0766f8ef11c8e73a7351fbbc5d5ae9f987941a54
angie
  Fri Mar 11 15:12:00 2011 -0800
Mark rightly pointed out that these programs I used for quick testingshould go in lib/tests with proper testcases, not in oneShot/.
Test cases coming up...

diff --git src/oneShot/vcfParseTest/vcfParseTest.c src/oneShot/vcfParseTest/vcfParseTest.c
deleted file mode 100644
index 3c8af00..0000000
--- src/oneShot/vcfParseTest/vcfParseTest.c
+++ /dev/null
@@ -1,56 +0,0 @@
-/* vcfParseTest - Parse VCF header and data lines in given position range.. */
-#include "common.h"
-#include "linefile.h"
-#include "hash.h"
-#include "options.h"
-#include "vcf.h"
-
-static char const rcsid[] = "$Id: newProg.c,v 1.30 2010/03/24 21:18:33 hiram Exp $";
-
-void usage()
-/* Explain usage and exit. */
-{
-errAbort(
-  "vcfParseTest - Parse VCF header and data lines in given position range.\n"
-  "usage:\n"
-  "   vcfParseTest fileOrUrl.vcf.gz seqName start end\n"
-  "\n"
-  "fileOrUrl.vcf.gz needs to have been compressed by tabix, and index file\n"
-  "fileOrUrl.vcf.gz.tbi must exist.\n"
-  );
-}
-
-static struct optionSpec options[] = {
-   {NULL, 0},
-};
-
-void vcfParseTest(char *fileOrUrl, char *seqName, int start, int end)
-/* vcfParseTest - Parse VCF header and data lines in given position range.. */
-{
-struct vcfFile *vcff = vcfTabixFileMayOpen(fileOrUrl, seqName, start, end, 100, stderr);
-if (vcff == NULL)
-    errAbort("Failed to parse \"%s\" and/or its index file \"%s.tbi\"", fileOrUrl, fileOrUrl);
-printf("Finished parsing \"%s\", got %d data rows\n", fileOrUrl, slCount(vcff->records));
-printf("First (up to) 100 rows in range:\n");
-int i = 0;
-struct vcfRecord *rec = vcff->records;
-while (rec != NULL && i < 100)
-    {
-    printf("%s\t%d\t%d\t%s:%s/%s\t%f\n",
-	   rec->chrom, rec->chromStart, rec->chromEnd,
-	   rec->name, rec->ref, rec->alt, rec->qual);
-    rec = rec->next;
-    i++;
-    }
-vcfFileFree(&vcff);
-}
-
-int main(int argc, char *argv[])
-/* Process command line. */
-{
-optionInit(&argc, argv, options);
-if (argc != 5)
-    usage();
-vcfParseTest(argv[1], argv[2], atoi(argv[3]), atoi(argv[4]));
-return 0;
-}