src/inc/bigWig.h 1.12

Index: src/inc/bigWig.h
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/inc/bigWig.h,v
retrieving revision 1.11
retrieving revision 1.12
diff -b -B -U 1000000 -r1.11 -r1.12
--- src/inc/bigWig.h	17 Jun 2009 15:19:00 -0000	1.11
+++ src/inc/bigWig.h	10 Nov 2009 05:45:47 -0000	1.12
@@ -1,67 +1,69 @@
 /* bigWig - interface to binary file with wiggle-style values (that is a bunch of
  * small non-overlapping regions each associated with a floating point value. 
  *
  * There are several ways to use this module.   To create a new bigWig file use the
  * bigWigCreate function, which takes as input an ascii file in fixedStep, variableStep
  * or bedGraph format.
  *
  * To get a section of of a bigWig for display on a browser, use the bigWigSummaryArray
  * function, which will fill in an array of doubles with on value for each pixel that
  * you want to display.
  *
  * To read all the data out of a bigWig get the chromosome info with bbiChromList
  * and then fetch all of it for each chromosome using bigWigIntervalQuery.
  *
  * See also the module bbiFile that has a description of they structure of
  * a bigWig file, and lower level routines used to implement this interface.
  */
 
 #ifndef BIGWIG_H
 #define BIGWIG_H
 
 #ifndef BBIFILE
 #include "bbiFile.h"
 #endif
 
 
 void bigWigFileCreate(
 	char *inName, 		/* Input file in ascii wiggle format. */
 	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.  512 is good. */
 	boolean clipDontDie,	/* If TRUE then clip items off end of chrom rather than dying. */
 	char *outName);
 /* Convert ascii format wig file (in fixedStep, variableStep or bedGraph format) 
  * to binary big wig format. */
 
 struct bbiFile *bigWigFileOpen(char *fileName);
 /* Open up big wig file.   Free this up with bbiFileClose */
 
+#define bigWigFileClose(a) bbiFileClose(a)
+
 struct bbiInterval *bigWigIntervalQuery(struct bbiFile *bwf, char *chrom, bits32 start, bits32 end,
 	struct lm *lm);
 /* Get data for interval.  Return list allocated out of lm. */
 
 int bigWigIntervalDump(struct bbiFile *bwf, char *chrom, bits32 start, bits32 end, int maxCount,
 	FILE *out);
 /* Print out info on bigWig parts that intersect chrom:start-end.   Set maxCount to 0 if you 
  * don't care how many are printed.  Returns number printed. */
 
-boolean bigWigSummaryArray(char *fileName, char *chrom, bits32 start, bits32 end,
+boolean bigWigSummaryArray(struct bbiFile *bwf, char *chrom, bits32 start, bits32 end,
 	enum bbiSummaryType summaryType, int summarySize, double *summaryValues);
 /* Fill in summaryValues with  data from indicated chromosome range in bigWig 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(0) depending on the application.)  Returns FALSE if no data
  * at that position. */
 
-boolean bigWigSummaryArrayExtended(char *fileName, char *chrom, bits32 start, bits32 end,
+boolean bigWigSummaryArrayExtended(struct bbiFile *bwf, char *chrom, bits32 start, bits32 end,
 	int summarySize, struct bbiSummaryElement *summary);
 /* Get extended summary information for summarySize evenely spaced elements into
  * the summary array. */
 
-double bigWigSingleSummary(char *fileName, char *chrom, int start, int end,
+double bigWigSingleSummary(struct bbiFile *bwf, char *chrom, int start, int end,
     enum bbiSummaryType summaryType, double defaultVal);
 /* Return the summarized single value for a range. */
 
 #endif /* BIGWIG_H */