Index: src/lib/bigBed.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/lib/bigBed.c,v
retrieving revision 1.26
retrieving revision 1.27
diff -b -B -U 1000000 -r1.26 -r1.27
--- src/lib/bigBed.c	5 Feb 2010 19:33:43 -0000	1.26
+++ src/lib/bigBed.c	6 Feb 2010 19:58:52 -0000	1.27
@@ -1,225 +1,225 @@
 /* bigBed - interface to binary file with bed-style values (that is a bunch of
  * possibly overlapping regions. */
 
 #include "common.h"
 #include "hash.h"
 #include "linefile.h"
 #include "localmem.h"
 #include "obscure.h"
 #include "dystring.h"
 #include "rangeTree.h"
 #include "cirTree.h"
 #include "bPlusTree.h"
 #include "basicBed.h"
 #include "asParse.h"
 #include "zlibFace.h"
 #include "sig.h"
 #include "udc.h"
 #include "bbiFile.h"
 #include "bigBed.h"
 
 struct bbiFile *bigBedFileOpen(char *fileName)
 /* Open up big bed file. */
 {
 return bbiFileOpen(fileName, bigBedSig, "big bed");
 }
 
 struct bigBedInterval *bigBedIntervalQuery(struct bbiFile *bbi, char *chrom, 
 	bits32 start, bits32 end, int maxItems, struct lm *lm)
 /* Get data for interval.  Return list allocated out of lm.  Set maxItems to maximum
  * number of items to return, or to 0 for all items. */
 {
 struct bigBedInterval *el, *list = NULL;
 int itemCount = 0;
 bbiAttachUnzoomedCir(bbi);
 bits32 chromId;
 struct fileOffsetSize *blockList = bbiOverlappingBlocks(bbi, bbi->unzoomedCir, 
 	chrom, start, end, &chromId);
 struct fileOffsetSize *block, *beforeGap, *afterGap;
 struct udcFile *udc = bbi->udc;
 boolean isSwapped = bbi->isSwapped;
 struct dyString *dy = dyStringNew(32);
 
 /* Set up for uncompression optionally. */
 char *uncompressBuf = NULL;
 if (bbi->uncompressBufSize > 0)
     uncompressBuf = needLargeMem(bbi->uncompressBufSize);
 
 for (block = blockList; block != NULL; )
     {
     /* Find contigious blocks and read them into mergedBuf. */
     fileOffsetSizeFindGap(block, &beforeGap, &afterGap);
     bits64 mergedOffset = block->offset;
     bits64 mergedSize = beforeGap->offset + beforeGap->size - mergedOffset;
     udcSeek(udc, mergedOffset);
     char *mergedBuf = needLargeMem(mergedSize);
     udcMustRead(udc, mergedBuf, mergedSize);
     char *blockBuf = mergedBuf;
 
     /* Loop through individual blocks within merged section. */
     for (;block != afterGap; block = block->next)
         {
 	/* Uncompress if necessary. */
 	char *blockPt, *blockEnd;
 	if (uncompressBuf)
 	    {
 	    blockPt = uncompressBuf;
 	    int uncSize = zUncompress(blockBuf, block->size, uncompressBuf, bbi->uncompressBufSize);
 	    blockEnd = blockPt + uncSize;
 	    }
 	else
 	    {
 	    blockPt = blockBuf;
 	    blockEnd = blockPt + block->size;
 	    }
 
 	while (blockPt < blockEnd)
 	    {
 	    /* Read next record into local variables. */
 	    bits32 chr = memReadBits32(&blockPt, isSwapped);	// Read and discard chromId
 	    bits32 s = memReadBits32(&blockPt, isSwapped);
 	    bits32 e = memReadBits32(&blockPt, isSwapped);
 	    int c;
 	    dyStringClear(dy);
 	    while ((c = *blockPt++) >= 0)
 		{
 		if (c == 0)
 		    break;
 		dyStringAppendC(dy, c);
 		}
 
