src/inc/bigBed.h 1.8

Index: src/inc/bigBed.h
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/inc/bigBed.h,v
retrieving revision 1.7
retrieving revision 1.8
diff -b -B -U 1000000 -r1.7 -r1.8
--- src/inc/bigBed.h	3 Feb 2009 08:18:24 -0000	1.7
+++ src/inc/bigBed.h	10 Feb 2009 22:07:49 -0000	1.8
@@ -1,57 +1,59 @@
 /* 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
 
 #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 bbiFile *bigBedFileOpen(char *fileName);
 /* Open up big bed file.   Free this up with bbiFileFree */
 
 struct bigBedInterval *bigBedIntervalQuery(struct bbiFile *bwf, 
 	char *chrom, bits32 start, bits32 end, struct lm *lm);
 /* Get data for interval.  Return list allocated out of lm. */
 
 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(char *fileName, 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(char *fileName, char *chrom, bits32 start, bits32 end,
 	int summarySize, struct bbiSummaryElement *summary);
 /* Get extended summary information for summarySize evenely spaced elements into
  * the summary array. */
 
 void bigBedFileCreate(
 	char *inName, 	  /* Input file in a tabular bed format <chrom><start><end> + whatever. */
 	char *chromSizes, /* Two column tab-separated file: <chromosome> <size>. */
 	int blockSize,	  /* Number of items to bundle in r-tree.  1024 is good. */
 	int itemsPerSlot, /* Number of items in lowest level of tree.  64 is good. */
+	bits16 definedFieldCount,  /* Number of defined bed fields - 3-16 or so.  0 means all fields
+				    * are the defined bed ones. */
 	char *outName);   /* BigBed output file name. */
 /* Convert tab-separated bed file to binary indexed, zoomed bigBed version. */
 
 #endif /* BIGBED_H */