e70152e44cc66cc599ff6b699eb8adc07f3e656a
kent
  Sat May 24 21:09:34 2014 -0700
Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
diff --git src/utils/faSimplify/faSimplify.c src/utils/faSimplify/faSimplify.c
index 5a9ab36..95829b1 100644
--- src/utils/faSimplify/faSimplify.c
+++ src/utils/faSimplify/faSimplify.c
@@ -1,74 +1,77 @@
 /* faSimplify - Simplify fasta record headers. */
+
+/* Copyright (C) 2011 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "faSimplify - Simplify fasta record headers\n"
   "usage:\n"
   "   faSimplify in.fa startPat endPat out.fa\n"
   "This will write out the stuff between startPat and\n"
   "endPat\n"
   "options:\n"
   "   -prefix=XXX This will add XXX as a prefix\n"
   "   -suffix=XXX This will add YYY as a suffix\n"
   );
 }
 
 static struct optionSpec options[] = {
    {"prefix", OPTION_STRING},
    {"suffix", OPTION_STRING},
    {NULL, 0},
 };
 
 char *prefix = "";
 char *suffix = "";
 
 void faSimplify(char *inName, char *startPat, char *endPat, char *outName)
 /* faFlyBaseToUcsc - Convert Flybase peptide fasta file to UCSC format. */
 {
 struct lineFile *lf = lineFileOpen(inName, TRUE);
 FILE *f = mustOpen(outName, "w");
 char *line;
 int startSize = strlen(startPat);
 
 while (lineFileNext(lf, &line, NULL))
     {
     if (line[0] == '>')
         {
 	char *s = stringIn(startPat, line), *e;
 	if (s == NULL)
 	   errAbort("No %s line %d of %s", startPat, lf->lineIx, lf->fileName);
 	s += startSize;
 	e = stringIn(endPat, s);
 	if (e == NULL)
 	   errAbort("No %s line %d of %s", endPat, lf->lineIx, lf->fileName);
 	*e = 0;
 	fprintf(f, ">%s%s%s\n", prefix, s, suffix);
 	}
     else
         {
 	fprintf(f, "%s\n", line);
 	}
     }
 carefulClose(&f);
 lineFileClose(&lf);
 }
 
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 5)
     usage();
 prefix = optionVal("prefix", prefix);
 suffix = optionVal("suffix", suffix);
 faSimplify(argv[1], argv[2], argv[3], argv[4]);
 return 0;
 }