4f36ff46dc1f285afd7478ddcf87f4777f7c4672
max
  Thu Aug 5 04:00:42 2021 -0700
improving chromToUcsc docs, refs #27919

diff --git src/utils/chromToUcsc/chromToUcsc src/utils/chromToUcsc/chromToUcsc
index f9e8066..a5b81a0 100755
--- src/utils/chromToUcsc/chromToUcsc
+++ src/utils/chromToUcsc/chromToUcsc
@@ -23,35 +23,35 @@
 
     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
     For BAM files use this program in a pipe with samtools:
         samtools view -h in.bam | ./chromToUcsc -a mm10.chromAlias.tsv | samtools -bS > out.bam
 
-    By default, this script expects the chromosome name in the first field, but you can change the field with -k.
-    This works for BED, bedGraph, GTF, wiggle, VCF.
+    By default, this script expects the chromosome name in the first field.
+    The default works for BED, bedGraph, GTF, wiggle, VCF.
     For the following file formats, you will need to set the -k option to these values manually:
     genePred: 2 -- PSL 10 (target) or 14 (query) -- chain: 2 (target) or 7 (query) -- SAM: 2
-    If any line starts with @ (SAM format), -k is automatically set to 2.
+    (If a line starts with @ (SAM format), -k is automatically set to 2.)
     """)
 
     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")
     parser.add_option("-a", "--chromAlias", dest="aliasFname", action="store", help="a UCSC chromAlias file in tab-sep format or the http/https URL to one")
     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("-d", "--debug", dest="debug", action="store_true", help="show debug messages")
     parser.add_option("-s", "--skipUnknown", dest="skipUnknown", action="store_true", help="skip unknown sequence rather than generate an error.")
     parser.add_option("-k", "--field", dest="fieldNo", action="store", type="int", \
             help="index of field to convert, default is %default (first field is 1). ", default=1)
 
     (options, args) = parser.parse_args()
 
     if options.downloadDb is None and options.aliasFname is None:
         parser.print_help()