/dports/biology/bamutil/bamUtil-1.0.15/libStatGen/bam/test/ |
H A D | TestCigarHelper.cpp | 40 CigarRoller newCigar; in testSoftClipBeginByRefPos() local 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() [all …]
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/dports/biology/bamutil/bamUtil-1.0.15/libStatGen/bam/ |
H A D | CigarHelper.cpp | 28 newCigar.clear(); in softClipBeginByRefPos() 48 newCigar.Set(record.getCigar()); in softClipBeginByRefPos() 64 newCigar += *op; in softClipBeginByRefPos() 138 newCigar += *op; in softClipBeginByRefPos() 154 newCigar += *op; in softClipBeginByRefPos() 188 newCigar.clear(); in softClipEndByRefPos() 261 newCigar += *op; in softClipEndByRefPos() 271 newCigar += *op; in softClipEndByRefPos() 290 newCigar.Remove(j); in softClipEndByRefPos() 298 newCigar.Remove(j); in softClipEndByRefPos() [all …]
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H A D | CigarHelper.h | 43 CigarRoller& newCigar, 61 CigarRoller& newCigar);
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/dports/biology/vcflib/vcflib-1.0.2/smithwaterman/ |
H A D | LeftAlign.cpp | 632 vector<pair<int, string> > newCigar; in leftAlign() local 647 cigar = joinCIGAR(newCigar); in leftAlign() 683 if (!newCigar.empty() && newCigar.back().second == "S") { in leftAlign() 684 newCigar.back().first += indel.length; in leftAlign() 695 pair<int, string>& op = newCigar.back(); in leftAlign() 701 …if (!newCigar.empty() && newCigar.back().second == "M") newCigar.back().first += indel.position - … in leftAlign() 710 for (vector<pair<int, string> >::iterator c = newCigar.begin(); c != newCigar.end(); ++c) in leftAlign() 720 if (newCigar.back().second == "M") newCigar.back().first += remainingReadBp; in leftAlign() 724 if (newCigar.back().second == "D") newCigar.pop_back(); // remove trailing deletions in leftAlign() 727 if (newCigar.back().second == "S") newCigar.back().first += softEnd.size(); in leftAlign() [all …]
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/dports/biology/freebayes/freebayes-1.3.5/vcflib/smithwaterman/ |
H A D | LeftAlign.cpp | 632 vector<pair<int, string> > newCigar; in leftAlign() local 647 cigar = joinCIGAR(newCigar); in leftAlign() 683 if (!newCigar.empty() && newCigar.back().second == "S") { in leftAlign() 684 newCigar.back().first += indel.length; in leftAlign() 695 pair<int, string>& op = newCigar.back(); in leftAlign() 701 …if (!newCigar.empty() && newCigar.back().second == "M") newCigar.back().first += indel.position - … in leftAlign() 710 for (vector<pair<int, string> >::iterator c = newCigar.begin(); c != newCigar.end(); ++c) in leftAlign() 720 if (newCigar.back().second == "M") newCigar.back().first += remainingReadBp; in leftAlign() 724 if (newCigar.back().second == "D") newCigar.pop_back(); // remove trailing deletions in leftAlign() 727 if (newCigar.back().second == "S") newCigar.back().first += softEnd.size(); in leftAlign() [all …]
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/dports/biology/smithwaterman/smithwaterman-2610e259611ae4cde8f03c72499d28f03f6d38a7/ |
H A D | LeftAlign.cpp | 632 vector<pair<int, string> > newCigar; in leftAlign() local 647 cigar = joinCIGAR(newCigar); in leftAlign() 683 if (!newCigar.empty() && newCigar.back().second == "S") { in leftAlign() 684 newCigar.back().first += indel.length; in leftAlign() 695 pair<int, string>& op = newCigar.back(); in leftAlign() 701 …if (!newCigar.empty() && newCigar.back().second == "M") newCigar.back().first += indel.position - … in leftAlign() 710 for (vector<pair<int, string> >::iterator c = newCigar.begin(); c != newCigar.end(); ++c) in leftAlign() 720 if (newCigar.back().second == "M") newCigar.back().first += remainingReadBp; in leftAlign() 724 if (newCigar.back().second == "D") newCigar.pop_back(); // remove trailing deletions in leftAlign() 727 if (newCigar.back().second == "S") newCigar.back().first += softEnd.size(); in leftAlign() [all …]
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/dports/biology/freebayes/freebayes-1.3.5/src/ |
H A D | LeftAlign.cpp | 246 CIGAR newCigar; in leftAlign() local 249 newCigar.ADDCIGAR(CIGOP('S', softBegin.size())); in leftAlign() 255 newCigar.ADDCIGAR(CIGOP('M', last.position)); in leftAlign() 258 newCigar.ADDCIGAR(CIGOP('I', last.length)); in leftAlign() 260 newCigar.ADDCIGAR(CIGOP('N', last.length)); in leftAlign() 262 newCigar.ADDCIGAR(CIGOP('D', last.length)); in leftAlign() 276 CIGOP& op = newCigar.back(); in leftAlign() 285 newCigar.ADDCIGAR(CIGOP('I', indel.length)); in leftAlign() 302 newCigar.ADDCIGAR(CIGOP('S', softEnd.size())); in leftAlign() 321 alignment.CigarData = newCigar; in leftAlign() [all …]
