6e5ee11ca95cd971984038cf65bae00d9c898707
galt
  Wed Jun 4 15:40:02 2014 -0700
Since we have git, it is easy to rename errabort.c to errAbort.c without losing any history.
diff --git src/utils/fastaToPsl/fastaToPsl.c src/utils/fastaToPsl/fastaToPsl.c
index 5fcbe2b..bd50f8d 100644
--- src/utils/fastaToPsl/fastaToPsl.c
+++ src/utils/fastaToPsl/fastaToPsl.c
@@ -1,102 +1,102 @@
 /* fastaToPsl - Convert FASTA alignments to PSL format. */
 
 /* Copyright (C) 2010 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 #include "common.h"
 #include "fa.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "dystring.h"
-#include "errabort.h"
+#include "errAbort.h"
 #include "psl.h"
 #include "sqlNum.h"
 #include "obscure.h"
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "fastaToPsl - Convert FASTA pair alignments to PSL format\n"
   "usage:\n"
   "   fastaToPsl  in.fasta out.psl\n"
   "\n"
   "If there are more than two sequences in the FASTA alignment.\n"
   "the first sequence is use as the query and the rest of the\n"
   "sequences are iterated over as the target to create a series\n"
   "of pair-wise alignments.\n"
   );
 }
 
 
 /* command line */
 static struct optionSpec optionSpec[] = {
     {NULL, 0}
 };
 
 void fastaToPsl(char *inName, char *outName)
 /* fastaToPsl - Convert axt to psl format. */
 {
 struct lineFile *inLF;
 FILE *outFh;
 boolean read;
 struct psl* pslAlign;
 
 DNA *qSeq;
 int qSize;
 int qSeqLen;
 char *qHeader;
 
 DNA *tSeq;
 int tSize;
 int tSeqLen;
 char *tHeader;
 
 int queryCounter;
 
 inLF  = lineFileOpen(inName, TRUE);
 outFh = mustOpen(outName, "w");
 
 /* read the target sequence */
 read = faMixedSpeedReadNext(inLF, &qSeq, &qSize, &qHeader);
 if (!read)
     errAbort("Could not read target FASTA entry.");
 qSeq    = cloneString(qSeq);
 qSeqLen = countNonDash(qSeq, qSize);
 qHeader = cloneString(qHeader);
 verbose(2, "Query sequence header: %s\n", qHeader);
 verbose(3, "Query sequence alignment length: %d\n", qSize);
 verbose(3, "Query sequence length: %d\n", qSeqLen);
 verbose(4, "Query sequence: %s\n", qSeq);
 
 /* read the rest of the sequences */
 queryCounter = 1;
 pslWriteHead(outFh);
 while (faMixedSpeedReadNext(inLF, &tSeq, &tSize, &tHeader))
     {
     tSeqLen = countNonDash(tSeq, tSize);
 
     verbose(2, "Target sequence (%d) header: %s\n", queryCounter, tHeader);
     verbose(3, "Target sequence (%d) length: %d\n", queryCounter, tSeqLen);
     verbose(4, "Target sequence (%d): %s\n", queryCounter, tSeq);
 
     pslAlign = pslFromAlign(qHeader, qSeqLen, 0, qSeqLen, qSeq,
                             tHeader, tSeqLen, 0, tSeqLen, tSeq,
                             "+", 0);
     pslTabOut(pslAlign, outFh);
 
     ++queryCounter;
     }
 
 lineFileClose(&inLF);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 optionInit(&argc, argv, optionSpec);
 if (argc != 3)
     usage();
 fastaToPsl(argv[1], argv[2]);
 return 0;
 }