/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/cramtools/ref/ |
H A D | ReferenceRegion.java | 26 public long alignmentStart; field in ReferenceRegion 41 if (alignmentStart < 1) in ReferenceRegion() 43 alignmentStart, bases.length)); in ReferenceRegion() 45 this.alignmentStart = alignmentStart; in ReferenceRegion() 54 byte[] copy = copySafe(bases, 1, (int) alignmentStart, (int) (alignmentEnd - alignmentStart + 1)); in copyRegion() 76 int from = arrayPosition(alignmentStart); in copy() 77 int to = arrayPosition(alignmentStart + alignmentSpan); in copy() 82 …return ReferenceRegion.copySafe(array, (int) this.alignmentStart, (int) alignmentStart, alignmentS… in copySafe() 105 int from = (int) (alignmentStart - refAlStart); in copySafe() 117 int from = (int) (alignmentStart - this.alignmentStart); in md5() [all …]
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/read/ |
H A D | ArtificialBAMBuilder.java | 32 int alignmentStart = 1; field in ArtificialBAMBuilder 106 …read = ArtificialReadUtils.createArtificialRead(header, readName, 0, alignmentStart + locus, readL… in makeReads() 160 public int getAlignmentStart() { return alignmentStart; } in getAlignmentStart() 162 public ArtificialBAMBuilder setAlignmentStart(final int alignmentStart) { in setAlignmentStart() argument 163 …Utils.validateArg(alignmentStart > 0, "alignmentStart should be positive but was " + alignmentStar… in setAlignmentStart() 164 this.alignmentStart = alignmentStart; in setAlignmentStart() 188 return alignmentStart + nLoci * (skipNLoci + 1) + readLength; in getAlignmentEnd() 202 ", alignmentStart=" + alignmentStart + in toString()
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H A D | ArtificialReadUtils.java | 134 …teArtificialRead(SAMFileHeader header, String name, int refIndex, int alignmentStart, int length) { in createArtificialRead() argument 135 …RecordToGATKReadAdapter(createArtificialSAMRecord(header, name, refIndex, alignmentStart, length)); in createArtificialRead() 150 …dToGATKReadAdapter(createArtificialSAMRecord(header, name, refIndex, alignmentStart, bases, qual)); in createArtificialRead() 266 read.setAlignmentStart(alignmentStart); in createArtificialUnmappedReadWithAssignedPosition() 349 …if ((refIndex == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX && alignmentStart != SAMRecord.NO_ALIGNMEN… in createArtificialSAMRecord() 350 …(refIndex != SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX && alignmentStart == SAMRecord.NO_ALIGNMENT_ST… in createArtificialSAMRecord() 351 …IllegalArgumentException("Invalid alignment start for artificial read, start = " + alignmentStart); in createArtificialSAMRecord() 355 record.setAlignmentStart(alignmentStart); in createArtificialSAMRecord() 391 … SAMRecord rec = createArtificialSAMRecord(header, name, refIndex, alignmentStart, bases.length); in createArtificialSAMRecord() 415 … SAMRecord rec = createArtificialSAMRecord(header, name, refIndex, alignmentStart, bases, qual); in createArtificialSAMRecord() [all …]
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H A D | AlignmentUtils.java | 517 …fset(final Cigar cigar, final PileupElement pileupElement, final int alignmentStart, final int ref… in calcAlignmentByteArrayOffset() argument 518 …ayOffset( cigar, pileupElement.getOffset(), pileupElement.isDeletion(), alignmentStart, refLocus ); in calcAlignmentByteArrayOffset() 531 …l Cigar cigar, final int offset, final boolean isDeletion, final int alignmentStart, final int ref… in calcAlignmentByteArrayOffset() argument 534 …if ( alignmentStart < 0 ) throw new IllegalArgumentException("attempting to find the alignment pos… in calcAlignmentByteArrayOffset() 542 pileupOffset = refLocus - alignmentStart; in calcAlignmentByteArrayOffset()
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H A D | ReadUtils.java | 682 …Integer, CigarOperator> getReadIndexForReferenceCoordinate(final int alignmentStart, final Cigar c… in getReadIndexForReferenceCoordinate() argument 683 if (refCoord < alignmentStart) { in getReadIndexForReferenceCoordinate() 687 int firstRefPosOfElement = alignmentStart; //inclusive in getReadIndexForReferenceCoordinate() 689 int lastRefPosOfElement = alignmentStart; //exclusive in getReadIndexForReferenceCoordinate()
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/transformers/ |
H A D | AdapterTrimTransformer.java | 43 … for (int alignmentStart = bases.length - minClipLength; alignmentStart >= 0; alignmentStart--) { in apply() 47 …f (!SequenceUtil.isNoCall((byte) adapterSequence.charAt(j)) && bases[alignmentStart + j] != adapte… in apply() 51 …atches < bestNumMismatches || (numMismatches == bestNumMismatches && alignmentStart < bestAlignmen… in apply() 54 bestAlignmentStart = alignmentStart; in apply()
