b1c2fdec9a31078a56333427830a760757d22a51
angie
  Fri Jun 17 14:44:44 2016 -0700
Command line wrapper script for hgVai: hg/utils/vai.pl .  hgVai has a new input parameter to specify a local file of variants instead of a custom track, and inhibits web output (e.g. Content-Type and cookies) when run on the command line.  Added support for reading pgSnp variants from input file without bin column instead of database (pgSnp.as includes bin, but pgSnp files do not).
Has been tested somewhat on GBiB.  Needs documentation.
refs #12216

diff --git src/hg/lib/customTrack.c src/hg/lib/customTrack.c
index 47dcd7c..d9a70e1 100644
--- src/hg/lib/customTrack.c
+++ src/hg/lib/customTrack.c
@@ -660,30 +660,32 @@
 // pull out file part from the URL, strip off the query part after "?"
 char fileName[2000];
 safecpy(fileName, sizeof(fileName), url);
 chopSuffixAt(fileName, '?');
 
 // based on udc cache dir analysis by hiram in rm #12813
 if (endsWith(fileName, ".bb") || endsWith(fileName, ".bigBed") || endsWith(fileName, ".bigbed"))
     return cloneString("bigBed");
 if (endsWith(fileName, ".bw") || endsWith(fileName, ".bigWig") ||  
             endsWith(fileName, ".bigwig") || endsWith(fileName, ".bwig"))
     return cloneString("bigWig");
 if (endsWith(fileName, ".bam") || endsWith(fileName, ".cram"))
     return cloneString("bam");
 if (endsWith(fileName, ".vcf.gz"))
     return cloneString("vcfTabix");
+if (endsWith(fileName, ".vcf"))
+    return cloneString("vcf");
 return NULL;
 }
 
 boolean customTrackIsBigData(char *fileName)
 /* Return TRUE if fileName has a suffix that we recognize as a bigDataUrl track type. */
 {
 char *fileNameDecoded = cloneString(fileName);
 cgiDecode(fileName, fileNameDecoded, strlen(fileName));
 
 boolean result;
 char *type = customTrackTypeFromBigFile(fileNameDecoded);
 result = (type!=NULL);
 
 freeMem(type);
 freeMem(fileNameDecoded);