/**
* 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;
}
}
}
}
}
}
