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/bedGraphToBigWig/bedGraphToBigWig.c src/utils/bedGraphToBigWig/bedGraphToBigWig.c
index 8115a24..6179af5 100644
--- src/utils/bedGraphToBigWig/bedGraphToBigWig.c
+++ src/utils/bedGraphToBigWig/bedGraphToBigWig.c
@@ -362,31 +362,31 @@
 return twiceReducedList;
 }
 
 void bedGraphToBigWig(char *inName, char *chromSizes, char *outName)
 /* bedGraphToBigWig - Convert a bedGraph program to bigWig.. */
 {
 verboseTimeInit();
 struct lineFile *lf = lineFileOpen(inName, TRUE);
 struct hash *chromSizesHash = bbiChromSizesFromFile(chromSizes);
 verbose(2, "%d chroms in %s\n", chromSizesHash->elCount, chromSizes);
 int minDiff = 0, i;
 double aveSize = 0;
 bits64 bedCount = 0;
 bits32 uncompressBufSize = 0;
 struct bbiChromUsage *usageList = bbiChromUsageFromBedFile(lf, chromSizesHash, NULL, 
-    &minDiff, &aveSize, &bedCount);
+    &minDiff, &aveSize, &bedCount, FALSE);
 verboseTime(2, "pass1");
 verbose(2, "%d chroms in %s, minDiff=%d, aveSize=%g, bedCount=%lld\n", 
     slCount(usageList), inName, minDiff, aveSize, bedCount);
 
 /* Write out dummy header, zoom offsets. */
 FILE *f = mustOpen(outName, "wb");
 bbiWriteDummyHeader(f);
 bbiWriteDummyZooms(f);
 
 /* Write out dummy total summary. */
 struct bbiSummaryElement totalSum;
 ZeroVar(&totalSum);
 bits64 totalSummaryOffset = ftell(f);
 bbiSummaryElementWrite(f, &totalSum);