9a6742a6bb8914efe0fd1c050bd5a9493bb0eaaa
krish
  Sat Dec 18 00:28:19 2010 -0800
fixed size bugs and makefile bug
diff --git src/hg/fastaToPsl/fastaToPsl.c src/hg/fastaToPsl/fastaToPsl.c
deleted file mode 100644
index c8cbbe5..0000000
--- src/hg/fastaToPsl/fastaToPsl.c
+++ /dev/null
@@ -1,86 +0,0 @@
-/* fastaToPsl - Convert FASTA alignments to PSL format. */
-#include "common.h"
-#include "fa.h"
-#include "linefile.h"
-#include "hash.h"
-#include "options.h"
-#include "dystring.h"
-#include "errabort.h"
-#include "psl.h"
-#include "sqlNum.h"
-#include "obscure.h"
-
-static char const rcsid[] = "$Id: spideyToPsl.c,v 1.4 2008/02/21 02:13:24 markd Exp $";
-
-void usage()
-/* Explain usage and exit. */
-{
-errAbort(
-  "fastaToPsl - Convert FASTA pair alignments to PSL format\n"
-  "usage:\n"
-  "   fastaToPsl [options] in.fa out.psl\n"
-  "\n"
-  "where in.fa is the FASTA pair alignment. \n"
-  );
-}
-
-
-/* command line */
-static struct optionSpec optionSpec[] = {
-    {NULL, 0}
-};
-
-void fastaToPsl(char *inName, char *outName)
-/* fastaToPsl - Convert axt to psl format. */
-{
-struct lineFile *inLF;
-DNA *tmpSeq;
-char *tmpHeader;
-int tmpSize;
-boolean read;
-struct psl* pslAlign;
-
-DNA *qSeq;
-int qSize;
-char *qHeader;
-
-DNA *tSeq;
-int tSize;
-char *tHeader;
-
-inLF  = lineFileOpen(inName, TRUE);
-
-/* read the query sequence */
-read = faMixedSpeedReadNext(inLF, &tmpSeq, &qSize, &tmpHeader);
-if (!read) errAbort("Could not read query FASTA entry.");
-qSeq    = cloneString(tmpSeq);
-qHeader = cloneString(tmpHeader);
-
-/* read the target sequence */
-read = faMixedSpeedReadNext(inLF, &tmpSeq, &tSize, &tmpHeader);
-if (!read) errAbort("Could not read target FASTA entry.");
-tSeq    = cloneString(tmpSeq);
-tHeader = cloneString(tmpHeader);
-
-/* try to read next sequence to see if there is one */
-read = faMixedSpeedReadNext(inLF, &tmpSeq, &tmpSize, &tmpHeader);
-if (read) warn("WARN: Found more than two FASTA entries, only processing the first two.");
-
-pslAlign = pslFromAlign(qHeader, countNonDash(qSeq, qSize), 0, qSize, qSeq,
-                        tHeader, countNonDash(tSeq, tSize), 0, tSize, tSeq,
-                        "+", 0);
-pslWriteAll(pslAlign, outName, TRUE);
-
-lineFileClose(&inLF);
-}
-
-int main(int argc, char *argv[])
-/* Process command line. */
-{
-optionInit(&argc, argv, optionSpec);
-if (argc != 3)
-    usage();
-//gUntranslated = optionExists("untranslated");
-fastaToPsl(argv[1], argv[2]);
-return 0;
-}