/**
* Creates an empty GATKSAMRecord with the read's header, read group and mate information, but
* empty (not-null) fields: - Cigar String - Read Bases - Base Qualities
*
* <p>Use this method if you want to create a new empty GATKSAMRecord based on another
* GATKSAMRecord
*
* @param read a read to copy the header from
* @return a read with no bases but safe for the GATK
*/
public static GATKSAMRecord emptyRead(GATKSAMRecord read) {
final GATKSAMRecord emptyRead = new GATKSAMRecord(read.getHeader());
emptyRead.setReferenceIndex(read.getReferenceIndex());
emptyRead.setAlignmentStart(0);
emptyRead.setMappingQuality(0);
// setting read indexing bin last
emptyRead.setFlags(read.getFlags());
emptyRead.setMateReferenceIndex(read.getMateReferenceIndex());
emptyRead.setMateAlignmentStart(read.getMateAlignmentStart());
emptyRead.setInferredInsertSize(read.getInferredInsertSize());
emptyRead.setCigarString("");
emptyRead.setReadBases(new byte[0]);
emptyRead.setBaseQualities(new byte[0]);
SAMReadGroupRecord samRG = read.getReadGroup();
emptyRead.clearAttributes();
if (samRG != null) {
GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord(samRG);
emptyRead.setReadGroup(rg);
}
GATKBin.setReadIndexingBin(emptyRead, 0);
return emptyRead;
}
@Override
public Integer map(
ReferenceContext referenceContext,
GATKSAMRecord read,
RefMetaDataTracker RefMetaDataTracker) {
final String rgID = read.getReadGroup().getId();
final PerReadGroupInfo info = readGroupInfo.get(rgID);
if (info.needsMoreData()) {
info.readLength.add(read.getReadLength());
info.nReadsSeen++;
if (read.getReadPairedFlag()) {
info.nReadsPaired++;
if (read.getInferredInsertSize() != 0) {
info.insertSize.add(Math.abs(read.getInferredInsertSize()));
}
}
}
return null;
}