 	    /* If we're actually in range then copy it into a new  element and add to list. */
 	    if (chr == chromId && rangeIntersection(s, e, start, end) > 0)
 		{
 		++itemCount;
 		if (maxItems > 0 && itemCount > maxItems)
 		    break;
 
 		lmAllocVar(lm, el);
 		el->start = s;
 		el->end = e;
 		if (dy->stringSize > 0)
 		    el->rest = lmCloneString(lm, dy->string);
 		slAddHead(&list, el);
 		}
 	    }
 	if (maxItems > 0 && itemCount > maxItems)
 	    break;
 	blockBuf += block->size;
         }
     if (maxItems > 0 && itemCount > maxItems)
         break;
     freez(&mergedBuf);
     }
 freeMem(uncompressBuf);
 dyStringFree(&dy);
 slFreeList(&blockList);
 slReverse(&list);
 return list;
 }
 
 int bigBedIntervalToRow(struct bigBedInterval *interval, char *chrom, char *startBuf, char *endBuf,
 	char **row, int rowSize)
 /* Convert bigBedInterval into an array of chars equivalent to what you'd get by
  * parsing the bed file. The startBuf and endBuf are used to hold the ascii representation of
  * start and end.  Note that the interval->rest string will have zeroes inserted as a side effect. 
  */
 {
 int fieldCount = 3;
 sprintf(startBuf, "%u", interval->start);
 sprintf(endBuf, "%u", interval->end);
 row[0] = chrom;
 row[1] = startBuf;
 row[2] = endBuf;
 if (!isEmpty(interval->rest))
     {
     int wordCount = chopByWhite(interval->rest, row+3, rowSize-3);
     fieldCount += wordCount;
     }
 return fieldCount;
 }
 
-struct bbiInterval *bigBedCoverageIntervals(struct bbiFile *bbi, 
+static struct bbiInterval *bigBedCoverageIntervals(struct bbiFile *bbi, 
 	char *chrom, bits32 start, bits32 end, struct lm *lm)
 /* Return intervals where the val is the depth of coverage. */
 {
 /* Get list of overlapping intervals */
 struct bigBedInterval *bi, *biList = bigBedIntervalQuery(bbi, chrom, start, end, 0, lm);
 if (biList == NULL)
     return NULL;
 
 /* Make a range tree that collects coverage. */
 struct rbTree *rangeTree = rangeTreeNew();
 for (bi = biList; bi != NULL; bi = bi->next)
     rangeTreeAddToCoverageDepth(rangeTree, bi->start, bi->end);
 struct range *range, *rangeList = rangeTreeList(rangeTree);
 
 /* Convert rangeList to bbiInterval list. */
 struct bbiInterval *bwi, *bwiList = NULL;
 for (range = rangeList; range != NULL; range = range->next)
     {
     lmAllocVar(lm, bwi);
     bwi->start = range->start;
     if (bwi->start < start)
        bwi->start = start;
     bwi->end = range->end;
     if (bwi->end > end)
        bwi->end = end;
     bwi->val = ptToInt(range->val);
     slAddHead(&bwiList, bwi);
     }
 slReverse(&bwiList);
 
 /* Clean up and go home. */
 rangeTreeFree(&rangeTree);
 return bwiList;
 }
 
 boolean bigBedSummaryArrayExtended(struct bbiFile *bbi, char *chrom, bits32 start, bits32 end,
 	int summarySize, struct bbiSummaryElement *summary)
 /* Get extended summary information for summarySize evenely spaced elements into
  * the summary array. */
 {
 return bbiSummaryArrayExtended(bbi, chrom, start, end, bigBedCoverageIntervals,
 	summarySize, summary);
 }
 
 boolean bigBedSummaryArray(struct bbiFile *bbi, char *chrom, bits32 start, bits32 end,
 	enum bbiSummaryType summaryType, int summarySize, double *summaryValues)
 /* Fill in summaryValues with  data from indicated chromosome range in bigBed 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("") depending on the application.)  Returns FALSE if no data
  * at that position. */
 {
 return bbiSummaryArray(bbi, chrom, start, end, bigBedCoverageIntervals,
 	summaryType, summarySize, summaryValues);
 }
 
 char *bigBedAutoSqlText(struct bbiFile *bbi)
 /* Get autoSql text if any associated with file.  Do a freeMem of this when done. */
 {
 if (bbi->asOffset == 0)
     return NULL;
 struct udcFile *f = bbi->udc;
 udcSeek(f, bbi->asOffset);
 return udcReadStringAndZero(f);
 }
 
 struct asObject *bigBedAs(struct bbiFile *bbi)
 /* Get autoSql object definition if any associated with file. */
 {
 if (bbi->asOffset == 0)
     return NULL;
 char *asText = bigBedAutoSqlText(bbi);
 struct asObject *as = asParseText(asText);
 freeMem(asText);
 return as;
 }
 
 bits64 bigBedItemCount(struct bbiFile *bbi)
 /* Return total items in file. */
 {
 udcSeek(bbi->udc, bbi->unzoomedDataOffset);
 return udcReadBits64(bbi->udc, bbi->isSwapped);
 }

