Index: src/lib/bbiWrite.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/lib/bbiWrite.c,v
retrieving revision 1.13
retrieving revision 1.14
diff -b -B -U 1000000 -r1.13 -r1.14
--- src/lib/bbiWrite.c	6 Apr 2010 23:06:42 -0000	1.13
+++ src/lib/bbiWrite.c	28 Apr 2010 16:44:28 -0000	1.14
@@ -1,578 +1,583 @@
 #include "common.h"
 #include "hash.h"
 #include "linefile.h"
 #include "sqlNum.h"
 #include "localmem.h"
 #include "zlibFace.h"
 #include "cirTree.h"
 #include "bPlusTree.h"
 #include "bbiFile.h"
+#include "obscure.h"
 
 void bbiWriteDummyHeader(FILE *f)
 /* Write out all-zero header, just to reserve space for it. */
 {
 repeatCharOut(f, 0, 64);
 }
 
 void bbiWriteDummyZooms(FILE *f)
 /* Write out zeroes to reserve space for ten zoom levels. */
 {
 repeatCharOut(f, 0, bbiMaxZoomLevels * 24);
 }
 
 void bbiSummaryElementWrite(FILE *f, struct bbiSummaryElement *sum)
 /* Write out summary element to file. */
 {
 writeOne(f, sum->validCount);
 writeOne(f, sum->minVal);
 writeOne(f, sum->maxVal);
 writeOne(f, sum->sumData);
 writeOne(f, sum->sumSquares);
 }
 
 static int bbiChromInfoCmp(const void *va, const void *vb)
 /* Sort bbiChromInfo.  Unlike most of our sorts this is single rather
  * than double indirect. */
 {
 const struct bbiChromInfo *a = (const struct bbiChromInfo *)va;
 const struct bbiChromInfo *b = (const struct bbiChromInfo *)vb;
 return strcmp(a->name, b->name);
 }
 
 
 void bbiWriteChromInfo(struct bbiChromUsage *usageList, int blockSize, FILE *f)
 /* Write out information on chromosomes to file. */
 {
 int chromCount = slCount(usageList);
 struct bbiChromUsage *usage;
 
 /* Allocate and fill in array from list. */
 struct bbiChromInfo *chromInfoArray;
 AllocArray(chromInfoArray, chromCount);
 int i;
 int maxChromNameSize = 0;
 for (i=0, usage = usageList; i<chromCount; ++i, usage = usage->next)
     {
     char *chromName = usage->name;
     int len = strlen(chromName);
     if (len > maxChromNameSize)
         maxChromNameSize = len;
     chromInfoArray[i].name = chromName;
     chromInfoArray[i].id = usage->id;
     chromInfoArray[i].size = usage->size;
     }
 
 /* Sort so the b-Tree actually works. */
 qsort(chromInfoArray, chromCount, sizeof(chromInfoArray[0]), bbiChromInfoCmp);
 
 /* Write chromosome bPlusTree */
 int chromBlockSize = min(blockSize, chromCount);
 bptFileBulkIndexToOpenFile(chromInfoArray, sizeof(chromInfoArray[0]), chromCount, chromBlockSize,
     bbiChromInfoKey, maxChromNameSize, bbiChromInfoVal, 
     sizeof(chromInfoArray[0].id) + sizeof(chromInfoArray[0].size), 
     f);
 
 freeMem(chromInfoArray);
 }
 
 void bbiWriteFloat(FILE *f, float val)
 /* Write out floating point val to file.  Mostly to convert from double... */
 {
 writeOne(f, val);
 }
 
 struct hash *bbiChromSizesFromFile(char *fileName)
 /* Read two column file into hash keyed by chrom. */
 {
 struct hash *hash = hashNew(0);
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[2];
 while (lineFileRow(lf, row))
     hashAddInt(hash, row[0], sqlUnsigned(row[1]));
 
 lineFileClose(&lf);
 return hash;
 }
 
 void bbiChromInfoKey(const void *va, char *keyBuf)
 /* Get key field out of bbiChromInfo. */
 {
 const struct bbiChromInfo *a = ((struct bbiChromInfo *)va);
 strcpy(keyBuf, a->name);
 }
 