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/haplotype/ |
H A D | Haplotype.java | 109 …final Cigar newCigar = AlignmentUtils.trimCigarByReference(getCigar(), newStart, newStop).getCigar… in trim() local 110 …final boolean leadingInsertion = !newCigar.getFirstCigarElement().getOperator().consumesReferenceB… in trim() 111 …final boolean trailingInsertion = !newCigar.getLastCigarElement().getOperator().consumesReferenceB… in trim() 113 … final int lastIndexToKeepExclusive = newCigar.numCigarElements() - (trailingInsertion ? 1 : 0); in trim() 119 … final Cigar leadingIndelTrimmedNewCigar = !(leadingInsertion || trailingInsertion) ? newCigar : in trim() 120 …new CigarBuilder(false).addAll(newCigar.getCigarElements().subList(firstIndexToKeepInclusive, last… in trim()
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/read/ |
H A D | CigarUtils.java | 363 final CigarBuilder newCigar = new CigarBuilder(); in clipCigar() local 370 newCigar.add(new CigarElement(element.getLength(), element.getOperator())); in clipCigar() 379 newCigar.add(new CigarElement(element.getLength(), operator)); in clipCigar() 387 newCigar.add(new CigarElement(element.getLength(), clippingOperator)); in clipCigar() 390 newCigar.add(new CigarElement(clippedLength, clippingOperator)); in clipCigar() 391 newCigar.add(new CigarElement(unclippedLength, operator)); in clipCigar() 393 newCigar.add(new CigarElement(unclippedLength, operator)); in clipCigar() 394 newCigar.add(new CigarElement(clippedLength, clippingOperator)); in clipCigar() 400 return newCigar.make(); in clipCigar()
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H A D | AlignmentUtils.java | 114 …final Cigar newCigar = appendClippedElementsFromCigarToCigar(leftAlignedReadToRefCigar, originalCi… in createReadAlignedToRef() local 115 copiedRead.setCigar(newCigar); in createReadAlignedToRef()
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/dports/biology/bamutil/bamUtil-1.0.15/src/ |
H A D | OverlapHandler.cpp | 114 static CigarRoller newCigar; // holds updated cigar. in handleNoOverlapWrongOrientation() local 125 newCigar) != CigarHelper::NO_CLIP) in handleNoOverlapWrongOrientation() 134 record.setCigar(newCigar); in handleNoOverlapWrongOrientation()
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H A D | OverlapClipLowerBaseQual.cpp | 260 static CigarRoller newCigar; in handleOverlapWithoutMate() local 279 newCigar); in handleOverlapWithoutMate() 313 record.setCigar(newCigar); in handleOverlapWithoutMate()
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/dports/biology/pbbam/pbbam-0.18.0/tests/src/ |
H A D | test_BamRecord.cpp | 322 const std::string& newCigar, in CheckBaseTagsClippedAndAligned() 324 { return MakeCigaredBaseRecord(newBases, newCigar, newStrand); }; in CheckBaseTagsClippedAndAligned() argument 353 const std::string& newCigar, in CheckFrameTagsClippedAndAligned() 383 const std::string& newCigar, in CheckQualityTagsClippedAndAligned() 431 const std::string& newCigar, in CheckQualitiesClippedAndAligned() 457 const std::string& newCigar, in CheckSequenceClippedAndAligned() 459 { return BamRecordTests::MakeCigaredRecord(newSeq, newCigar, newStrand); }; in CheckSequenceClippedAndAligned() argument 483 const std::string& newCigar, in CheckPulseBaseTags() 519 const std::string& newCigar, in CheckPulseFrameTags() 563 const std::string& newCigar, in CheckPulseQualityTags() [all …]
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/dports/biology/vcflib/vcflib-1.0.2/src/ |
H A D | vcfleftalign.cpp | 389 Cigar newCigar; in leftAlign() local 392 newCigar.push_back(make_pair(softBegin.size(), "S")); in leftAlign() 398 newCigar.push_back(make_pair(last.position, "M")); in leftAlign() 399 newCigar.push_back(make_pair(last.length, (last.insertion ? "I" : "D"))); in leftAlign() 401 newCigar.push_back(make_pair(last.length, (last.insertion ? "I" : "D"))); in leftAlign() 414 pair<int, string>& op = newCigar.back(); in leftAlign() 417 newCigar.push_back(make_pair(indel.position - lastend, "M")); in leftAlign() 418 newCigar.push_back(make_pair(indel.length, (indel.insertion ? "I" : "D"))); in leftAlign() 425 newCigar.push_back(make_pair(alignedLength - lastend, "M")); in leftAlign() 429 newCigar.push_back(make_pair(softEnd.size(), "S")); in leftAlign() [all …]
