49340bc650cba71856dc15f8972b804faf0035ec
max
  Thu Feb 2 11:20:54 2023 +0100
modifying the -k docs for chromToUcsc, refs #30567

diff --git src/utils/chromToUcsc/chromToUcsc src/utils/chromToUcsc/chromToUcsc
index df8a345..090c802 100755
--- src/utils/chromToUcsc/chromToUcsc
+++ src/utils/chromToUcsc/chromToUcsc
@@ -37,31 +37,32 @@
 
     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 (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)
+            help="Index of field (1-based) that contains the chromosome name. No other field is touched by this program, unless the "
+            "SAM format is detected. Default is %default (first field).", default=1)
 
     (options, args) = parser.parse_args()
 
     if options.downloadDb 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)
     return args, options
 
 # ----------- main --------------
 def splitLines(ifh):