ce16b1fd8bd824c6da07e6f427c389bdbb27ddc6
markd
  Sun Apr 24 17:01:44 2022 -0700
corrected help doc on PSL column names

diff --git src/utils/chromToUcsc/chromToUcsc src/utils/chromToUcsc/chromToUcsc
index c1f884f..df8a345 100755
--- src/utils/chromToUcsc/chromToUcsc
+++ src/utils/chromToUcsc/chromToUcsc
@@ -26,31 +26,31 @@
 
     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.
     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
+    genePred: 2 -- PSL: 10 (query) or 14 (target) -- chain: 2 (target) or 7 (query) -- SAM: 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: