70d4208efa11f262ba5591198214c9ccdc6b54ae
angie
  Mon Aug 22 22:24:05 2011 -0700
Feature #3707 (VCF+tabix support in hgTables):Basic hgTables support for VCF, modeled after BAM code.  Tested all fields,
selected fields, bed output; filter, intersection, schema
on 3 flavors of vcfTabix:
ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20101123/interim_phase1_release/ALL.chr17.phase1.projectConsensus.genotypes.vcf.gz
ftp://ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp/release/20100804/AFR.dindel.20100804.sites.vcf.gz
ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/v4.0/ByChromosomeNoGeno/00-All.vcf.gz

diff --git src/hg/hgTables/joining.c src/hg/hgTables/joining.c
index 0c288cc..e794c4f 100644
--- src/hg/hgTables/joining.c
+++ src/hg/hgTables/joining.c
@@ -344,30 +344,40 @@
 makeOrderedCommaFieldList(fieldList, dtfList, dy);
 slFreeList(&fieldList);
 hFreeConn(&conn);
 }
 
 static void makeBamOrderedCommaFieldList(struct joinerDtf *dtfList,
 	struct dyString *dy)
 /* Make comma-separated field list in same order as fields are in
  * big bed. */
 {
 struct slName *fieldList = bamGetFields(dtfList->table);
 makeOrderedCommaFieldList(fieldList, dtfList, dy);
 slFreeList(&fieldList);
 }
 
+static void makeVcfOrderedCommaFieldList(struct joinerDtf *dtfList,
+	struct dyString *dy)
+/* Make comma-separated field list in same order as fields are in
+ * big bed. */
+{
+struct slName *fieldList = vcfGetFields(dtfList->table);
+makeOrderedCommaFieldList(fieldList, dtfList, dy);
+slFreeList(&fieldList);
+}
+
 
 struct tableJoiner
 /* List of fields in a single table. */
     {
     struct tableJoiner *next;	/* Next in list. */
     char *database;		/* Database we're in.  Not alloced here. */
     char *table;		/* Table we're in.  Not alloced here. */
     struct joinerDtf *fieldList;	/* Fields. */
     struct slRef *keysOut;	/* Keys that connect to output.
                                  * Value is joinerPair. */
     boolean loaded;	/* If true is loaded. */
     };
 
 void tableJoinerFree(struct tableJoiner **pTf)
 /* Free up memory associated with tableJoiner. */
@@ -989,30 +999,32 @@
 {
 struct joinerDtf *dtfList = NULL;
 struct joinerDtf *filterTables = NULL;
 boolean doJoin = joinRequired(primaryDb, primaryTable,
 			      fieldList, &dtfList, &filterTables);
 
 if (! doJoin)
     {
     struct sqlConnection *conn = hAllocConn(dtfList->database);
     struct dyString *dy = dyStringNew(0);
     
     if (isBigBed(database, dtfList->table, NULL, ctLookupName))
 	makeBigBedOrderedCommaFieldList(dtfList, dy);
     else if (isBamTable(dtfList->table))
         makeBamOrderedCommaFieldList(dtfList, dy);
+    else if (isVcfTable(dtfList->table))
+        makeVcfOrderedCommaFieldList(dtfList, dy);
     else if (isCustomTrack(dtfList->table))
         makeCtOrderedCommaFieldList(dtfList, dy);
     else
 	makeDbOrderedCommaFieldList(conn, dtfList->table, dtfList, dy);
     doTabOutTable(dtfList->database, dtfList->table, f, conn, dy->string);
     hFreeConn(&conn);
     }
 else
     {
     struct joiner *joiner = allJoiner;
     struct joinedTables *joined = joinedTablesCreate(joiner, 
     	primaryDb, primaryTable, dtfList, filterTables, 1000000, getRegions());
     if (f == NULL)
         joinedTablesTabOut(joined);
     else