 void *bbiChromInfoVal(const void *va)
 /* Get val field out of bbiChromInfo. */
 {
 const struct bbiChromInfo *a = ((struct bbiChromInfo *)va);
 return (void*)(&a->id);
 }
 
 void bbiChromUsageFree(struct bbiChromUsage **pUsage)
 /* free a single bbiChromUsage structure */
 {
 struct bbiChromUsage *usage = *pUsage;
 if (usage != NULL)
     {
     freeMem(usage->name);
     freez(pUsage);
     }
 }
 
 void bbiChromUsageFreeList(struct bbiChromUsage **pList)
 /* free a list of bbiChromUsage structures */
 {
 struct bbiChromUsage *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     bbiChromUsageFree(&el);
     }
 *pList = NULL;
 }
 
 struct bbiChromUsage *bbiChromUsageFromBedFile(struct lineFile *lf, 
 	struct hash *chromSizesHash, int *retMinDiff, double *retAveSize, bits64 *retBedCount)
 /* Go through bed file and collect chromosomes and statistics. */
 {
 char *row[3];
 struct hash *uniqHash = hashNew(0);
 struct bbiChromUsage *usage = NULL, *usageList = NULL;
 int lastStart = -1;
 bits32 id = 0;
 bits64 totalBases = 0, bedCount = 0;
 int minDiff = BIGNUM;
 for (;;)
     {
     int rowSize = lineFileChopNext(lf, row, ArraySize(row));
     if (rowSize == 0)
         break;
     lineFileExpectWords(lf, 3, rowSize);
     char *chrom = row[0];
     int start = lineFileNeedNum(lf, row, 1);
     int end = lineFileNeedNum(lf, row, 2);
     if (start >= end)
         {
 	if (start == end)
 	    errAbort("line %d of %s: start and end coordinates the same\n"
 	             "They need to be at least one apart"
 		     , lf->lineIx, lf->fileName);
 	else
 	    errAbort("end (%d) before start (%d) line %d of %s",
 	    	end, start, lf->lineIx, lf->fileName);
 	}
     ++bedCount;
     totalBases += (end - start);
     if (usage == NULL || differentString(usage->name, chrom))
         {
 	if (hashLookup(uniqHash, chrom))
 	    {
 	    errAbort("%s is not sorted at line %d.  Please use \"sort -k1,1 -k2,2n\" or bedSort and try again.",
 	    	lf->fileName, lf->lineIx);
 	    }
 	hashAdd(uniqHash, chrom, NULL);
+	struct hashEl *chromHashEl = hashLookup(chromSizesHash, chrom);
+	if (chromHashEl == NULL)
+	    errAbort("%s is not found in chromosome sizes file", chrom);
+	int chromSize = ptToInt(chromHashEl->val);
 	AllocVar(usage);
 	usage->name = cloneString(chrom);
 	usage->id = id++;
-	usage->size = hashIntVal(chromSizesHash, chrom);
+	usage->size = chromSize;
 	slAddHead(&usageList, usage);
 	lastStart = -1;
 	}
     if (end > usage->size)
         errAbort("End coordinate %d bigger than %s size of %d line %d of %s", end, usage->name, usage->size, lf->lineIx, lf->fileName);
     usage->itemCount += 1;
     if (lastStart >= 0)
         {
 	int diff = start - lastStart;
 	if (diff < minDiff)
 	    {
 	    if (diff < 0)
 		errAbort("%s is not sorted at line %d.  Please use \"sort -k1,1 -k2,2n\" or bedSort and try again.",
 		    lf->fileName, lf->lineIx);
 	    minDiff = diff;
 	    }
 	}
     lastStart = start;
     }
 slReverse(&usageList);
 *retMinDiff = minDiff;
 *retAveSize = (double)totalBases/bedCount;
 *retBedCount = bedCount;
 freeHash(&uniqHash);
 return usageList;
 }
 
