a44421a79fb36cc2036fe116b97ea3bc9590cd0c
braney
  Fri Dec 2 09:34:39 2011 -0800
removed rcsid (#295)
diff --git src/utils/faAlign/faAlign.c src/utils/faAlign/faAlign.c
index a4e69eb..188251e 100644
--- src/utils/faAlign/faAlign.c
+++ src/utils/faAlign/faAlign.c
@@ -1,67 +1,66 @@
 /* faAlign - Align two fasta files. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "dnaseq.h"
 #include "fa.h"
 #include "axt.h"
 
-static char const rcsid[] = "$Id: faAlign.c,v 1.2 2005/01/10 00:45:33 kent Exp $";
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "faAlign - Align two fasta files\n"
   "usage:\n"
   "   faAlign target.fa query.fa output.axt\n"
   "options:\n"
   "   -dna - use DNA scoring scheme\n"
   );
 }
 
 static struct optionSpec options[] = {
    {"dna", OPTION_BOOLEAN},
    {NULL, 0},
 };
 
 void faAlign(char *targetFile, char *queryFile, char *outFile, boolean isDna)
 /* faAlign - Align two fasta files. */
 {
 bioSeq *targetList = faReadAllMixed(targetFile);
 bioSeq *queryList = faReadAllMixed(queryFile);
 bioSeq *target, *query;
 struct axtScoreScheme *ss;
 FILE *f = mustOpen(outFile, "w");
 
 if (isDna)
     ss = axtScoreSchemeDefault();
 else
     ss = axtScoreSchemeProteinDefault();
 for (query = queryList; query != NULL; query = query->next)
     {
     for (target = targetList; target != NULL; target = target->next)
        {
        struct axt *axt = axtAffine(query, target, ss);
        if (axt != NULL)
            {
 	   axtWrite(axt, f);
 	   axtFree(&axt);
 	   }
        }
     }
 carefulClose(&f);
 freeDnaSeq(&targetList);
 freeDnaSeq(&queryList);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, options);
 if (argc != 4)
     usage();
 faAlign(argv[1], argv[2], argv[3], optionExists("dna"));
 return 0;
 }