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/dports/biology/gatk/gatk-4.2.0.0/src/testUtils/java/org/broadinstitute/hellbender/testutils/testers/ |
H A D | SamFileTester.java | 155 …public void addMappedFragment(final int referenceSequenceIndex, final int alignmentStart, final bo… in addMappedFragment() argument 157 …addFragment(referenceSequenceIndex, alignmentStart, false, isDuplicate, null, null, defaultQuality… in addMappedFragment() 160 …public void addMappedFragment(final int referenceSequenceIndex, final int alignmentStart, final bo… in addMappedFragment() argument 162 …addFragment(referenceSequenceIndex, alignmentStart, false, isDuplicate, null, null, defaultQuality… in addMappedFragment() 165 …public void addMappedFragment(final int referenceSequenceIndex, final int alignmentStart, final bo… in addMappedFragment() argument 167 …addFragment(referenceSequenceIndex, alignmentStart, false, isDuplicate, cigar, null, defaultQualit… in addMappedFragment() 170 …public void addMappedFragment(final int referenceSequenceIndex, final int alignmentStart, final bo… in addMappedFragment() argument 173 …addFragment(referenceSequenceIndex, alignmentStart, false, isDuplicate, cigar, qualityString, defa… in addMappedFragment() 176 …t(final String readName, final int referenceSequenceIndex, final int alignmentStart, final boolean… in addMappedFragment() argument 242 …addFragment("READ" + readNameCounter++, referenceSequenceIndex, alignmentStart, recordUnmapped, is… in addFragment() [all …]
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/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/test/evosuite-tests/uk/ac/sanger/artemis/cramtools/ref/ |
H A D | ReferenceRegion_ESTest.java | 69 referenceRegion0.alignmentStart = (long) (byte)4; in test05() 70 referenceRegion0.alignmentStart = (long) (byte)0; in test05() 91 referenceRegion1.alignmentStart = (long) (byte) (-1); in test07() 388 assertEquals(1L, referenceRegion0.alignmentStart); in test27() 410 assertEquals(1L, referenceRegion0.alignmentStart); in test29() 446 assertEquals(1L, referenceRegion0.alignmentStart); in test32() 464 assertEquals(1L, referenceRegion0.alignmentStart); in test34() 490 assertEquals(77L, referenceRegion0.alignmentStart); in test36()
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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/ |
H A D | UniqueAltReadCountUnitTest.java | 70 final int alignmentStart = 100; in createTestLikelihoods() local 84 …int startPosition = shiftModulus.isPresent() ? alignmentStart + (i % shiftModulus.get()) : alignme… in createTestLikelihoods() 92 …= ArtificialReadUtils.createArtificialRead(SAM_HEADER, "Read" + j, chromosomeIndex, alignmentStart, in createTestLikelihoods()
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/dports/biology/edlib/edlib-d5774b4/test/ |
H A D | runTests.cpp | 126 int alignmentStart = getAlignmentStart(result.alignment, result.alignmentLength, in runRandomTests() local 128 if (result.startLocations[0] != alignmentStart) { in runRandomTests() 131 result.startLocations[0], alignmentStart); in runRandomTests() 184 int alignmentStart = getAlignmentStart(result3.alignment, result3.alignmentLength, in runRandomTests() local 186 if (result3.startLocations[0] != alignmentStart) { in runRandomTests() 189 result3.startLocations[0], alignmentStart); in runRandomTests() 254 …int alignmentStart = getAlignmentStart(result.alignment, result.alignmentLength, result.endLocatio… in executeTest() local 255 if (result.startLocations[0] != alignmentStart) { in executeTest() 258 result.startLocations[0], alignmentStart); in executeTest()
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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/engine/filters/ |
H A D | ReadGroupBlackListReadFilterUnitTest.java | 108 int alignmentStart = 0; in testFilterOutByReadGroup() local 112 …Read record = ArtificialReadUtils.createArtificialRead(header, "readUno", 0, ++alignmentStart, 20); in testFilterOutByReadGroup() 148 int alignmentStart = 0; in testFilterOutByAttribute() local 152 …Read record = ArtificialReadUtils.createArtificialRead(header, "readUno", 0, ++alignmentStart, 20); in testFilterOutByAttribute()
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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/read/ |
