4f577798b6f2ace7507b711d3189e42650ca7f83
max
  Wed Oct 30 22:04:47 2019 -0700
docs for chromFixer, refs #24407

diff --git src/utils/chromFixer/chromFixer src/utils/chromFixer/chromFixer
index bbf8216..657647a 100755
--- src/utils/chromFixer/chromFixer
+++ src/utils/chromFixer/chromFixer
@@ -7,35 +7,35 @@
     from urllib2 import urlopen # py3
 try:
     from cStringIO import StringIO # py2
 except ImportError:
     from io import StringIO # py3
 
 # ==== functions =====
 def parseArgs():
     " setup logging, parse command line arguments and options. -h shows auto-generated help page "
     parser = optparse.OptionParser("""usage: %prog [options] filename - change NCBI or Ensembl chromosome names to UCSC names using the chromAlias table of the genome browser.
 
     Examples:
         %prog -i test.bed -o test.ucsc.bed -g hg19
         %prog -g mm10 --get
         %prog -i test2.bed -o test2.ucsc.bed -a mm10.chromAlias.tsv
-        cat test.bed | %prog -a mm10.chromAlias.tsv > test.ucsc.edb
+        cat test.bed | %prog -a mm10.chromAlias.tsv > test.ucsc.bed
     """)
 
-    parser.add_option("-g", "--genomeDb", dest="db", action="store", help="a UCSC assembly ID, like hg19, mm10 or similar. Not required if -a is used.")
-    parser.add_option("-a", "--chromAlias", dest="aliasFname", action="store", help="a UCSC chromAlias table in tab-sep format.")
+    parser.add_option("-g", "--genomeDb", dest="db", action="store", help="a UCSC assembly ID, like hg19, hg38 or similar. Not required if -a is used. ")
+    parser.add_option("-a", "--chromAlias", dest="aliasFname", action="store", help="a UCSC chromAlias table in tab-sep format. The alias tables for hg19 or hg38 are hardcoded in the script, they do not require a chromAlias table..")
     parser.add_option("-i", "--in", dest="inFname", action="store", help="input filename, default: /dev/stdin")
     parser.add_option("-o", "--out", dest="outFname", action="store", help="output filename, default: /dev/stdout")
     parser.add_option("", "--get", dest="doDownload", action="store_true", help="download a chrom alias table from UCSC for --genomeDb into the current directory and exit")
     parser.add_option("-d", "--debug", dest="debug", action="store_true", help="show debug messages")
     #parser.add_option("", "--test", dest="test", action="store_true", help="do something") 
     (options, args) = parser.parse_args()
 
     if options.db is None and options.aliasFname is None:
         parser.print_help()
         exit(1)
 
     if options.debug:
         logging.basicConfig(level=logging.DEBUG)
     else:
         logging.basicConfig(level=logging.INFO)