a44421a79fb36cc2036fe116b97ea3bc9590cd0c
braney
  Fri Dec 2 09:34:39 2011 -0800
removed rcsid (#295)
diff --git src/utils/faTrimPolyA/faTrimPolyA.c src/utils/faTrimPolyA/faTrimPolyA.c
index 67b4a12..e426c9a 100644
--- src/utils/faTrimPolyA/faTrimPolyA.c
+++ src/utils/faTrimPolyA/faTrimPolyA.c
@@ -1,81 +1,80 @@
 /* faTrimPolyA - trim Poly-A tail*/
 #include "common.h"
 #include "options.h"
 #include "linefile.h"
 #include "fa.h"
 #include "dnautil.h"
 
-static char const rcsid[] = "$Id: faTrimPolyA.c,v 1.2 2005/04/08 18:42:33 markd Exp $";
 
 /* Command line option specifications */
 static struct optionSpec optionSpecs[] = {
     {"polyA", OPTION_BOOLEAN},
     {"polyT", OPTION_BOOLEAN},
     {NULL, 0}
 };
 boolean trimPolyA = FALSE;
 boolean trimPolyT = FALSE;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "faTrimPolyA - trim poly-A tails\n"
   "usage:\n"
   "   faTrimPolyA in.fa out.fa \n"
   "Options:\n"
   "  -polyA - trim poly-As at the end of the sequence.  This is the\n"
   "   default if no trim option is specified.\n" 
   "  -polyT - trim poly-Ts at the beginning of the sequence.  To trim both,\n"
   "   specify both options.\n"
   );
 }
 
 void polyTrimSeq(struct dnaSeq *seq, FILE *fh)
 /*  trim a sequence */
 {
 if (trimPolyA)
     {
     int sz = maskTailPolyA(seq->dna, seq->size);
     seq->size -= sz;
     seq->dna[seq->size] = '\0';
     }
 if (trimPolyT)
     {
     int sz = maskHeadPolyT(seq->dna, seq->size);
     seq->size -= sz;
     seq->dna += sz;
     }
 
 faWriteNext(fh, seq->name, seq->dna, seq->size);
 }
 
 void faTrimPolyA(char *inFile, char *outFile)
 /* faTrimPolyA - trim Poly-A tail*/
 {
 struct dnaSeq seq;
 struct lineFile *lf = lineFileOpen(inFile, TRUE);
 FILE *fh = mustOpen(outFile, "w");
 ZeroVar(&seq);
 
 while (faSomeSpeedReadNext(lf, &seq.dna, &seq.size, &seq.name, FALSE))
     polyTrimSeq(&seq, fh);
 carefulClose(&fh);
 lineFileClose(&lf);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 dnaUtilOpen();
 optionInit(&argc, argv, optionSpecs);
 if (argc != 3 )
     usage();
 trimPolyA = optionExists("polyA");
 trimPolyT = optionExists("polyT");
 if (!(trimPolyA || trimPolyT))
     trimPolyA = TRUE;
 
 faTrimPolyA(argv[1], argv[2]);
 return 0;
 }