83b6e55d2e100cb7c6e92e5c57d934040d8a524d
max
  Tue Jan 26 06:59:34 2021 -0800
adding * as a valid chrom name to chromToUcsc, refs #26839

diff --git src/utils/chromToUcsc/chromToUcsc src/utils/chromToUcsc/chromToUcsc
index eb8b316..6e17808 100755
--- src/utils/chromToUcsc/chromToUcsc
+++ src/utils/chromToUcsc/chromToUcsc
@@ -123,31 +123,31 @@
         elif row[0][0]== "@":
             fieldIdx = 2 # SAM format detected
             isSam = True
             if row[0]=="@SQ":
                 # @SQ     SN:1    LN:195471971
                 chrom = row[1].split(":")[1]
                 if chrom not in ucscChroms:
                     ucscChrom = toUcsc.get(chrom)
                     if ucscChrom is None:
                         logging.error("SAM format, header line %d: chrom name %s is not in chromAlias table" % (lineNo, repr(chrom)))
                         exit(1)
                     row[1] = "SN:%s" % ucscChrom
         else:
             # just pass through any UCSC chrom names
             chrom = row[fieldIdx]
-            if row[0].startswith("#") or chrom in ucscChroms:
+            if row[0].startswith("#") or chrom in ucscChroms or chrom=="*":
                 ucscChrom = chrom
             else:
                 ucscChrom = toUcsc.get(chrom)
                 if ucscChrom is None:
                     logging.error("line %d: chrom name %s is not in chromAlias table" % (lineNo, repr(chrom)))
                     exit(1)
             if isSam:
                 mateChrom = row[6]
                 if mateChrom!="=":
                     row[6] = toUcsc[mateChrom]
 
             row[fieldIdx] = ucscChrom
 
         line = sep.join(row)
         ofh.write(line)