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Searched refs:newCigar (Results 1 – 22 of 22) sorted by relevance

/dports/biology/bamutil/bamUtil-1.0.15/libStatGen/bam/test/
H A DTestCigarHelper.cpp40 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 …]
/dports/biology/bamutil/bamUtil-1.0.15/libStatGen/bam/
H A DCigarHelper.cpp28 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 …]
H A DCigarHelper.h43 CigarRoller& newCigar,
61 CigarRoller& newCigar);
/dports/biology/vcflib/vcflib-1.0.2/smithwaterman/
H A DLeftAlign.cpp632 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()
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/dports/biology/freebayes/freebayes-1.3.5/vcflib/smithwaterman/
H A DLeftAlign.cpp632 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 …]
/dports/biology/smithwaterman/smithwaterman-2610e259611ae4cde8f03c72499d28f03f6d38a7/
H A DLeftAlign.cpp632 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()
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/dports/biology/freebayes/freebayes-1.3.5/src/
H A DLeftAlign.cpp246 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()
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/haplotype/
H A DHaplotype.java109 …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()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/read/
H A DCigarUtils.java363 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()
H A DAlignmentUtils.java114 …final Cigar newCigar = appendClippedElementsFromCigarToCigar(leftAlignedReadToRefCigar, originalCi… in createReadAlignedToRef() local
115 copiedRead.setCigar(newCigar); in createReadAlignedToRef()
/dports/biology/bamutil/bamUtil-1.0.15/src/
H A DOverlapHandler.cpp114 static CigarRoller newCigar; // holds updated cigar. in handleNoOverlapWrongOrientation() local
125 newCigar) != CigarHelper::NO_CLIP) in handleNoOverlapWrongOrientation()
134 record.setCigar(newCigar); in handleNoOverlapWrongOrientation()
H A DOverlapClipLowerBaseQual.cpp260 static CigarRoller newCigar; in handleOverlapWithoutMate() local
279 newCigar); in handleOverlapWithoutMate()
313 record.setCigar(newCigar); in handleOverlapWithoutMate()
/dports/biology/pbbam/pbbam-0.18.0/tests/src/
H A Dtest_BamRecord.cpp322 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()
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/dports/biology/vcflib/vcflib-1.0.2/src/
H A Dvcfleftalign.cpp389 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()
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/dports/biology/freebayes/freebayes-1.3.5/vcflib-temp/src/
H A Dvcfleftalign.cpp380 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()
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/dports/biology/freebayes/freebayes-1.3.5/vcflib/src/
H A Dvcfleftalign.cpp380 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()
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/clipping/
H A DClippingOp.java98 … 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()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/
H A DReadAnonymizer.java126 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()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/read/mergealignment/
H A DAbstractAlignmentMerger.java526 Cigar newCigar = null; in createNewCigarIfMapsOffEndOfReference() local
537 newCigar = new Cigar(newCigarElements); in createNewCigarIfMapsOffEndOfReference()
540 return newCigar; in createNewCigarIfMapsOffEndOfReference()
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/read/
H A DGATKReadAdaptersUnitTest.java478 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()
H A DAlignmentUtilsUnitTest.java1126 final Cigar newCigar = AlignmentUtils.removeTrailingDeletions(originalCigar); in testRemoveTrailingDeletions() local
1128 Assert.assertEquals(originalCigar.equals(newCigar), !cigar.endsWith("D")); in testRemoveTrailingDeletions()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/alignment/
H A DContigAlignmentsModifier.java171 …final Cigar newCigar = new CigarBuilder().addAll(leftClippings).addAll(newMiddleSection).addAll(ri… local
184 return new Tuple2<>(newRefSpan, newCigar);