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 */