191a740d41e1bcaf9d012380f0ec5d23904f223d
markd
  Fri May 3 02:38:26 2024 -0700
updated confusing doc

diff --git src/hg/getRnaPred/getRnaPred.c src/hg/getRnaPred/getRnaPred.c
index fea038e..3442102 100644
--- src/hg/getRnaPred/getRnaPred.c
+++ src/hg/getRnaPred/getRnaPred.c
@@ -6,45 +6,45 @@
 #include "linefile.h"
 #include "genePred.h"
 #include "psl.h"
 #include "fa.h"
 #include "jksql.h"
 #include "hdb.h"
 #include "nibTwo.h"
 #include "dnautil.h"
 #include "options.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
-  "getRnaPred - Get virtual RNA for gene predictions\n"
+  "getRnaPred - Get genome putative RNA for gene predictions\n"
   "usage:\n"
   "   getRnaPred [options] database table chromosome output.fa\n"
   "table can be a table or a file.  Specify chromosome of 'all' to\n"
   "to process all chromosome\n"
   "\n"
   "options:\n"
   "   -weird - only get ones with weird splice sites\n"
   "   -cdsUpper - output CDS in upper case\n"
   "   -cdsOnly - only output CDS\n"
   "   -cdsOut=file - write CDS to this tab-separated file, in the form\n"
   "      acc  start  end\n"
   "    where start..end are genbank style, one-based coordinates\n"
   "   -keepMasking - un/masked in upper/lower case.\n"
-  "   -pslOut=psl - output a PSLs for the virtual mRNAs.  Allows virtual\n"
+  "   -pslOut=psl - output a PSLs for the genomic mRNAs.  Allows \n"
   "    mRNA to be analyzed by tools that work on PSLs\n"
   "   -suffix=suf - append suffix to each id to avoid confusion with mRNAs\n"
   "    use to define the genes.\n"
   "   -peptides - out the translation of the CDS to a peptide sequence.\n"
   "    The newer program genePredToProt maybe produce better results in cases\n"
   "    were there are frame-shifting indels in the CDS.\n"
   "   -exonIndices - output indices of exon boundaries after sequence name,\n"
   "    e.g., \"103 243 290\" says positions 1-103 are from the first exon,\n"
   "    positions 104-243 are from the second exon, etc. \n"
   "   -maxSize=size - output a maximum of size characters.  Useful when\n"
   "    testing gene predictions by RT-PCR.\n"
   "   -genomeSeqs=spec - get genome sequences from the specified nib directory\n"
   "    or 2bit file instead of going though the path found in chromInfo.\n"
   "   -includeCoords - include the genomic coordinates as a comment in the\n"
   "    fasta header.  This is necessary when there are multiple genePreds\n"
@@ -193,31 +193,31 @@
 
 if (cdsUpper)
     toUpperN(dnaBuf->string+cdsStart, (cdsEnd-cdsStart));
 
 if (cdsBuf != NULL)
     {
     dyStringClear(cdsBuf);
     dyStringAppendN(cdsBuf, dnaBuf->string+cdsStart, (cdsEnd-cdsStart));
     }
 
 if (cdsFh != NULL)
     fprintf(cdsFh,"%s\t%d\t%d\n", gp->name, cdsStart+1, cdsEnd);
 }
 
 void writePsl(char *db, struct genePred *gp, FILE* pslFh)
-/* create a PSL for the virtual mRNA */
+/* create a PSL for the genomic mRNA */
 {
 int rnaSize = genePredBases(gp);
 int qStart = 0, iExon;
 struct psl psl;
 ZeroVar(&psl);
 
 psl.match = rnaSize;
 psl.tNumInsert = gp->exonCount-1;
 psl.strand[0] = gp->strand[0];
 psl.qName = gp->name;
 psl.qSize = rnaSize;
 psl.qStart = 0;
 psl.qEnd = rnaSize;
 psl.tName = gp->chrom;
 psl.tSize =  hChromSize(db, gp->chrom);