RefHanger.Hanger rhanger = readHanger.popLeft();
RefHanger.Hanger ohanger = offsetHanger.popLeft();
return new LocusContext(rhanger.loc, rhanger.data, ohanger.data);
}
protected void hangRead(final SAMRecord read) {
<BUG>GenomeLoc readLoc = new GenomeLoc(read.getReferenceName(), read.getAlignmentStart());
</BUG>
for ( AlignmentBlock block : read.getAlignmentBlocks() ) {
if ( DEBUG )
logger.debug(String.format("Processing block %s len=%d%n", block, block.getLength()));

RefHanger.Hanger rhanger = readHanger.popLeft();
RefHanger.Hanger ohanger = offsetHanger.popLeft();
return new LocusContext(rhanger.loc, rhanger.data, ohanger.data);
}
protected void hangRead(final SAMRecord read) {
GenomeLoc readLoc = new GenomeLoc(read.getReferenceIndex(), read.getAlignmentStart());
for ( AlignmentBlock block : read.getAlignmentBlocks() ) {
if ( DEBUG )
logger.debug(String.format("Processing block %s len=%d%n", block, block.getLength()));
