68315931f4a9ec4272a8df76e6a881339717ac16
braney
  Wed Jun 1 15:37:37 2016 -0700
changes to support longTabix files in hgIntegrator

diff --git src/hg/lib/hAnno.c src/hg/lib/hAnno.c
index a76b333..71bdc5e 100644
--- src/hg/lib/hAnno.c
+++ src/hg/lib/hAnno.c
@@ -10,30 +10,31 @@
 #include "hdb.h"
 #include "hubConnect.h"
 #include "hui.h"
 #include "jksql.h"
 #include "pgSnp.h"
 #include "trackHub.h"
 #include "vcf.h"
 #include "annoGratorQuery.h"
 #include "annoGratorGpVar.h"
 #include "annoStreamBigBed.h"
 #include "annoStreamBigWig.h"
 #include "annoStreamDb.h"
 #include "annoStreamDbFactorSource.h"
 #include "annoStreamTab.h"
 #include "annoStreamVcf.h"
+#include "annoStreamTabix.h"
 #include "annoStreamWig.h"
 #include "annoGrateWigDb.h"
 #include "annoFormatTab.h"
 #include "annoFormatVep.h"
 
 //#*** duplicated in hgVarAnnoGrator and annoGratorTester
 struct annoAssembly *hAnnoGetAssembly(char *db)
 /* Make annoAssembly for db. */
 {
 static struct annoAssembly *aa = NULL;
 if (aa == NULL)
     {
     if (trackHubDatabase(db))
         {
         struct trackHubGenome *thg = trackHubGetGenome(db);
@@ -170,30 +171,35 @@
 /* Figure out the source and type of data and make an annoStreamer. */
 {
 struct annoStreamer *streamer = NULL;
 char *db = assembly->name, *dataDb = db, *dbTable = selTable;
 if (chrom == NULL)
     chrom = hDefaultChrom(db);
 if (isCustomTrack(selTable))
     {
     dbTable = trackDbSetting(tdb, "dbTableName");
     if (dbTable != NULL)
 	// This is really a database table, not a bigDataUrl CT.
 	dataDb = CUSTOM_TRASH;
     }
 if (startsWithWord("wig", tdb->type))
     streamer = annoStreamWigDbNew(dataDb, dbTable, assembly, maxOutRows);
+else if (sameString("longTabix", tdb->type))
+    {
+    char *fileOrUrl = getBigDataFileName(dataDb, tdb, selTable, chrom);
+    streamer = annoStreamTabixNew(fileOrUrl,  assembly, maxOutRows);
+    }
 else if (sameString("vcfTabix", tdb->type))
     {
     char *fileOrUrl = getBigDataFileName(dataDb, tdb, selTable, chrom);
     streamer = annoStreamVcfNew(fileOrUrl, TRUE, assembly, maxOutRows);
     }
 else if (sameString("vcf", tdb->type))
     {
     char *fileOrUrl = getBigDataFileName(dataDb, tdb, dbTable, chrom);
     streamer = annoStreamVcfNew(fileOrUrl, FALSE, assembly, maxOutRows);
     }
 else if (sameString("bam", tdb->type))
     {
     warn("Sorry, BAM is not yet supported");
     }
 else if (startsWith("bigBed", tdb->type) || sameString("bigGenePred", tdb->type))