 int bbiCountSectionsNeeded(struct bbiChromUsage *usageList, int itemsPerSlot)
 /* Count up number of sections needed for data. */
 {
 struct bbiChromUsage *usage;
 int count = 0;
 for (usage = usageList; usage != NULL; usage = usage->next)
     {
     int countOne = (usage->itemCount + itemsPerSlot - 1)/itemsPerSlot;
     count += countOne;
     verbose(2, "%s %d, %d blocks of %d\n", usage->name, usage->itemCount, countOne, itemsPerSlot);
     }
 return count;
 }
 
 
 void bbiAddToSummary(bits32 chromId, bits32 chromSize, bits32 start, bits32 end, 
 	bits32 validCount, double minVal, double maxVal, double sumData, double sumSquares,  
 	int reduction, struct bbiSummary **pOutList)
 /* Add data range to summary - putting it onto top of list if possible, otherwise
  * expanding list. */
 {
 struct bbiSummary *sum = *pOutList;
 if (end > chromSize)	// Avoid pathological clipping situation on bad input
     end = chromSize;
 while (start < end)
     {
     /* See if need to allocate a new summary. */
     if (sum == NULL || sum->chromId != chromId || sum->end <= start)
         {
 	struct bbiSummary *newSum;
 	AllocVar(newSum);
 	newSum->chromId = chromId;
 	if (sum == NULL || sum->chromId != chromId || sum->end + reduction <= start)
 	    newSum->start = start;
 	else
 	    newSum->start = sum->end;
 	newSum->end = newSum->start + reduction;
 	if (newSum->end > chromSize)
 	    newSum->end = chromSize;
 	newSum->minVal = minVal;
 	newSum->maxVal = maxVal;
 	sum = newSum;
 	slAddHead(pOutList, sum);
 	}
 
     /* Figure out amount of overlap between current summary and item */
     int overlap = rangeIntersection(start, end, sum->start, sum->end);
     if (overlap <= 0) 
 	{
         warn("%u %u doesn't intersect %u %u, chromId %u chromSize %u", start, end, sum->start, sum->end, chromId, chromSize);
 	internalErr();
 	}
     int itemSize = end - start;
     double overlapFactor = (double)overlap/itemSize;
 
     /* Fold overlapping bits into output. */
     sum->validCount += overlapFactor * validCount;
     if (sum->minVal > minVal)
         sum->minVal = minVal;
     if (sum->maxVal < maxVal)
         sum->maxVal = maxVal;
     sum->sumData += overlapFactor * sumData;
     sum->sumSquares += overlapFactor * sumSquares;
 
     /* Advance over overlapping bits. */
     start += overlap;
     }
 }
 
 void bbiAddRangeToSummary(bits32 chromId, bits32 chromSize, bits32 start, bits32 end, 
 	double val, int reduction, struct bbiSummary **pOutList)
 /* Add chromosome range to summary - putting it onto top of list if possible, otherwise
  * expanding list. */
 {
 int size = end-start;
 double sum = size*val;
 double sumSquares = sum*val;
 bbiAddToSummary(chromId, chromSize, start, end, size, val, val, sum, sumSquares, reduction, pOutList);
 }
 
 struct bbiSummary *bbiReduceSummaryList(struct bbiSummary *inList, 
 	struct bbiChromInfo *chromInfoArray, int reduction)
 /* Reduce summary list to another summary list. */
 {
 struct bbiSummary *outList = NULL;
 struct bbiSummary *sum;
 for (sum = inList; sum != NULL; sum = sum->next)
     bbiAddToSummary(sum->chromId, chromInfoArray[sum->chromId].size, sum->start, sum->end, sum->validCount, sum->minVal,
     	sum->maxVal, sum->sumData, sum->sumSquares, reduction, &outList);
 slReverse(&outList);
 return outList;
 }
 
 bits64 bbiTotalSummarySize(struct bbiSummary *list)
 /* Return size on disk of all summaries. */
 {
 struct bbiSummary *el;
 bits64 total = 0;
 for (el = list; el != NULL; el = el->next)
     total += sizeof(struct bbiSummaryOnDisk);
 return total;
 }
 
