/** * HACK TO CREATE GATKSAMRECORD BASED ONLY A SAMRECORD FOR TESTING PURPOSES ONLY * * @param read */ public GATKSAMRecord(final SAMRecord read) { super(read.getHeader()); super.setReferenceIndex(read.getReferenceIndex()); super.setAlignmentStart(read.getAlignmentStart()); super.setReadName(read.getReadName()); super.setMappingQuality(read.getMappingQuality()); // indexing bin done below super.setCigar(read.getCigar()); super.setFlags(read.getFlags()); super.setMateReferenceIndex(read.getMateReferenceIndex()); super.setMateAlignmentStart(read.getMateAlignmentStart()); super.setInferredInsertSize(read.getInferredInsertSize()); SAMReadGroupRecord samRG = read.getReadGroup(); SAMBinaryTagAndValue samAttr = GATKBin.getReadBinaryAttributes(read); if (samAttr == null) { clearAttributes(); } else { setAttributes(samAttr); } if (samRG != null) { GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord(samRG); setReadGroup(rg); } super.setFileSource(read.getFileSource()); super.setReadName(read.getReadName()); super.setCigarString(read.getCigarString()); super.setReadBases(read.getReadBases()); super.setBaseQualities(read.getBaseQualities()); // From SAMRecord constructor: Do this after the above because setCigarString will clear it. GATKBin.setReadIndexingBin(this, GATKBin.getReadIndexingBin(read)); }
private void collectReadData(final SAMRecord record, final ReferenceSequence ref) { metrics.TOTAL_READS++; readLengthHistogram.increment(record.getReadBases().length); if (!record.getReadFailsVendorQualityCheckFlag()) { metrics.PF_READS++; if (isNoiseRead(record)) metrics.PF_NOISE_READS++; if (record.getReadUnmappedFlag()) { // If the read is unmapped see if it's adapter sequence final byte[] readBases = record.getReadBases(); if (!(record instanceof BAMRecord)) StringUtil.toUpperCase(readBases); if (isAdapterSequence(readBases)) { this.adapterReads++; } } else if (doRefMetrics) { metrics.PF_READS_ALIGNED++; if (!record.getReadNegativeStrandFlag()) numPositiveStrand++; if (record.getReadPairedFlag() && !record.getMateUnmappedFlag()) { metrics.READS_ALIGNED_IN_PAIRS++; // Check that both ends have mapq > minimum final Integer mateMq = record.getIntegerAttribute("MQ"); if (mateMq == null || mateMq >= MAPPING_QUALITY_THRESOLD && record.getMappingQuality() >= MAPPING_QUALITY_THRESOLD) { ++this.chimerasDenominator; // With both reads mapped we can see if this pair is chimeric if (Math.abs(record.getInferredInsertSize()) > maxInsertSize || !record.getReferenceIndex().equals(record.getMateReferenceIndex())) { ++this.chimeras; } } } } } }