// 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;
}
