1156e1e9fd3c14d702772fdd0ff3978049f9e764
kent
  Tue Mar 29 14:33:06 2011 -0700
Having bigWigValsOnChromFetchData read bigWig directly rather than going through bigWigIntervalQuery in hopes of speeding up particularly on things that have a value for each base and are stored as fixedStep.   It does speed it up by 2x when you are not too i/o bound.
diff --git src/inc/bwgInternal.h src/inc/bwgInternal.h
index 3c6bad3..fab20ab 100644
--- src/inc/bwgInternal.h
+++ src/inc/bwgInternal.h
@@ -1,97 +1,113 @@
 /* bwgInternal - stuff to create and use bigWig files.  Generally you'll want to use the
  * simpler interfaces in the bigWig module instead.  This file is good reading though
  * if you want to extend the bigWig interface, or work with bigWig files directly
  * without going through the Kent library. */
 
 #ifndef BIGWIGFILE_H
 #define BIGWIGFILE_H
 
 enum bwgSectionType 
 /* Code to indicate section type. */
     {
     bwgTypeBedGraph=1,
     bwgTypeVariableStep=2,
     bwgTypeFixedStep=3,
     };
 
 struct bwgBedGraphItem
 /* An bedGraph-type item in a bwgSection. */
     {
     struct bwgBedGraphItem *next;	/* Next in list. */
     bits32 start,end;		/* Range of chromosome covered. */
     float val;			/* Value. */
     };
 
 struct bwgVariableStepItem
 /* An variableStep type item in a bwgSection. */
     {
     struct bwgVariableStepItem *next;	/* Next in list. */
     bits32 start;		/* Start position in chromosome. */
     float val;			/* Value. */
     };
 
 struct bwgVariableStepPacked
 /* An variableStep type item in a bwgSection. */
     {
     bits32 start;		/* Start position in chromosome. */
     float val;			/* Value. */
     };
 
 struct bwgFixedStepItem
 /* An fixedStep type item in a bwgSection. */
     {
     struct bwgFixedStepItem *next;	/* Next in list. */
     float val;			/* Value. */
     };
 
 struct bwgFixedStepPacked
 /* An fixedStep type item in a bwgSection. */
     {
     float val;			/* Value. */
     };
 
 union bwgItem
 /* Union of item pointers for all possible section types. */
     {
     struct bwgBedGraphItem *bedGraphList;		/* A linked list */
     struct bwgFixedStepPacked *fixedStepPacked;		/* An array */
     struct bwgVariableStepPacked *variableStepPacked;	/* An array */
     /* No packed format for bedGraph... */
     };
 
 struct bwgSection
 /* A section of a bigWig file - all on same chrom.  This is a somewhat fat data
  * structure used by the bigWig creation code.  See also bwgSection for the
  * structure returned by the bigWig reading code. */
     {
     struct bwgSection *next;		/* Next in list. */
     char *chrom;			/* Chromosome name. */
     bits32 start,end;			/* Range of chromosome covered. */
     enum bwgSectionType type;
     union bwgItem items;		/* List/array of items in this section. */
     bits32 itemStep;			/* Step within item if applicable. */
     bits32 itemSpan;			/* Item span if applicable. */
     bits16 itemCount;			/* Number of items in section. */
     bits32 chromId;			/* Unique small integer value for chromosome. */
     bits64 fileOffset;			/* Offset of section in file. */
     };
 
+struct bwgSectionHead
+/* A header from a bigWig file section - similar to above bug what is on disk. */
+    {
+    bits32 chromId;	/* Chromosome short identifier. */
+    bits32 start,end;	/* Range covered. */
+    bits32 itemStep;	/* For some section types, the # of bases between items. */
+    bits32 itemSpan;	/* For some section types, the # of bases in each item. */
+    UBYTE type;		/* Type byte. */
+    UBYTE reserved;	/* Always zero for now. */
+    bits16 itemCount;	/* Number of items in block. */
+    };
+
+void bwgSectionHeadFromMem(char **pPt, struct bwgSectionHead *head, boolean isSwapped);
+/* Read section header. */
+
+
 int bwgSectionCmp(const void *va, const void *vb);
 /* Compare to sort based on chrom,start,end.  */
 
 struct bwgSection *bwgParseWig(
 	char *fileName,       /* Name of ascii wig file. */
 	boolean clipDontDie,  /* Skip items outside chromosome rather than aborting. */
 	struct hash *chromSizeHash,  /* If non-NULL items checked to be inside chromosome. */
 	int maxSectionSize,   /* Biggest size of a section.  100 - 100,000 is usual range. */
 	struct lm *lm);	      /* Memory pool to allocate from. */
 /* Parse out ascii wig file - allocating memory in lm. */
 
 int bwgAverageResolution(struct bwgSection *sectionList);
 /* Return the average resolution seen in sectionList. */
 
 struct bbiSummary *bwgReduceSectionList(struct bwgSection *sectionList, 
 	struct bbiChromInfo *chromInfoArray, int reduction);
 /* Return summary of section list reduced by given amount. */
 
 #endif /* BIGWIGFILE_H */