/**
* 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;
}
// copied from LocusViewTemplate
protected GATKSAMRecord buildSAMRecord(
final String readName, final String contig, final int alignmentStart) {
GATKSAMRecord record = new GATKSAMRecord(header);
record.setReadName(readName);
record.setReferenceIndex(dictionary.getSequenceIndex(contig));
record.setAlignmentStart(alignmentStart);
record.setCigarString("1M");
record.setReadString("A");
record.setBaseQualityString("A");
record.setReadGroup(readGroup);
return record;
}