src/inc/bwgInternal.h 1.10

Index: src/inc/bwgInternal.h
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/inc/bwgInternal.h,v
retrieving revision 1.9
retrieving revision 1.10
diff -b -B -U 4 -r1.9 -r1.10
--- src/inc/bwgInternal.h	4 Feb 2009 22:27:20 -0000	1.9
+++ src/inc/bwgInternal.h	29 May 2010 22:28:44 -0000	1.10
@@ -13,10 +13,79 @@
     bwgTypeVariableStep=2,
     bwgTypeFixedStep=3,
     };
 
-struct bwgSection *bwgParseWig(char *fileName, boolean clipDontDie, struct hash *chromSizeHash,
-	int maxSectionSize, struct lm *lm);
+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. */
+    };
+
+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. */