src/utils/bedGraphToBigWig/bedGraphToBigWig.c 1.16

Index: src/utils/bedGraphToBigWig/bedGraphToBigWig.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/utils/bedGraphToBigWig/bedGraphToBigWig.c,v
retrieving revision 1.15
retrieving revision 1.16
diff -b -B -U 4 -r1.15 -r1.16
--- src/utils/bedGraphToBigWig/bedGraphToBigWig.c	10 Sep 2009 01:49:38 -0000	1.15
+++ src/utils/bedGraphToBigWig/bedGraphToBigWig.c	5 Nov 2009 19:35:38 -0000	1.16
@@ -174,10 +174,10 @@
     }
 assert(sectionIx == sectionCount);
 }
 
-struct bbiSummary *writeReducedOnceReturnReducedTwice(struct bbiChromUsage *usageList, 
-	struct lineFile *lf, int initialReduction, int initialReductionCount, 
+static struct bbiSummary *writeReducedOnceReturnReducedTwice(struct bbiChromUsage *usageList, 
+	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
@@ -191,8 +191,9 @@
 boundsPt = AllocArray(boundsArray, initialReductionCount);
 boundsEnd = boundsPt + initialReductionCount;
 
 *retDataStart = ftell(f);
+writeOne(f, initialReductionCount);
 for (;;)
     {
     /* Get next line of input if any. */
     char *row[5];
@@ -252,9 +253,9 @@
 	sum->validCount += overlap;
 	if (sum->minVal > val) sum->minVal = val;
 	if (sum->maxVal < val) sum->maxVal = val;
 	sum->sumData += val * overlap;
-	sum->sumSquares += val * overlap;
+	sum->sumSquares += val*val * overlap;
 	bbiOutputOneSummaryFurtherReduce(sum, &twiceReducedList, doubleReductionSize, 
 		&boundsPt, boundsEnd, usage->size, lm, f);
 
 	/* Move summary to next part. */
@@ -271,9 +272,9 @@
     sum->validCount += size;
     if (sum->minVal > val) sum->minVal = val;
     if (sum->maxVal < val) sum->maxVal = val;
     sum->sumData += val * size;
-    sum->sumSquares += val * size;
+    sum->sumSquares += val*val * size;
     }
 
 /* Write out 1st zoom index. */
 int indexOffset = *retIndexStart = ftell(f);
@@ -293,11 +294,12 @@
 verboseTime(2, NULL);
 struct lineFile *lf = lineFileOpen(inName, TRUE);
 struct hash *chromSizesHash = bbiChromSizesFromFile(chromSizes);
 verbose(2, "%d chroms in %s\n", chromSizesHash->elCount, chromSizes);
-int minDiff, i;
-double aveSize;
-struct bbiChromUsage *usageList = bbiChromUsageFromBedFile(lf, chromSizesHash, &minDiff, &aveSize);
+int minDiff = 0, i;
+double aveSize = 0;
+bits64 bedCount = 0;
+struct bbiChromUsage *usageList = bbiChromUsageFromBedFile(lf, chromSizesHash, &minDiff, &aveSize, &bedCount);
 verboseTime(2, "pass1");
 verbose(2, "%d chroms in %s\n", slCount(usageList), inName);
 
 /* Write out dummy header, zoom offsets. */
@@ -327,9 +329,10 @@
     resTryCount = 0;
 
 /* Write out primary full resolution data in sections, collect stats to use for reductions. */
 bits64 dataOffset = ftell(f);
-bits32 sectionCount = bbiCountSectionsNeeded(usageList, itemsPerSlot);
+bits64 sectionCount = bbiCountSectionsNeeded(usageList, itemsPerSlot);
+writeOne(f, sectionCount);
 struct bbiBoundsArray *boundsArray;
 AllocArray(boundsArray, sectionCount);
 lineFileRewind(lf);
 writeSections(usageList, lf, itemsPerSlot, boundsArray, sectionCount, f,
@@ -407,9 +410,9 @@
 
 /* Go back and rewrite header. */
 rewind(f);
 bits32 sig = bigWigSig;
-bits16 version = 1;
+bits16 version = bbiCurrentVersion;
 bits16 summaryCount = zoomLevels;
 bits32 reserved32 = 0;
 bits32 reserved64 = 0;