76ae0eba49560eee79493370778b4283f8033639
braney
  Mon Oct 12 13:56:59 2015 -0700
a tweak to allow bedToBigBed to work with tab separated files and extra
indices.  Bug found by Hiram.  No redmine

diff --git src/utils/bedToBigBed/bedToBigBed.c src/utils/bedToBigBed/bedToBigBed.c
index 988355e..8bba347 100644
--- src/utils/bedToBigBed/bedToBigBed.c
+++ src/utils/bedToBigBed/bedToBigBed.c
@@ -566,31 +566,31 @@
 
 struct bbExIndexMaker *eim = NULL;
 if (extraIndexList != NULL)
     eim = bbExIndexMakerNew(extraIndexList, as);
 
 /* Load in chromosome sizes. */
 struct hash *chromSizesHash = bbiChromSizesFromFile(chromSizes);
 verbose(2, "Read %d chromosomes and sizes from %s\n",  chromSizesHash->elCount, chromSizes);
 
 /* Do first pass, mostly just scanning file and counting hits per chromosome. */
 int minDiff = 0;
 double aveSize = 0;
 bits64 bedCount = 0;
 bits32 uncompressBufSize = 0;
 struct bbiChromUsage *usageList = bbiChromUsageFromBedFile(lf, chromSizesHash, eim, 
-    &minDiff, &aveSize, &bedCount);
+    &minDiff, &aveSize, &bedCount, tabSep);
 verboseTime(1, "pass1 - making usageList (%d chroms)", slCount(usageList));
 verbose(2, "%d chroms in %s. Average span of beds %f\n", slCount(usageList), inName, aveSize);
 
 /* Open output file and write dummy header. */
 FILE *f = mustOpen(outName, "wb");
 bbiWriteDummyHeader(f);
 bbiWriteDummyZooms(f);
 
 /* Write out autoSql string */
 bits64 asOffset = ftell(f);
 mustWrite(f, asText, strlen(asText) + 1);
 verbose(2, "as definition has %d columns\n", fieldCount);
 
 /* Write out dummy total summary. */
 struct bbiSummaryElement totalSum;