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/dports/biology/freebayes/freebayes-1.3.5/vcflib-temp/src/ |
H A D | vcfleftalign.cpp | 380 Cigar newCigar; in leftAlign() local 383 newCigar.push_back(make_pair(softBegin.size(), "S")); in leftAlign() 389 newCigar.push_back(make_pair(last.position, "M")); in leftAlign() 390 newCigar.push_back(make_pair(last.length, (last.insertion ? "I" : "D"))); in leftAlign() 392 newCigar.push_back(make_pair(last.length, (last.insertion ? "I" : "D"))); in leftAlign() 405 pair<int, string>& op = newCigar.back(); in leftAlign() 408 newCigar.push_back(make_pair(indel.position - lastend, "M")); in leftAlign() 409 newCigar.push_back(make_pair(indel.length, (indel.insertion ? "I" : "D"))); in leftAlign() 416 newCigar.push_back(make_pair(alignedLength - lastend, "M")); in leftAlign() 420 newCigar.push_back(make_pair(softEnd.size(), "S")); in leftAlign() [all …]
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/dports/biology/freebayes/freebayes-1.3.5/vcflib/src/ |
H A D | vcfleftalign.cpp | 380 Cigar newCigar; in leftAlign() local 383 newCigar.push_back(make_pair(softBegin.size(), "S")); in leftAlign() 389 newCigar.push_back(make_pair(last.position, "M")); in leftAlign() 390 newCigar.push_back(make_pair(last.length, (last.insertion ? "I" : "D"))); in leftAlign() 392 newCigar.push_back(make_pair(last.length, (last.insertion ? "I" : "D"))); in leftAlign() 405 pair<int, string>& op = newCigar.back(); in leftAlign() 408 newCigar.push_back(make_pair(indel.position - lastend, "M")); in leftAlign() 409 newCigar.push_back(make_pair(indel.length, (indel.insertion ? "I" : "D"))); in leftAlign() 416 newCigar.push_back(make_pair(alignedLength - lastend, "M")); in leftAlign() 420 newCigar.push_back(make_pair(softEnd.size(), "S")); in leftAlign() [all …]
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/clipping/ |
H A D | ClippingOp.java | 98 … final Cigar newCigar = CigarUtils.clipCigar(oldCigar, start, myStop + 1, CigarOperator.SOFT_CLIP); in applySoftClipBases() local 99 readCopied.setCigar(newCigar); in applySoftClipBases() 195 …final Cigar newCigar = read.isUnmapped() ? new Cigar() : CigarUtils.clipCigar(cigar, start, stop +… in applyHardClipBases() local 208 hardClippedRead.setCigar(newCigar); in applyHardClipBases()
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/ |
H A D | ReadAnonymizer.java | 126 final List<CigarElement> newCigar = new ArrayList<>(); in anonymizeRead() local 200 newCigar.add(new CigarElement(currentNewCigarOpCount, currentNewCigarOp)); in anonymizeRead() 216 newCigar.add(new CigarElement(currentNewCigarOpCount, currentNewCigarOp)); in anonymizeRead() 219 read.setCigar(new Cigar(newCigar)); in anonymizeRead()
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/read/mergealignment/ |
H A D | AbstractAlignmentMerger.java | 526 Cigar newCigar = null; in createNewCigarIfMapsOffEndOfReference() local 537 newCigar = new Cigar(newCigarElements); in createNewCigarIfMapsOffEndOfReference() 540 return newCigar; in createNewCigarIfMapsOffEndOfReference()
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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/read/ |
H A D | GATKReadAdaptersUnitTest.java | 478 final Cigar newCigar = TextCigarCodec.decode("4M"); in testGetAndSetCigar() local 479 read.setCigar(newCigar); in testGetAndSetCigar() 480 Assert.assertEquals(read.getCigar(), newCigar, "Wrong cigar for read after setCigar()"); in testGetAndSetCigar() local 481 …Assert.assertEquals(read.numCigarElements(), newCigar.numCigarElements(), "Wrong numCigarElements … in testGetAndSetCigar() 482 …Assert.assertEquals(read.getCigarElement(0), newCigar.getCigarElement(0), "Wrong numCigarElement f… in testGetAndSetCigar() 1017 final Cigar newCigar = TextCigarCodec.decode("4M"); in testSAMStringCigar() local 1018 read.setCigar(newCigar); in testSAMStringCigar()
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H A D | AlignmentUtilsUnitTest.java | 1126 final Cigar newCigar = AlignmentUtils.removeTrailingDeletions(originalCigar); in testRemoveTrailingDeletions() local 1128 Assert.assertEquals(originalCigar.equals(newCigar), !cigar.endsWith("D")); in testRemoveTrailingDeletions()
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/alignment/ |
H A D | ContigAlignmentsModifier.java | 171 …final Cigar newCigar = new CigarBuilder().addAll(leftClippings).addAll(newMiddleSection).addAll(ri… local 184 return new Tuple2<>(newRefSpan, newCigar);
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