| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/discovery/alignment/ |
| H A D | ContigAlignmentsModifierUnitTest.java | 39 1, cigar.getReadLength())).collect(Collectors.toList()); in testGappedAlignmentBreaker_OneInsertion()
57 1, cigar.getReadLength())).collect(Collectors.toList()); in testGappedAlignmentBreaker_OneDeletion()
75 1, cigar.getReadLength())).collect(Collectors.toList()); in testGappedAlignmentBreaker_Complex()
108 cigar.getReadLength())).collect(Collectors.toList()); in testGappedAlignmentBreaker_GapSizeSensitivity()
131 1, cigar.getReadLength()+1+8)).collect(Collectors.toList()); in testGappedAlignmentBreaker_HardAndSoftClip()
154 cigar.getReadLength())).collect(Collectors.toList()); in testGappedAlignmentBreaker_TerminalInsertionOperatorToSoftClip()
223 1, cigar.getReadLength())).collect(Collectors.toList()); in testGappedAlignmentBreaker_NegativeStrand()
255 …readStart, readStart+cigar.getReadLength() - CigarUtils.countClippedBases(cigar, CigarOperator.SOF… in willThrowOnInvalidCigar()
269 …ContigAlignmentsModifier.splitGappedAlignment(alignment, 1, cigar.getReadLength() + CigarUtils.cou… in testGappedAlignmentBreaker_NoLongerExpectException()
275 …ContigAlignmentsModifier.splitGappedAlignment(alignment, 1, cigar.getReadLength() + CigarUtils.cou… in testGappedAlignmentBreaker_NoLongerExpectException()
[all …]
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/read/ |
| H A D | ArtificialBAMBuilderUnitTest.java | 52 Assert.assertEquals(bamBuilder.getReadLength(), readLength); in testBamProvider()
86 Assert.assertEquals(read.getReadLength(), bamBuilder.getReadLength()); in assertGoodRead()
87 Assert.assertEquals(read.getReadBases().length, bamBuilder.getReadLength()); in assertGoodRead()
88 Assert.assertEquals(read.getBaseQualities().length, bamBuilder.getReadLength()); in assertGoodRead()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/htsjdk/samtools/ |
| H A D | SAMRecordSparkCodec.java | 69 final int readLength = alignment.getReadLength(); in encode()
100 this.binaryCodec.writeInt(alignment.getReadLength()); in encode()
110 if (alignment.getReadLength() != alignment.getBaseQualities().length && in encode()
113 alignment.getReadName() + "; read length: " + alignment.getReadLength() + in encode()
126 qualities = new byte[alignment.getReadLength()]; in encode()
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| /dports/biology/velvet/velvet_1.2.10/contrib/VelvetOptimiser-2.2.4/VelvetOpt/ |
| H A D | Utils.pm | 179 my $l = &getReadLength($file, 'Fasta');
187 my $l = &getReadLength($file, 'Fastq');
209 sub getReadLength { subroutine
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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 | 459 CigarUtil.softClip3PrimeEndOfRead(pos, Math.min(pos.getReadLength(), in clipForOverlappingReads()
460 pos.getReadLength() - posDiff + 1)); in clipForOverlappingReads()
464 CigarUtil.softClip3PrimeEndOfRead(neg, Math.min(neg.getReadLength(), in clipForOverlappingReads()
465 neg.getReadLength() - negDiff + 1)); in clipForOverlappingReads()
556 rec.getReadLength(), in createNewCigarsIfMapsOffEndOfReference()
568 mateCigar.getReadLength(), in createNewCigarsIfMapsOffEndOfReference()
576 final int alignmentReadLength = alignment.getReadLength(); in updateCigarForTrimmedOrClippedBases()
577 final int originalReadLength = rec.getReadLength(); in updateCigarForTrimmedOrClippedBases()
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| H A D | EarliestFragmentPrimaryAlignmentSelectionStrategy.java | 66 …return rec.getReadLength() - CoordMath.getEnd(alignmentBlock.getReadStart(), alignmentBlock.getLen… in getIndexOfFirstAlignedBase()
|
| /dports/biology/bamutil/bamUtil-1.0.15/libStatGen/bam/ |
| H A D | SamQuerySeqWithRefHelper.cpp | 47 myQueryIndex = myRecord.getReadLength() - 1; in SamQuerySeqWithRefIter()
88 myQueryIndex = myRecord.getReadLength() - 1; in reset()
134 while((myQueryIndex < myRecord.getReadLength()) && in getNextMatchMismatch()
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| H A D | SamStatistics.cpp | 50 int32_t readLen = samRecord.getReadLength(); in updateStatistics()
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| H A D | SamValidation.cpp | 547 samRecord.getReadLength(), in isValidCigar()
620 samRecord.getReadLength(), in isValidQuality()
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| H A D | CigarHelper.cpp | 308 int32_t numSoftClips = record.getReadLength() - readClipPosition; in softClipEndByRefPos()
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| H A D | SamFilter.cpp | 37 int32_t readLength = record.getReadLength(); in clipOnMismatchThreshold()
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| H A D | SamRecord.h | 342 int32_t getReadLength();
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| /dports/biology/bamutil/bamUtil-1.0.15/src/ |
