final SAMReadGroupRecord rg = rec.getRecord().getReadGroup(); final FingerprintIdDetails details; if (rg == null || !fingerprintIdDetailsMap.containsKey(rg)) { final FingerprintIdDetails unknownFPDetails = createUnknownFP(samFile, rec.getRecord()); fingerprintIdDetailsMap.put(null, unknownFPDetails); details = fingerprintIdDetailsMap.get(rg); final String readName = rec.getRecord().getReadName(); if (!usedReadNames.contains(readName)) { final HaplotypeProbabilitiesFromSequence probs = (HaplotypeProbabilitiesFromSequence) fingerprintsByReadGroup.get(details).get(haplotypeBlock); final byte base = StringUtil.toUpperCase(rec.getReadBase()); final byte qual = rec.getBaseQuality();
SamLocusIterator.RecordAndOffset recordAndOffset1 = new SamLocusIterator.RecordAndOffset(samRecord1, i); SamLocusIterator.RecordAndOffset recordAndOffset2 = new SamLocusIterator.RecordAndOffset(samRecord2, i); locusInfo.add(recordAndOffset1); locusInfo.add(recordAndOffset2);
Assert.assertEquals(li.getRecordAndOffsets().size(), expectedReadOffsets[i].length); for (int j = 0; j < expectedReadOffsets[i].length; ++j) { Assert.assertEquals(li.getRecordAndOffsets().get(j).getOffset(), expectedReadOffsets[i][j]);
Assert.assertEquals(li.getInsertedInRecord().get(0).getOffset(), expectedInsertionOffset); Assert.assertEquals(li.getInsertedInRecord().get(1).getOffset(), expectedInsertionOffset); } else { Assert.assertEquals(li.getInsertedInRecord().size(), 0); Assert.assertEquals(li.getDeletedInRecord().get(0).getOffset(), expectedReadOffsets[i]); Assert.assertEquals(li.getDeletedInRecord().get(1).getOffset(), expectedReadOffsets[i]); } else { Assert.assertEquals(li.size(), coverage); Assert.assertEquals(li.getRecordAndOffsets().get(0).getOffset(), expectedReadOffsets[i]); Assert.assertEquals(li.getRecordAndOffsets().get(1).getOffset(), expectedReadOffsets[i]);
Assert.assertEquals(li.getRecordAndOffsets().size(), expectedReadOffsets[i].length); for (int j = 0; j < expectedReadOffsets[i].length; ++j) { Assert.assertEquals(li.getRecordAndOffsets().get(j).getOffset(), expectedReadOffsets[i][j]); Assert.assertEquals(li.getDeletedInRecord().get(0).getOffset(), expectedDelOffset);
char rb= Character.toUpperCase((char)recOff.getReadBase()); boolean isTopStrand= (new ReadFromTopStrandFilter(true)).filterOut(recOff.getRecord());
final SAMReadGroupRecord rg = rec.getRecord().getReadGroup(); if (rg == null || !fingerprintsBySample.containsKey(rg.getSample())) { final PicardException e = new PicardException("Unknown sample: " + (rg != null ? rg.getSample() : "(null readgroup)")); throw e; } else { final String readName = rec.getRecord().getReadName(); if (!usedReadNames.contains(readName)) { final HaplotypeProbabilitiesFromContaminatorSequence probs = (HaplotypeProbabilitiesFromContaminatorSequence) fingerprintsBySample.get(rg.getSample()).get(haplotypeBlock); final byte base = StringUtil.toUpperCase(rec.getReadBase()); final byte qual = rec.getBaseQuality();
final SAMReadGroupRecord rg = rec.getRecord().getReadGroup(); final FingerprintIdDetails details; if (rg == null || !fingerprintIdDetailsMap.containsKey(rg)) { final FingerprintIdDetails unknownFPDetails = createUnknownFP(samFile, rec.getRecord()); fingerprintIdDetailsMap.put(null, unknownFPDetails); details = fingerprintIdDetailsMap.get(rg); final String readName = rec.getRecord().getReadName(); if (!usedReadNames.contains(readName)) { final HaplotypeProbabilitiesFromSequence probs = (HaplotypeProbabilitiesFromSequence) fingerprintsByReadGroup.get(details).get(haplotypeBlock); final byte base = StringUtil.toUpperCase(rec.getReadBase()); final byte qual = rec.getBaseQuality();
final SAMReadGroupRecord rg = rec.getRecord().getReadGroup(); if (rg == null || !fingerprintsBySample.containsKey(rg.getSample())) { final PicardException e = new PicardException("Unknown sample: " + (rg != null ? rg.getSample() : "(null readgroup)")); throw e; } else { final String readName = rec.getRecord().getReadName(); if (!usedReadNames.contains(readName)) { final HaplotypeProbabilitiesFromContaminatorSequence probs = (HaplotypeProbabilitiesFromContaminatorSequence) fingerprintsBySample.get(rg.getSample()).get(haplotypeBlock); final byte base = StringUtil.toUpperCase(rec.getReadBase()); final byte qual = rec.getBaseQuality();
final SAMRecord samrec = rec.getRecord(); if (oqs != null) qual = oqs[rec.getOffset()]; else qual = rec.getBaseQuality(); } else { qual = rec.getBaseQuality(); final byte base = rec.getReadBase(); final byte baseAsRead = samrec.getReadNegativeStrandFlag() ? SequenceUtil.complement(base) : base; final int read = samrec.getReadPairedFlag() && samrec.getSecondOfPairFlag() ? 2 : 1;
public void addBase(final SamLocusIterator.RecordAndOffset recordAndOffset, final SamLocusAndReferenceIterator.SAMLocusAndReference locusAndRef) { super.addBase(recordAndOffset, locusAndRef); final byte readBase = recordAndOffset.getReadBase(); final SAMRecord record = recordAndOffset.getRecord(); .filter(putative -> areReadsMates(record, putative.getRecord())) .findFirst() .orElse(null); final byte mateBase = mate.getReadBase(); if (SequenceUtil.isNoCall(readBase)) return; if (SequenceUtil.isNoCall(mateBase)) return;
boolean readIsTopStrand= !(new ReadFromTopStrandFilter(true)).filterOut(recOff.getRecord()); char readBase= Character.toUpperCase((char)recOff.getReadBase());
accumulator.get(refOffset).add(new RecordAndOffset(rec, readOffset));
public void addBase(final SamLocusIterator.RecordAndOffset recordAndOffset, final SamLocusAndReferenceIterator.SAMLocusAndReference locusAndRef) { super.addBase(recordAndOffset, locusAndRef); final byte readBase = recordAndOffset.getReadBase(); final SAMRecord record = recordAndOffset.getRecord(); .filter(putative -> areReadsMates(record, putative.getRecord())) .findFirst() .orElse(null); final byte mateBase = mate.getReadBase(); if (SequenceUtil.isNoCall(readBase)) return; if (SequenceUtil.isNoCall(mateBase)) return;
final SAMRecord samrec = rec.getRecord(); if (oqs != null) qual = oqs[rec.getOffset()]; else qual = rec.getBaseQuality(); } else { qual = rec.getBaseQuality(); final byte base = rec.getReadBase(); final byte baseAsRead = samrec.getReadNegativeStrandFlag() ? SequenceUtil.complement(base) : base; final int read = samrec.getReadPairedFlag() && samrec.getSecondOfPairFlag() ? 2 : 1;
accumulator.get(refOffset).add(new RecordAndOffset(rec, readOffset));