bd1404d9126eb1575ed20098204038364ea90308
kent
  Tue Mar 5 10:04:23 2013 -0800
Big bed extra indexes seem to work now.  Code still needs a little polish and testing.
diff --git src/inc/bbiFile.h src/inc/bbiFile.h
index 3eb1c31..d050c7b 100644
--- src/inc/bbiFile.h
+++ src/inc/bbiFile.h
@@ -117,35 +117,30 @@
     bits64 unzoomedIndexOffset;	/* Start of unzoomed index. */
     bits16 fieldCount;		/* Number of columns in bed version. */
     bits16 definedFieldCount;   /* Number of columns using bed standard definitions. */
     bits64 asOffset;		/* Offset to embedded null-terminated AutoSQL file. */
     bits64 totalSummaryOffset;	/* Offset to total summary information if any.  
 				   (On older files have to calculate) */
     bits32 uncompressBufSize;	/* Size of uncompression buffer, 0 if uncompressed */
     bits64 extensionOffset;	/* Start of header extension block or 0 if none. */
     struct cirTreeFile *unzoomedCir;	/* Unzoomed data index in memory - may be NULL. */
     struct bbiZoomLevel *levelList;	/* List of zoom levels. */
 
     /* Fields based on extension block. */
     bits16 extensionSize;   /* Size of extension block */
     bits16 extraIndexCount; /* Number of extra indexes (on fields other than chrom,start,end */ 
     bits64 extraIndexListOffset;    /* Offset to list of extra indexes */
-
-    struct bptFile *uglyOldNameBpt;	/* Index of names, may be NULL */ // uglyf - remove
-
-    /* Some fields that should not be accessed directly as they may not have good values. */
-    struct asObject *cachedAs;	/* Cached parsed version.  Use bigBedAsOrDefault() to get this. */
     };
 
 
 struct bbiFile *bbiFileOpen(char *fileName, bits32 sig, char *typeName);
 /* Open up big wig or big bed file. */
 
 void bbiFileClose(struct bbiFile **pBwf);
 /* Close down a big wig/big bed file. */
 
 struct fileOffsetSize *bbiOverlappingBlocks(struct bbiFile *bbi, struct cirTreeFile *ctf,
 	char *chrom, bits32 start, bits32 end, bits32 *retChromId);
 /* Fetch list of file blocks that contain items overlapping chromosome range. */
  
 struct bbiChromIdSize
 /* We store an id/size pair in chromBpt bPlusTree */