94672ce4f2953546899086d417a191e04aa9bf2f
kent
  Wed Feb 27 09:55:10 2013 -0800
Adding chromId to bigBedInterval structure for item name based queries.  Removing unused ppBed structure.
diff --git src/inc/bigBed.h src/inc/bigBed.h
index 8aee277..b0702f0 100644
--- src/inc/bigBed.h
+++ src/inc/bigBed.h
@@ -1,83 +1,73 @@
 /* bigBed - interface to binary file with bed-style values (that is a bunch of
  * possibly overlapping regions.
  *
  * This shares a lot with the bigWig module. */
 
 #ifndef BIGBED_H
 #define BIGBED_H
 
 #include "asParse.h"
 
 #ifndef BBIFILE
 #include "bbiFile.h"
 #endif
 
 struct bigBedInterval
 /* A partially parsed out bed record plus some extra fields. */
     {
     struct bigBedInterval *next;	/* Next in list. */
     bits32 start, end;		/* Range inside chromosome - half open zero based. */
     char *rest;			/* Rest of line. May be NULL*/
-    };
-
-struct ppBed
-/* A partially parsed out bed record plus some extra fields. */
-    {
-    struct ppBed *next;	/* Next in list. */
-    char *chrom;		/* Chromosome name (not allocated here) */
-    bits32 start, end;		/* Range inside chromosome - half open zero based. */
-    char *rest;			/* The rest of the bed. */
-    bits64 fileOffset;		/* File offset. */
-    bits32 chromId;		/* Chromosome ID. */
+    bits32 chromId;             /* ID of chromosome.  */
     };
 
 struct bbiFile *bigBedFileOpen(char *fileName);
 /* Open up big bed file.   Free this up with bbiFileClose. */
 
 #define bigBedFileClose(a) bbiFileClose(a)
 
 struct bigBedInterval *bigBedIntervalQuery(struct bbiFile *bbi, char *chrom,
 	bits32 start, bits32 end, int maxItems, struct lm *lm);
 /* Get data for interval.  Return list allocated out of lm.  Set maxItems to maximum
  * number of items to return, or to 0 for all items. */
 
 int bigBedIntervalToRow(struct bigBedInterval *interval, char *chrom, char *startBuf, char *endBuf,
 	char **row, int rowSize);
 /* Convert bigBedInterval into an array of chars equivalent to what you'd get by
  * parsing the bed file. The startBuf and endBuf are used to hold the ascii representation of
  * start and end.  Note that the interval->rest string will have zeroes inserted as a side effect.
  * Returns number of fields in row.  */
 
 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. */
 
 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);
 // Get asObject associated with bigBed file, or the default.
 
 boolean bigBedFileCheckSigs(char *fileName);
 /* check file signatures at beginning and end of file */
 
 #endif /* BIGBED_H */