cf1446a79ba6729f0d88f1ccca523d9604d758ca
max
  Tue Dec 15 02:09:54 2020 -0800
fixing up the chromToUcsc test case to use a more realistic vcf.gz file, refs #26672

diff --git src/utils/chromToUcsc/chromToUcsc src/utils/chromToUcsc/chromToUcsc
index 3760c0f..6a15512 100755
--- src/utils/chromToUcsc/chromToUcsc
+++ src/utils/chromToUcsc/chromToUcsc
@@ -152,27 +152,29 @@
     args, options = parseArgs()
 
     aliasFname = options.aliasFname
     inFname = options.inFname
     outFname = options.outFname
 
     if options.downloadDb:
         download(options.downloadDb)
 
     if aliasFname is None:
         logging.error("You need to provide an alias table with the -a option or use --get to download one.")
         exit(1)
 
     if inFname is None:
         ifh = stdin
+    elif inFname.endswith(".gz"):
+        ifh = gzip.open(inFname)
     else:
         ifh = open(inFname)
 
     if outFname is None:
         ofh = stdout
     else:
         ofh = open(outFname, "w")
 
     fieldIdx = options.fieldNo-1
     chromToUcsc(aliasFname, fieldIdx, ifh, ofh)
 
 main()