2124d33552ad625470e6136295530e804a2ed8c7
markd
  Fri Sep 23 22:30:04 2016 -0700
fixed confused help message (that I wrote)

diff --git src/hg/mrnaToGene/mrnaToGene.c src/hg/mrnaToGene/mrnaToGene.c
index bd013b3..fc913a5 100644
--- src/hg/mrnaToGene/mrnaToGene.c
+++ src/hg/mrnaToGene/mrnaToGene.c
@@ -57,33 +57,33 @@
   "usage:\n"
   "   mrnaToGene [options] psl genePredFile\n"
   "\n"
   "Convert PSL alignments with CDS annotation from genbank to  gene\n"
   "annotations in genePred format.  Accessions without valids CDS are\n"
   "optionally dropped. A best attempt is made to convert incomplete CDS\n"
   "annotations.\n"
   "\n"
   "The psl argument may either be a PSL file or a table in a databases,\n"
   "depending on options.  CDS maybe obtained from the database or file.\n"
   "Accession in PSL files are tried with and with out genbank versions.\n"
   "\n"
   "Options:\n"
   "  -db=db - get PSLs and CDS from this database, psl specifies the table.\n"
   "  -cdsDb=db - get CDS from this database, psl is a file.\n"
-  "  -cdsFile=file - get CDS from this database, psl is a file.\n"
-  "   File is table seperate with accession as the first column and\n"
-  "   CDS the second\n"
+  "  -cdsFile=file - get CDS from this file, psl is a file.\n"
+  "   File is tab separate with name as the first column and\n"
+  "   NCBI CDS the second\n"
   "  -insertMergeSize=%d - Merge inserts (gaps) no larger than this many bases.\n"
   "   A negative size disables merging of blocks.  This differs from specifying zero\n"
   "   in that adjacent blocks will not be merged, allowing tracking of frame for\n"
   "   each block. Defaults to %d unless -cdsMergeSize or -utrMergeSize are specified,\n"
   "   if either of these are specified, this option is ignored.\n"
   "  -smallInsertSize=n - alias for -insertMergetSize\n"
   "  -cdsMergeSize=-1 - merge gaps in CDS no larger than this size.\n"
   "   A negative values disables.\n"
   "  -cdsMergeMod3 - only merge CDS gaps if they mod 3\n"
   "  -utrMergeSize=-1  - merge gaps in UTR no larger than this size.\n"
   "   A negative values disables.\n"
   "  -requireUtr - Drop sequences that don't have both 5' and 3' UTR annotated.\n"
   "  -genePredExt - create a extended genePred, including frame information.\n"
   "  -allCds - consider PSL to be all CDS.\n"
   "  -noCds - consider PSL to not contain any CDS.\n"