src/utils/bedToBigBed/bedToBigBed.c 1.12

Index: src/utils/bedToBigBed/bedToBigBed.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/bedToBigBed/bedToBigBed.c,v
retrieving revision 1.11
retrieving revision 1.12
diff -b -B -U 4 -r1.11 -r1.12
--- src/utils/bedToBigBed/bedToBigBed.c	28 Sep 2009 18:20:28 -0000	1.11
+++ src/utils/bedToBigBed/bedToBigBed.c	5 Nov 2009 19:35:01 -0000	1.12
@@ -248,10 +248,10 @@
     }
 return tree;
 }
 
-struct bbiSummary *writeReducedOnceReturnReducedTwice(struct bbiChromUsage *usageList, 
-	int fieldCount, struct lineFile *lf, int initialReduction, int initialReductionCount, 
+static struct bbiSummary *writeReducedOnceReturnReducedTwice(struct bbiChromUsage *usageList, 
+	int fieldCount, struct lineFile *lf, bits32 initialReduction, bits32 initialReductionCount, 
 	int zoomIncrement, int blockSize, int itemsPerSlot, 
 	struct lm *lm, FILE *f, bits64 *retDataStart, bits64 *retIndexStart)
 /* Write out data reduced by factor of initialReduction.  Also calculate and keep in memory
  * next reduction level.  This is more work than some ways, but it keeps us from having to
@@ -264,8 +264,9 @@
 boundsPt = AllocArray(boundsArray, initialReductionCount);
 boundsEnd = boundsPt + initialReductionCount;
 
 *retDataStart = ftell(f);
+writeOne(f, initialReductionCount);
 
 /* This gets a little complicated I'm afraid.  The strategy is to:
  *   1) Build up a range tree that represents coverage depth on that chromosome
  *      This also has the nice side effect of getting rid of overlaps.
@@ -385,9 +386,10 @@
 
 /* Do first pass, mostly just scanning file and counting hits per chromosome. */
 int minDiff = 0;
 double aveSpan = 0;
-struct bbiChromUsage *usageList = bbiChromUsageFromBedFile(lf, chromSizesHash, &minDiff, &aveSpan);
+bits64 bedCount = 0;
+struct bbiChromUsage *usageList = bbiChromUsageFromBedFile(lf, chromSizesHash, &minDiff, &aveSpan, &bedCount);
 verboseTime(1, "pass1 - making usageList");
 verbose(2, "%d chroms in %s. Average span of beds %f\n", slCount(usageList), inName, aveSpan);
 
 /* Open output file and write dummy header. */
@@ -428,8 +430,9 @@
     }
 
 /* Write out primary full resolution data in sections, collect stats to use for reductions. */
 bits64 dataOffset = ftell(f);
+writeOne(f, bedCount);
 bits32 blockCount = bbiCountSectionsNeeded(usageList, itemsPerSlot);
 struct bbiBoundsArray *boundsArray;
 AllocArray(boundsArray, blockCount);
 lineFileRewind(lf);
@@ -509,9 +512,9 @@
     }
 /* Go back and rewrite header. */
 rewind(f);
 bits32 sig = bigBedSig;
-bits16 version = 1;
+bits16 version = bbiCurrentVersion;
 bits16 summaryCount = zoomLevels;
 bits32 reserved32 = 0;
 bits32 reserved64 = 0;