110329b274d3e77d46cedfea05ac44a20682719e
braney
  Wed Feb 5 13:12:28 2020 -0800
use mitochondrial code on chrMT

diff --git src/hg/bedItemOverlapCount/bedItemOverlapCount.c src/hg/bedItemOverlapCount/bedItemOverlapCount.c
index 22d0aba..e8d128d 100644
--- src/hg/bedItemOverlapCount/bedItemOverlapCount.c
+++ src/hg/bedItemOverlapCount/bedItemOverlapCount.c
@@ -241,31 +241,31 @@
 	if ((char *)NULL == prevChrom)  // begin a chr
 	    {
 	    if (hashLookup(seenHash, bed->chrom))
 		errAbort("ERROR:input file not sorted. %s seen before on line %d\n",
 		    bed->chrom, bf->lineIx);
 
 	    hashAdd(seenHash, bed->chrom, NULL);
 	    prevChrom = cloneString(bed->chrom);
 	    chromSize = chromosomeSize(prevChrom);
 	    verbose(2,"#\tchrom %s starting, size %d\n", prevChrom,chromSize);
 	    }
 	if (bed->chromEnd > chromSize)
 	    {
 	    // check for circular chrM
 	    if (doBed12 || bed->chromStart>=chromSize 
-		|| differentWord(bed->chrom,"chrM")) 
+		|| !isMito(bed->chrom))
 		{
 		warn("ERROR: %s\t%d\t%d", bed->chrom, bed->chromStart,
 		bed->chromEnd);
 		errAbort("chromEnd > chromSize ?  %d > %d", 
 		    bed->chromEnd,chromSize);
 		}
 
 	    for (i = bed->chromStart; i < chromSize; ++i)
 		INCWOVERFLOW(counts,i);
 	    for (i = 0; i < (bed->chromEnd - chromSize); ++i)
 		INCWOVERFLOW(counts,i);
 	    }
 	else if (doBed12)
 	    {
 	    int *starts = bed->chromStarts;