadEvidence
468 if ( getCigarString() == null || getCigarString().isEmpty() ) { in SplitRead()
514 …return super.toString()+"\tSplit\t"+getCigarString()+"\t"+(tagSA == null ? " SA: None" : (" SA: " … in toString()
723 if ( getCigarString() == null || getCigarString().isEmpty() ) in LargeIndel()
749 public String toString() {return super.toString() + "\tIndel\t" + getCigarString();} in toString()
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| H A D | XGBoostEvidenceFilter.java | 391 final String cigarString = ((ReadEvidence) evidence).getCigarString(); in CigarQualityInfo()
|
| /dports/biology/seqan1/seqan-1.3.1/seqan/store/ |
| H A D | store_io_sam.h | 116 getCigarString( in getCigarString() function
187 getCigarString( in getCigarString() function
192 return getCigarString(cigar, gaps1, gaps2, 20); in getCigarString()
203 getCigarString( in getCigarString() function
1066 getCigarString(cigar, contigGaps, readGaps); in _writeAlignments()
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| H A D | store_io_bam.h | 538 getCigarString(cigar, contigGaps, readGaps); in _writeAlignments()
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| H A D | store_generated_forwards.h | 839 …gar, typename TGaps1, typename TGaps2, typename TThresh> inline void getCigarString( TCigar &cigar…
840 template <typename TCigar, typename TGaps1, typename TGaps2> inline void getCigarString( TCigar &ci…
841 …pec, typename TGaps1, typename TGaps2, typename TThresh> inline void getCigarString( String<CigarE…
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/yara/ |
| H A D | mapper_aligner.h | 220 getCigarString(me.cigar, contigGaps, readGaps, length(contigInfix)); in _alignMatchImpl()
|
| /dports/biology/bamutil/bamUtil-1.0.15/libStatGen/general/test/cigar/ |
| H A D | CigarRollerTest.cpp | 272 cigar.getCigarString(str); in test()
327 cigar.getCigarString(str); in test()
496 cigar.getCigarString(cigarString); in test()
906 cigar.getCigarString(cigarString); in test()
|
| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/mason2/ |
| H A D | mason_simulator.cpp | 240 getCigarString(record.cigar, gapsContig, gapsRead, std::numeric_limits<int>::max()); in _alignAndSetCigar()
561 getCigarString(record.cigar, gapsContig, gapsRead, std::numeric_limits<int>::max()); in _alignAndSetCigar()
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| /dports/biology/bamutil/bamUtil-1.0.15/libStatGen/bam/ |
| H A D | SamRecord.cpp | 281 cigar.getCigarString(myCigar); in setCigar()
2837 myCigarRoller.getCigarString(myCigar); in parseCigarBinary()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/alignment/ |
| H A D | AlignmentIntervalUnitTest.java | 227 …tart(), samRecord.getReadNegativeStrandFlag() ? "-" : "+", samRecord.getCigarString(), "" + samRec… in testConstructionFromStr()
|
| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/bs_tools/ |
| H A D | bisar.h | 242 getCigarString(cigar, contigGaps, readGaps); in writeBsAlignment()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/read/ |
| H A D | GATKReadAdaptersUnitTest.java | 64 record.setCigar(sam.getCigarString()); in basicReadBackedByADAMRecord()
|
| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/components/alignment/ |
| H A D | BamView.java | 4186 viewer.appendString("Cigar String "+sam.getCigarString()+"\n", Level.DEBUG); in appendToDetailView()
4200 viewer.appendString("Mate Cigar String "+mate.getCigarString()+"\n", Level.DEBUG); in appendToDetailView()
|