dff08fa790cf447dfc913940ce110ca45143e1b2
markd
  Thu Jun 9 00:16:44 2022 -0700
core dump freeing memory

diff --git src/isPcr/gfPcr/gfPcr.c src/isPcr/gfPcr/gfPcr.c
index 89cd261..23e32ff 100644
--- src/isPcr/gfPcr/gfPcr.c
+++ src/isPcr/gfPcr/gfPcr.c
@@ -1,115 +1,115 @@
 /* gfPcr - In silico PCR using gfServer index...
  * Copyright 2004 Jim Kent.  All rights reserved. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "genoFind.h"
 #include "gfPcrLib.h"
 
 
 /* Command line overridable variables. */
 int maxSize = 4000; /* corresponds to maxSize= parameter. */
 int minPerfect = 15;
 int minGood = 18;
 char *clName = NULL;  /* corresponds to name= parameter */
 char *clOut = "fa";  /* corresponds to out= parameter */
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "gfPcr - In silico PCR version %s using gfServer index.\n"
   "usage:\n"
   "   gfPcr host port seqDir fPrimer rPrimer output\n"
   "or\n"
   "   gfPcr host port seqDir batch output\n"
   "Where:\n"
   "   host is the name of the machine running the gfServer\n"
   "   port is the gfServer port (usually 17779)\n"
   "   seqDir is where the nib or 2bit files for the genome database are\n"
   "   fPrimer is the forward strand primer\n"
   "   rPrimer is the reverse strand primer\n"
   "   output is the output file.  Use 'stdout' for output to standard output\n"
   "   batch is a space or tab delimited file with the following fields on each line\n"
   "       name/fPrimer/rPrimer/maxProductSize\n"
   "options:\n"
   "   -maxSize=N - Maximum size of PCR product (default %d)\n"
   "   -minPerfect=N - Minimum size of perfect match at 3' end of primer (default %d)\n"
   "   -minGood=N - Minimum size where there must be 2 matches for each mismatch (default %d)\n"
   "   -out=XXX - Output format.  Either\n"
   "      fa - fasta with position, primers in header (default)\n"
   "      bed - tab delimited format. Fields: chrom/start/end/name/score/strand\n"
   "      psl - blat format.\n"
   "   -name=XXX - Name to use in bed output.\n"
   "   -genome=name  When using a dynamic gfServer, The genome name is used to \n"
   "                 find the data files relative to the dynamic gfServer root, named \n"
   "                 in the form $genome.2bit, and $genome.untrans.gfidx.\n"
   "   -genomeDataDir=path\n"
   "                 When using a dynamic gfServer, this is the dynamic gfServer root directory\n"
   "                 that contained the genome data files.  Defaults to being the root directory.\n"
   "                \n"
   , gfVersion, maxSize, minPerfect, minGood
   );
 }
 
 static struct optionSpec options[] = {
    {"maxSize", OPTION_INT},
    {"minPerfect", OPTION_INT},
    {"minGood", OPTION_INT},
    {"out", OPTION_STRING},
    {"name", OPTION_STRING},
    {"genome", OPTION_STRING},
    {"genomeDataDir", OPTION_STRING},
    {NULL, 0},
 };
 
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 struct gfPcrInput *inList = NULL;
 struct gfPcrOutput *outList = NULL;
 char *host, *port, *seqDir, *outFile = NULL;
 char *genome, *genomeDataDir = NULL;
 
 optionInit(&argc, argv, options);
 maxSize = optionInt("maxSize", maxSize);
 minPerfect = optionInt("minPerfect", minPerfect);
 minGood = optionInt("minGood", minGood);
 if (minGood < minPerfect)
     minGood = minPerfect;
 clOut = optionVal("out", clOut);
 clName = optionVal("name", clName);
 if (argc == 6)	/* Batch */
     {
     inList = gfPcrInputLoadAll(argv[4]);
     outFile = argv[5];
     }
 else if (argc == 7) /* One primer pair */
     {
     AllocVar(inList);
-    inList->name = clName;
+    inList->name = cloneString(clName);
     inList->fPrimer = cloneString(argv[4]);
     inList->rPrimer = cloneString(argv[5]);
     outFile = argv[6];
     }
 else
     usage();
 host = argv[1];
 port = argv[2];
 seqDir = argv[3];
 genome = optionVal("genome", NULL);
 genomeDataDir = optionVal("genomeDataDir", NULL);
 if ((genomeDataDir != NULL) && (genome == NULL))
     errAbort("-genomeDataDir requires the -genome option");
 if ((genome != NULL) && (genomeDataDir == NULL))
     genomeDataDir = ".";
 struct gfConnection *conn = gfConnect(host, port, genome, genomeDataDir);
 outList = gfPcrViaNet(conn, seqDir, inList, maxSize, minPerfect, minGood);
 gfDisconnect(&conn);
 gfPcrOutputWriteAll(outList, clOut, NULL, outFile);
 gfPcrOutputFreeList(&outList);
 gfPcrInputFreeList(&inList);
 return 0;
 }