572f8e2a5e67250ee2802f039a8b97d2322cc99a
max
  Tue Dec 15 02:16:25 2020 -0800
documenting supported file formats, refs #26689

diff --git src/utils/chromToUcsc/chromToUcsc src/utils/chromToUcsc/chromToUcsc
index 6a15512..683b3f0 100755
--- src/utils/chromToUcsc/chromToUcsc
+++ src/utils/chromToUcsc/chromToUcsc
@@ -5,30 +5,33 @@
 
 try:
     from urllib.request import urlopen # py2
 except ImportError:
     from urllib2 import urlopen # py3
 try:
     from cStringIO import StringIO # py2
 except ImportError:
     from io import BytesIO # 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 in tabular or wiggle files, using a chromAlias table.
 
+    Supports at least these file formats: BED, PSL, genePred, VCF, wiggle (bedgraph, span and fixed and mixes thereof), SAM, chain, interact,
+    pgSNP, GTF/GFF.
+
     Requires a <genome>.chromAlias.tsv file which can be downloaded like this:
         %prog --get hg19              # download the file hg19.chromAlias.tsv into current directory
 
     If you do not want to use the --get option to retrieve the mapping tables, you can also download the alias mapping
     files yourself, e.g. for mm10 with 'wget https://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/chromAlias.txt.gz'
 
     Then the script can be run like this:
         %prog -i in.bed -o out.bed -a hg19.chromAlias.tsv
         %prog -i in.bed -o out.bed -a https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/chromAlias.txt.gz
     Or in pipes, like this:
         cat test.bed | %prog -a mm10.chromAlias.tsv > test.ucsc.bed
 
     """)
 
     parser.add_option("", "--get", dest="downloadDb", action="store", help="download a chrom alias table from UCSC for the genomeDb into the current directory and exit")