 
 static bits64 bbiSummaryFetchOffset(const void *va, void *context)
 /* Fetch bbiSummary file offset for r-tree */
 {
 const struct bbiSummary *a = *((struct bbiSummary **)va);
 return a->fileOffset;
 }
 
 static struct cirTreeRange bbiSummaryFetchKey(const void *va, void *context)
 /* Fetch bbiSummary key for r-tree */
 {
 struct cirTreeRange res;
 const struct bbiSummary *a = *((struct bbiSummary **)va);
 res.chromIx = a->chromId;
 res.start = a->start;
 res.end = a->end;
 return res;
 }
 
 
 static bits64 bbiWriteSummaryAndIndexComp(struct bbiSummary *summaryList, 
 	int blockSize, int itemsPerSlot, FILE *f)
 /* Write out summary and index to summary uncompressed, returning start position of
  * summary index. */
 {
 bits32 i, count = slCount(summaryList);
 struct bbiSummary **summaryArray;
 AllocArray(summaryArray, count);
 writeOne(f, count);
 struct bbiSummary *summary = summaryList;
 
 /* Figure out max size of uncompressed and compressed blocks. */
 bits32 itemSize = sizeof(summary->chromId) + sizeof(summary->start) + sizeof(summary->end) + sizeof(summary->validCount) + 4*sizeof(float);
 int uncBufSize = itemSize * itemsPerSlot;
 char uncBuf[uncBufSize];
 int compBufSize = zCompBufSize(uncBufSize);
 char compBuf[compBufSize];
 
 /* Loop through compressing and writing one slot at a time. */
 bits32 itemsLeft = count;
 int sumIx = 0;
 while (itemsLeft > 0)
     {
     bits32 itemsInSlot = itemsLeft;
     if (itemsInSlot > itemsPerSlot)
          itemsInSlot = itemsPerSlot;
     char *writePt = uncBuf;
 
     bits64 filePos = ftell(f);
     for (i=0; i<itemsInSlot; ++i)
         {
 	summaryArray[sumIx++] = summary;
 	memWriteOne(&writePt, summary->chromId);
 	memWriteOne(&writePt, summary->start);
 	memWriteOne(&writePt, summary->end);
 	memWriteOne(&writePt, summary->validCount);
 	memWriteFloat(&writePt, summary->minVal);
 	memWriteFloat(&writePt, summary->maxVal);
 	memWriteFloat(&writePt, summary->sumData);
 	memWriteFloat(&writePt, summary->sumSquares);
 	summary->fileOffset = filePos;
 	summary = summary->next;
 	if (summary == NULL)
 	    break;
 	}
 
     bits32 uncSize = writePt - uncBuf;
     int compSize = zCompress(uncBuf, uncSize, compBuf, compBufSize);
     mustWrite(f, compBuf, compSize);
 
     itemsLeft -= itemsInSlot;
     }
 bits64 indexOffset = ftell(f);
 cirTreeFileBulkIndexToOpenFile(summaryArray, sizeof(summaryArray[0]), count,
     blockSize, itemsPerSlot, NULL, bbiSummaryFetchKey, bbiSummaryFetchOffset, 
     indexOffset, f);
 freez(&summaryArray);
 return indexOffset;
 }
 
 static bits64 bbiWriteSummaryAndIndexUnc(struct bbiSummary *summaryList, 
 	int blockSize, int itemsPerSlot, FILE *f)
 /* Write out summary and index to summary compressed, returning start position of
  * summary index. */
 {
 bits32 i, count = slCount(summaryList);
 struct bbiSummary **summaryArray;
 AllocArray(summaryArray, count);
 writeOne(f, count);
 struct bbiSummary *summary;
 for (summary = summaryList, i=0; summary != NULL; summary = summary->next, ++i)
     {
     summaryArray[i] = summary;
     summary->fileOffset = ftell(f);
     writeOne(f, summary->chromId);
     writeOne(f, summary->start);
     writeOne(f, summary->end);
     writeOne(f, summary->validCount);
     bbiWriteFloat(f, summary->minVal);
     bbiWriteFloat(f, summary->maxVal);
     bbiWriteFloat(f, summary->sumData);
     bbiWriteFloat(f, summary->sumSquares);
     }
 bits64 indexOffset = ftell(f);
 cirTreeFileBulkIndexToOpenFile(summaryArray, sizeof(summaryArray[0]), count,
     blockSize, itemsPerSlot, NULL, bbiSummaryFetchKey, bbiSummaryFetchOffset, 
     indexOffset, f);
 freez(&summaryArray);
 return indexOffset;
 }
 
