a44421a79fb36cc2036fe116b97ea3bc9590cd0c
braney
  Fri Dec 2 09:34:39 2011 -0800
removed rcsid (#295)
diff --git src/utils/faGapLocs/faGapLocs.c src/utils/faGapLocs/faGapLocs.c
index 5b29168..7b8eb58 100644
--- src/utils/faGapLocs/faGapLocs.c
+++ src/utils/faGapLocs/faGapLocs.c
@@ -1,88 +1,87 @@
 /* faGapLocs - report location of gaps and sequences in a FASTA file. */
 #include "common.h"
 #include "linefile.h"
 #include "fa.h"
 #include "dnautil.h"
 #include "options.h"
 
-static char const rcsid[] = "$Id: faGapLocs.c,v 1.1 2007/08/17 01:15:44 markd Exp $";
 
 /* command line options */
 static struct optionSpec optionSpecs[] =
 {
     {NULL, 0}
 };
 
 static void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "faGapLocs - report location of gaps and sequences in a FASTA file\n"
   "usage:\n"
   "   faGapLocs in.fa out.lift\n"
   "options:\n"
 
   "Output is in the format of a lift file, with entries named in the form:\n"
   "   seqid_gap_N\n"
   "   seqid_blk_N\n"
   );
 }
 
 static int processGap(char *seqId, int seqSize, DNA *seq, int iSeq, int nGap, FILE *liftFh)
 /* write out one gap and return next position in sequence */
 {
 int len = strspn(seq+iSeq, "n");
 fprintf(liftFh, "%d\t%s_gap_%d\t%d\t%s\t%d\n",
         iSeq, seqId, nGap, len, seqId, seqSize);
 return iSeq+len;
 }
 
 static int processBlk(char *seqId, int seqSize, DNA *seq, int iSeq, int nBlk, FILE *liftFh)
 /* write out one block of sequence and return next position in sequence */
 {
 int len = strcspn(seq+iSeq, "n");
 fprintf(liftFh, "%d\t%s_seq_%d\t%d\t%s\t%d\n",
         iSeq, seqId, nBlk, len, seqId, seqSize);
 return iSeq+len;
 }
 
 
 static void processSeq(char *seqId, int seqSize, DNA *seq, FILE *liftFh)
 /* process one fasta sequence, writing gap and blk information to file */
 {
 int nGap = 0, nBlk = 0, iSeq;
 
 for (iSeq = 0; iSeq < seqSize; )
     {
     if (seq[iSeq] == 'n')
         iSeq = processGap(seqId, seqSize, seq, iSeq, nGap++, liftFh);
     else
         iSeq = processBlk(seqId, seqSize, seq, iSeq, nBlk++, liftFh);
     }
 }
 
 static void faGapLocs(char *faIn, char* liftOut)
 /* faGapLocs - report location of gaps and sequences in a FASTA file. */
 {
 struct lineFile *faLf = lineFileOpen(faIn, TRUE);
 FILE *liftFh = mustOpen(liftOut, "w");
 char *seqId;
 int seqSize;
 DNA *seq;
 
 while (faSpeedReadNext(faLf, &seq, &seqSize, &seqId))
     processSeq(seqId, seqSize, seq, liftFh);
 
 carefulClose(&liftFh);
 lineFileClose(&faLf);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, optionSpecs);
 if (argc != 3)
     usage();
 faGapLocs(argv[1], argv[2]);
 return 0;
 }