| H A D | OverlapClipLowerBaseQual.cpp | 87 firstRecord.getReadLength()-1); in handleOverlapPair()
239 if(myUnmap && (secondClipPos >= (secondRecord.getReadLength()-1))) in handleOverlapPair()
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| H A D | Recab.cpp | 377 int seqLen = samRecord.getReadLength(); in processReadBuildTable()
673 int seqLen = samRecord.getReadLength(); in processReadApplyTable()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/read/ |
| H A D | AlignmentUtils.java | 103 …otypeSWAlignment.getAlignmentOffset(), rightPaddedHaplotypeVsRefCigar.getReadLength() - 1).getCiga… in createReadAlignedToRef()
117 … if ( leftAlignedReadToRefCigar.getReadLength() + softClippedBases != copiedRead.getLength() ) { in createReadAlignedToRef()
118 …ar " + leftAlignedReadToRefCigar + " with read length " + leftAlignedReadToRefCigar.getReadLength() in createReadAlignedToRef()
119 …ring() + "\nhapToRef " + haplotypeToRef + " length " + haplotypeToRef.getReadLength() + "/" + hapl… in createReadAlignedToRef()
120 …+ "\nreadToHap " + swCigar + " length " + swCigar.getReadLength() + "/" + swCigar.getReferenceLeng… in createReadAlignedToRef()
186 …if ( bases.length != basesToRefCigar.getReadLength() ) throw new IllegalArgumentException("Mismatc… in getBasesCoveringRefInterval()
536 …if ( offset >= cigar.getReadLength() ) throw new IllegalArgumentException("attempting to find the … in calcAlignmentByteArrayOffset()
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| H A D | ArtificialBAMBuilder.java | 169 public int getReadLength() { return readLength; } in getReadLength() method in ArtificialBAMBuilder
|
| /dports/biology/bamutil/bamUtil-1.0.15/libStatGen/bam/examples/printRefPositions/ |
| H A D | PrintRefPositions.cpp | 42 for(int i = 0; i < record.getReadLength(); i++) in printRefPositions()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/haplotype/ |
| H A D | Haplotype.java | 212 …this.cigar.getReadLength() == length(), () -> "Read length " + length() + " not equal to the read … in setCigar()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/locusiterator/ |
| H A D | LIBSTest.java | 21 this.readLength = cigar.getReadLength(); in LIBSTest()
|
| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/components/alignment/ |
| H A D | SAMRecordList.java | 208 thisRead.getReadLength(), in paintComponent()
233 thisWidth = (String.valueOf(thisRead.getReadLength()) ).length(); in getFormatString()
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| /dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/ |
| H A D | BwaMemIntegrationTest.java | 106 … final int maxDistance = chimeric.get(0).getReadLength() + chimeric.get(1).getReadLength() + 100; in testChimericUnpairedMapping()
|
| /dports/biology/bamutil/bamUtil-1.0.15/libStatGen/bam/test/ |
| H A D | TestValidate.cpp | 91 assert(samRecord.getReadLength() == expectedRecordPtr->myReadLength); in validateRead1()
373 assert(samRecord.getReadLength() == expectedRecordPtr->myReadLength); in validateRead2()
543 assert(samRecord.getReadLength() == expectedRecordPtr->myReadLength); in validateRead3()
754 assert(samRecord.getReadLength() == expectedRecordPtr->myReadLength); in validateRead4()
940 assert(samRecord.getReadLength() == expectedRecordPtr->myReadLength); in validateRead5()
1190 assert(samRecord.getReadLength() == expectedRecordPtr->myReadLength); in validateRead6()
1336 assert(samRecord.getReadLength() == expectedRecordPtr->myReadLength); in validateRead7()
1498 assert(samRecord.getReadLength() == expectedRecordPtr->myReadLength); in validateRead8()
1620 assert(samRecord.getReadLength() == expectedRecordPtr->myReadLength); in validateRead9()
1777 assert(samRecord.getReadLength() == expectedRecordPtr->myReadLength); in validateRead10()
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| /dports/biology/gatk/gatk-4.2.0.0/src/testUtils/java/org/broadinstitute/hellbender/testutils/ |
| H A D | ReadClipperTestUtils.java | 60 int readLength = cigar.getReadLength(); in makeReadFromCigar()
|
| /dports/cad/sweethome3d/SweetHome3D-6.6.4-src/src/com/eteks/sweethome3d/j3d/ |
| H A D | Max3DSLoader.java | 1453 public long getReadLength() { in getReadLength() method in Max3DSLoader.Chunk3DS
1501 if (chunk.getLength() != chunk.getReadLength()) { in releaseChunk()
1503 …d to read " + chunk.getLength() + " bytes, but actually read " + chunk.getReadLength() + " bytes"); in releaseChunk()
1515 return chunk.getLength() == chunk.getReadLength(); in isChunckEndReached()
1523 long remainingLength = chunk.getLength() - chunk.getReadLength(); in readUntilChunkEnd()
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| /dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/interfaces/loader/ |
| H A D | common-reader-priv.h | 132 rc_t ( *getReadLength ) ( const SEQUENCE_IMPL *self, uint32_t *length ); member
|