2bc47d2d3a50670423fee6be8ae3fc0b825b859b
hiram
  Wed Jan 22 14:42:04 2014 -0800
correctly recognize _alt as a haplotype for hg38 refs #11681
diff --git src/hg/featureBits/featureBits.c src/hg/featureBits/featureBits.c
index 1c3db75..496e6a9 100644
--- src/hg/featureBits/featureBits.c
+++ src/hg/featureBits/featureBits.c
@@ -194,31 +194,32 @@
 else if (hasSuffixCompress(cleaned, suffix, "Z"))
     return TRUE;
 else if (hasSuffixCompress(cleaned, suffix, "bz2"))
     return TRUE;
 else
     return FALSE;
 }
 
 bool inclChrom(char *name)
 /* check if a chromosome should be included */
 {
 return  !((noRandom && (endsWith(name, "_random")
                         || startsWith("chrUn", name)
                         || sameWord("chrNA", name) /* danRer */
                         || sameWord("chrU", name)))  /* dm */
-          || (noHap && stringIn( "_hap", name)));
+          || (noHap && stringIn( "_hap", name))
+          || (noHap && stringIn( "_alt", name)));
 }
 
 void bitsToBins(Bits *bits, char *chrom, int chromSize, FILE *binFile, int binSize, int binOverlap)
 /* Write out binned counts of bits. */
 {
 int bin, count;
 
 if (!binFile)
     return;
 for (bin=0; bin+binSize<chromSize; bin=bin+binOverlap)
     {
     count = bitCountRange(bits, bin, binSize);
     fprintf(binFile, "%s\t%d\t%d\t%d\t%s.%d\n", chrom, bin, bin+binSize, count, chrom, bin/binOverlap+1);
     }
 count = bitCountRange(bits, bin, chromSize-bin);