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Searched refs:alignmentStart (Results 1 – 23 of 23) sorted by relevance

/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/cramtools/ref/
H A DReferenceRegion.java26 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()
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/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/read/
H A DArtificialBAMBuilder.java32 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()
H A DArtificialReadUtils.java134 …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 …]
H A DAlignmentUtils.java517 …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()
H A DReadUtils.java682 …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()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/transformers/
H A DAdapterTrimTransformer.java43 … 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()
/dports/biology/gatk/gatk-4.2.0.0/src/testUtils/java/org/broadinstitute/hellbender/testutils/testers/
H A DSamFileTester.java155 …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 …]
/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/test/evosuite-tests/uk/ac/sanger/artemis/cramtools/ref/
H A DReferenceRegion_ESTest.java69 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()
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/mutect/
H A DUniqueAltReadCountUnitTest.java70 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()
/dports/biology/edlib/edlib-d5774b4/test/
H A DrunTests.cpp126 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()
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/engine/filters/
H A DReadGroupBlackListReadFilterUnitTest.java108 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()
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/read/
H A DArtificialReadUtilsUnitTest.java28 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
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/clipping/
H A DReadClipper.java331 …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()
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/clipping/
H A DReadClipperUnitTest.java226 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
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/locusiterator/
H A DPerSampleReadStateManagerUnitTest.java86 final int alignmentStart = 1; in makeReadStacks() local
88 …rtificialReads(readCountsPerAlignmentStart.get(n), header, "foo", 0, alignmentStart, readLengths.g… in makeReadStacks()
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/walkers/realignmentfilter/
H A DRealignmentEngineUnitTest.java104 …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()
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/
H A DReferenceConfidenceModel.java756 …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()
/dports/biology/bowtie2/bowtie2-2.4.4/
H A Daligner_result.cpp933 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()
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/fragments/
H A DFragmentUtilsUnitTest.java26 … final int alignmentStart, final int leftSoftclip, final int rightSoftclip) { in makeOverlappingRead() argument
31 …read = ArtificialReadUtils.createArtificialRead(header, "myRead", 0, alignmentStart + leftSoftclip… in makeOverlappingRead()
/dports/biology/freebayes/freebayes-1.3.5/src/
H A DAllele.h140 long int alignmentStart; variable
199 , alignmentStart(bas) in Allele()
H A DAllele.cpp19 return position - alignmentStart; in bpLeft()
H A DAlleleParser.cpp2606 if (*a != NULL && allele->alignmentStart <= position && allele->alignmentEnd > position) {
/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/genotyper/
H A DAlleleLikelihoodsUnitTest.java592 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}, …