1a98c031559edae71e6272570a671c8a107c81a1
max
  Thu Aug 26 01:34:44 2021 -0700
small change to bamToPsl.c docs, refs #28044

diff --git src/utils/bamToPsl/bamToPsl.c src/utils/bamToPsl/bamToPsl.c
index c21c1fd..31143bc 100644
--- src/utils/bamToPsl/bamToPsl.c
+++ src/utils/bamToPsl/bamToPsl.c
@@ -18,32 +18,35 @@
   "   bamToPsl [options] in.bam out.psl\n"
   "options:\n"
   "   -fasta=output.fa - output query sequences to specified file\n"
   "   -chromAlias=file - specify a two-column file: 1: alias, 2: other name\n"
   "          for target name translation from column 1 name to column 2 name\n"
   "          names not found are passed through intact\n"
   "   -nohead          - do not output the PSL header, default has header output\n"
   "   -allowDups       - for fasta output, allow duplicate query sequences output\n"
   "                    - default is to eliminate duplicate sequences\n"
   "                    - runs much faster without the duplicate check\n"
   "   -noSequenceVerify - when checking for dups, do not verify each sequence\n"
   "                    - when the same name is identical, assume they are\n"
   "                    - helps speed up the dup check but not thorough\n"
   "   -dots=N          - output progress dot(.) every N alignments processed\n"
   "\n"
-  "note: a chromAlias file can be obtained from a UCSC database, e.g.:\n"
-  " hgsql -N -e 'select alias,chrom from chromAlias;' hg38 > hg38.chromAlias.tab"
+  "Note: a chromAlias file can be obtained from a UCSC database, e.g.:\n"
+  " hgsql -N -e 'select alias,chrom from chromAlias;' hg38 > hg38.chromAlias.tab\n"
+  " Or from the downloads server:\n"
+  "  wget https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/chromAlias.txt.gz\n"
+  "See also our tool chromToUcsc\n"
   );
 }
 
 /* Command line validation table. */
 static struct optionSpec options[] = {
    {"fasta", OPTION_STRING},
    {"chromAlias", OPTION_STRING},
    {"nohead", OPTION_BOOLEAN},
    {"allowDups", OPTION_BOOLEAN},
    {"noSequenceVerify", OPTION_BOOLEAN},
    {"dots", OPTION_INT},
    {NULL, 0},
 };
 
 static int dots = 0;