String newErrMsg = "Syzygy input file error: could not read first line of "+pathToSyzygyFile;
throw new StingException(newErrMsg,e);
}
}
@Override
<BUG>public Pair<Integer,Integer> map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context)

{
Pair<Pair<List<SAMRecord>, List<SAMRecord>>,Pair<List<Integer>,List<Integer>>> splitReads = PoolUtils.splitReadsByReadDirection(context.getReads(),context.getOffsets());</BUG>
if ( !super.suppress_printing )

String newErrMsg = "Syzygy input file error: could not read first line of "+pathToSyzygyFile;
throw new StingException(newErrMsg,e);
}
}
@Override
public Pair<Integer,Integer> map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext rawContext)
