cfa3310ec7d0c3ef45a3f647c7e7164453d9d4e0
kent
  Tue Mar 5 01:01:42 2013 -0800
A little more progress on multiple extra index change. First time reader and writer have both worked in any small way together.
diff --git src/inc/bigBed.h src/inc/bigBed.h
index 959a578..bd7c4db 100644
--- src/inc/bigBed.h
+++ src/inc/bigBed.h
@@ -44,56 +44,54 @@
 boolean bigBedSummaryArray(struct bbiFile *bbi, char *chrom, bits32 start, bits32 end,
 	enum bbiSummaryType summaryType, int summarySize, double *summaryValues);
 /* Fill in summaryValues with  data from indicated chromosome range in bigBed file.
  * Be sure to initialize summaryValues to a default value, which will not be touched
  * for regions without data in file.  (Generally you want the default value to either
  * be 0.0 or nan("") depending on the application.)  Returns FALSE if no data
  * at that position. */
 
 boolean bigBedSummaryArrayExtended(struct bbiFile *bbi, char *chrom, bits32 start, bits32 end,
 	int summarySize, struct bbiSummaryElement *summary);
 /* Get extended summary information for summarySize evenely spaced elements into
  * the summary array. */
 
 /*** Some routines for accessing bigBed items via name. ***/
 
-struct bigBedInterval *bigBedNameQuery(struct bbiFile *bbi, char *name, struct lm *lm);
+struct bigBedInterval *bigBedNameQuery(struct bbiFile *bbi, struct bptFile *index,
+    char *name, struct lm *lm);
 /* Return list of intervals matching file. These intervals will be allocated out of lm. */
 
-struct bigBedInterval *bigBedMultiNameQuery(struct bbiFile *bbi, char **names, 
-    int nameCount, struct lm *lm);
+struct bigBedInterval *bigBedMultiNameQuery(struct bbiFile *bbi, struct bptFile *index,
+    char **names, int nameCount, struct lm *lm);
 /* Fetch all records matching any of the names. Return list is allocated out of lm. */
 
 int bigBedIntervalToRowLookupChrom(struct bigBedInterval *interval, 
     struct bigBedInterval *prevInterval, struct bbiFile *bbi,
     char *chromBuf, int chromBufSize, char *startBuf, char *endBuf, char **row, int rowSize);
 /* Convert bigBedInterval to array of chars equivalend to what you'd get by parsing the
  * bed file.  If you already know what chromosome the interval is on use the simpler
  * bigBedIntervalToRow.  This one will look up the chromosome based on the chromId field
  * of the interval,  which is relatively time consuming.  To avoid doing this unnecessarily
  * pass in a non-NULL prevInterval,  and if the chromId is the same on prevInterval as this,
  * it will avoid the lookup.  The chromBufSize should be at greater or equal to 
  * bbi->chromBpt->keySize+1.  The startBuf and endBuf are used to hold the ascii representation of
  * start and end, and should be 16 bytes.  Note that the interval->rest string will have zeroes 
  * inserted as a side effect.  Returns number of fields in row.  */
 
 void bigBedIntervalListToBedFile(struct bbiFile *bbi, struct bigBedInterval *intervalList, FILE *f);
 /* Write out big bed interval list to bed file, looking up chromosome. */
 
-void bigBedAttachNameIndex(struct bbiFile *bbi);
-/* Attach name index part of bbiFile to bbi.  Not normally needed to call directly. */
-
 /** Routines to access other data from a bigBed file. */
 
 bits64 bigBedItemCount(struct bbiFile *bbi);
 /* Return total items in file. */
 
 char *bigBedAutoSqlText(struct bbiFile *bbi);
 /* Get autoSql text if any associated with file.  Do a freeMem of this when done. */
 
 struct asObject *bigBedAs(struct bbiFile *bbi);
 /* Get autoSql object definition if any associated with file. */
 
 struct asObject *bigBedAsOrDefault(struct bbiFile *bbi);
 // Get asObject associated with bigBed - if none exists in file make it up from field counts.
 
 struct asObject *bigBedFileAsObjOrDefault(char *fileName);