H A D | ArtificialReadUtilsUnitTest.java | 28 int alignmentStart= 19; in testCreateIdenticalArtificialReads() local 31 …cialReadUtils.createIdenticalArtificialReads(10, header, "name", refIndex, alignmentStart, length); in testCreateIdenticalArtificialReads() 35 Assert.assertEquals(read.getStart(), alignmentStart); in testCreateIdenticalArtificialReads() local
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/clipping/ |
H A D | ReadClipper.java | 331 …inal GATKRead read, final int refStart, final int refStop, final int alignmentStart, final int ali… in hardClipToRegion() argument 333 if (alignmentStart <= refStop && alignmentStop >= refStart) { in hardClipToRegion() 334 if (alignmentStart < refStart && alignmentStop > refStop) { in hardClipToRegion() 336 } else if (alignmentStart < refStart) { in hardClipToRegion()
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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/clipping/ |
H A D | ReadClipperUnitTest.java | 226 for ( final int alignmentStart : Arrays.asList(1, 10) ) { in makeRevertSoftClipsBeforeContig() 227 tests.add(new Object[]{softStart, alignmentStart}); in makeRevertSoftClipsBeforeContig() 235 …void testRevertSoftClippedBasesBeforeStartOfContig(final int softStart, final int alignmentStart) { in testRevertSoftClippedBasesBeforeStartOfContig() argument 237 final int nSoft = -1 * (softStart - alignmentStart); in testRevertSoftClippedBasesBeforeStartOfContig() 240 read.setPosition(read.getContig(), alignmentStart); in testRevertSoftClippedBasesBeforeStartOfContig() local 243 Assert.assertEquals(read.getStart(), alignmentStart); in testRevertSoftClippedBasesBeforeStartOfContig() local
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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/locusiterator/ |
H A D | PerSampleReadStateManagerUnitTest.java | 86 final int alignmentStart = 1; in makeReadStacks() local 88 …rtificialReads(readCountsPerAlignmentStart.get(n), header, "foo", 0, alignmentStart, readLengths.g… in makeReadStacks()
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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/realignmentfilter/ |
H A D | RealignmentEngineUnitTest.java | 104 …private GATKRead makeRead(final String name, final int alignmentStart, final String baseString, fi… in makeRead() argument 108 …return ArtificialReadUtils.createArtificialRead(HEADER, name, REF_INDEX, alignmentStart, bases, qu… in makeRead()
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ |
H A D | ReferenceConfidenceModel.java | 756 …final int alignmentStart = activeRegion.getPaddedSpan().getStart() - paddedReferenceLoc.getStart(); in createReferenceHaplotype() local 757 if ( alignmentStart < 0 ) { in createReferenceHaplotype() 758 …row new IllegalStateException("Bad alignment start in createReferenceHaplotype " + alignmentStart); in createReferenceHaplotype() 761 refHaplotype.setAlignmentStartHapwrtRef(alignmentStart); in createReferenceHaplotype()
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/dports/biology/bowtie2/bowtie2-2.4.4/ |
H A D | aligner_result.cpp | 933 const size_t alignmentStart = res.trimmedLeft(true); in add() local 941 for(size_t i = alignmentStart; i < alignmentStart + len; i++) { in add() 951 if(i < alignmentStart + len - 1) { in add() 984 const size_t alignmentStart = res.trimmedLeft(true); in overlap() local 993 for(size_t i = alignmentStart; i < alignmentStart + len; i++) { in overlap() 1003 if(i < alignmentStart + len - 1) { in overlap()
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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/fragments/ |
H A D | FragmentUtilsUnitTest.java | 26 … final int alignmentStart, final int leftSoftclip, final int rightSoftclip) { in makeOverlappingRead() argument 31 …read = ArtificialReadUtils.createArtificialRead(header, "myRead", 0, alignmentStart + leftSoftclip… in makeOverlappingRead()
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/dports/biology/freebayes/freebayes-1.3.5/src/ |
H A D | Allele.h | 140 long int alignmentStart; variable 199 , alignmentStart(bas) in Allele()
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H A D | Allele.cpp | 19 return position - alignmentStart; in bpLeft()
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H A D | AlleleParser.cpp | 2606 if (*a != NULL && allele->alignmentStart <= position && allele->alignmentEnd > position) {
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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/genotyper/ |
H A D | AlleleLikelihoodsUnitTest.java | 592 final int alignmentStart = (r & 1) == 0 ? EVEN_READ_START : ODD_READ_START; 594 …"RRR" + sample + "00" + r, 0, alignmentStart, "AAAAA".getBytes(), new byte[]{30, 30, 30, 30, 30}, …
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