ca09a10b768ab143bdf3ae6edf6df6aafe06ce56,java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java,IndelGenotyperWalker,map,#char[]#SAMRecord#,125
Before Change
if ( read.getAlignmentStart() < coverage.getStart() ) {
// should never happen
throw new StingException("Read "+read.getReadName()+": out of order on the contig");
}
// a little trick here: we want to make sure that current read completely fits into the current
After Change
if ( read.getAlignmentStart() < coverage.getStart() ) {
// should never happen
throw new StingException("Read "+read.getReadName()+": out of order on the contig\n"+
"Read starts at "+read.getReferenceName()+":"+read.getAlignmentStart()+ " (cigar="+read.getCigarString()+
"); window starts at "+coverage.getStart());
}