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/inc/bbiFile.h src/inc/bbiFile.h
index e582038..587dcfe 100644
--- src/inc/bbiFile.h
+++ src/inc/bbiFile.h
@@ -365,31 +365,31 @@
 
 struct bbExIndexMaker
 /* A helper structure to make indexes beyond primary one.  Just used for bigBeds */
     {
     bits16 indexCount;          /* Number of extra indexes. */
         /* Kind of wish next four fields,  all of which are arrays indexed
          * by the same thing,  were a single array of a structure instead. */
     bits16 *indexFields;        /* array of field ids, one for each extra index. */
     int *maxFieldSize;          /* array of maximum sizes seen for this field. */
     struct bbNamedFileChunk **chunkArrayArray; /* where we keep name/start/size triples */
     bits64 *fileOffsets;        /* array of file offsets where indexes starts. */
     int recordCount;            /* number of records in file. */
     };
 
 struct bbiChromUsage *bbiChromUsageFromBedFile(struct lineFile *lf, struct hash *chromSizesHash, 
-	struct bbExIndexMaker *eim, int *retMinDiff, double *retAveSize, bits64 *retBedCount);
+	struct bbExIndexMaker *eim, int *retMinDiff, double *retAveSize, bits64 *retBedCount, boolean tabSep);
 /* Go through bed file and collect chromosomes and statistics.  If eim parameter is non-NULL
  * collect max field sizes there too. */
 
 #define bbiMaxZoomLevels 10	/* Max number of zoom levels */
 #define bbiResIncrement 4	/* Amount to reduce at each zoom level */
 
 int bbiCalcResScalesAndSizes(int aveSize, 
     int resScales[bbiMaxZoomLevels], int resSizes[bbiMaxZoomLevels]);
 /* Fill in resScales with amount to zoom at each level, and zero out resSizes based
  * on average span. Returns the number of zoom levels we actually will use. */
 
 typedef struct bbiSummary *bbiWriteReducedOnceReturnReducedTwice(
 	struct bbiChromUsage *usageList, int fieldCount,
 	struct lineFile *lf, bits32 initialReduction, bits32 initialReductionCount, 
 	int zoomIncrement, int blockSize, int itemsPerSlot, boolean doCompress,