d7e3477e89a22c7a00c5ac85528d2d21477695f8
markd
  Sun Jun 6 22:06:34 2021 -0700
allow mate chrom name of "*"

diff --git src/utils/chromToUcsc/chromToUcsc src/utils/chromToUcsc/chromToUcsc
index 2e8cdf1..c666c20 100755
--- src/utils/chromToUcsc/chromToUcsc
+++ src/utils/chromToUcsc/chromToUcsc
@@ -155,31 +155,31 @@
                         continue
                     row[1] = "SN:%s" % ucscChrom
         else:
             # just pass through any UCSC chrom names
             chrom = row[fieldIdx]
             if row[0].startswith("#") or chrom in ucscChroms or chrom=="*":
                 ucscChrom = chrom
             else:
                 ucscChrom = toUcsc.get(chrom)
                 if ucscChrom is None:
                     handledUnmappedChrom(chrom, skipUnknown, skipWarned,
                                          "line %d: chrom name %s is not in chromAlias table" % (lineNo, repr(chrom)))
                     continue
             if isSam:
                 mateChrom = row[6]
-                if mateChrom!="=":
+                if mateChrom not in ("=", "*"):
                     row[6] = toUcsc[mateChrom]
 
             row[fieldIdx] = ucscChrom
 
         line = sep.join(row)
         ofh.write(line)
         ofh.write("\n")
 
 def download(db):
     url = "http://hgdownload.soe.ucsc.edu/goldenPath/%s/database/chromAlias.txt.gz" % db
     gzData = urlopen(url).read()
 
     if 'cStringIO' in modules:
         data = StringIO(gzData)
     else: