491395482b817cfe82cbdef4dd7f8ee0723c1a4a
angie
  Wed Mar 23 21:01:49 2011 -0700
Feature #2822, #2823 (VCF customFactory + track handler):Added a new track type, vcfTabix, with handlers in hgTracks and hgc
and a customFactory.  It is a new bigDataUrl type of track; the
remote VCF file must be compressed and indexed by tabix, so like
BAM a separate index file is required.  If the VCF file has
genotypes, then each sample's two haplotypes are graphed in a
line, with one line per sample.  Otherwise, alleles and counts
(if available) are drawn using Belinda's pgSnp methods.
The source code has to be compiled with USE_TABIX=1 (which is
automatically set for us by common.mk when it finds the local
installation) in order for the CGIs to recognize the track type.

diff --git src/lib/tests/vcfParseTest.c src/lib/tests/vcfParseTest.c
index 7dd2474..280f52a 100644
--- src/lib/tests/vcfParseTest.c
+++ src/lib/tests/vcfParseTest.c
@@ -1,60 +1,60 @@
 /* vcfParseTest - Parse VCF header and data lines in given position range.. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "options.h"
 #include "sqlNum.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);
+struct vcfFile *vcff = vcfTabixFileMayOpen(fileOrUrl, seqName, start, end, 100);
 if (vcff == NULL)
     errAbort("Failed to parse \"%s\" and/or its index file \"%s.tbi\"", fileOrUrl, fileOrUrl);
 int recCount = slCount(vcff->records);
 printf("Finished parsing \"%s\" items in %s:%d-%d, got %d data rows\n",
        fileOrUrl, seqName, start+1, end, recCount);
 if (recCount > 0)
     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], sqlUnsigned(argv[3]), sqlUnsigned(argv[4]));
 return 0;
 }