 bits64 bbiWriteSummaryAndIndex(struct bbiSummary *summaryList, 
 	int blockSize, int itemsPerSlot, boolean doCompress, FILE *f)
 /* Write out summary and index to summary, returning start position of
  * summary index. */
 {
 if (doCompress)
     return bbiWriteSummaryAndIndexComp(summaryList, blockSize, itemsPerSlot, f);
 else
     return bbiWriteSummaryAndIndexUnc(summaryList, blockSize, itemsPerSlot, f);
 }
 
 struct cirTreeRange bbiBoundsArrayFetchKey(const void *va, void *context)
 /* Fetch bbiBoundsArray key for r-tree */
 {
 const struct bbiBoundsArray *a = ((struct bbiBoundsArray *)va);
 return a->range;
 }
 
 bits64 bbiBoundsArrayFetchOffset(const void *va, void *context)
 /* Fetch bbiBoundsArray file offset for r-tree */
 {
 const struct bbiBoundsArray *a = ((struct bbiBoundsArray *)va);
 return a->offset;
 }
 
 struct bbiSumOutStream *bbiSumOutStreamOpen(int allocCount, FILE *f, boolean doCompress)
 /* Allocate new bbiSumOutStream. */
 {
 struct bbiSumOutStream *stream;
 AllocVar(stream);
 AllocArray(stream->array, allocCount);
 stream->allocCount = allocCount;
 stream->f = f;
 stream->doCompress = doCompress;
 return stream;
 }
 
 void bbiSumOutStreamFlush(struct bbiSumOutStream *stream)
 /* Flush out any pending input. */
 {
 if (stream->elCount != 0)
     {
     int uncSize = stream->elCount * sizeof(stream->array[0]);
     if (stream->doCompress)
         {
 	int compBufSize = zCompBufSize(uncSize);
 	char compBuf[compBufSize];
 	int compSize = zCompress(stream->array, uncSize, compBuf, compBufSize);
 	mustWrite(stream->f, compBuf, compSize);
 	}
     else
         {
 	mustWrite(stream->f, stream->array, uncSize);
 	}
     stream->elCount = 0;
     }
 }
 
 void bbiSumOutStreamClose(struct bbiSumOutStream **pStream)
 /* Free up bbiSumOutStream */
 {
 struct bbiSumOutStream *stream = *pStream;
 if (stream != NULL)
     {
     bbiSumOutStreamFlush(stream);
     freeMem(stream->array);
     freez(pStream);
     }
 }
 
 void bbiSumOutStreamWrite(struct bbiSumOutStream *stream, struct bbiSummary *sum)
 /* Write out next one to stream. */
 {
 int elCount = stream->elCount;
 struct bbiSummaryOnDisk *a = &stream->array[elCount];
 a->chromId = sum->chromId;
 a->start = sum->start;
 a->end = sum->end;
 a->validCount = sum->validCount;
 a->minVal = sum->minVal;
 a->maxVal = sum->maxVal;
 a->sumData = sum->sumData;
 a->sumSquares = sum->sumSquares;
 elCount += 1;
 stream->elCount = elCount;
 if (elCount >= stream->allocCount)
     bbiSumOutStreamFlush(stream);    
 }
 
 void bbiOutputOneSummaryFurtherReduce(struct bbiSummary *sum, 
 	struct bbiSummary **pTwiceReducedList, 
 	int doubleReductionSize, struct bbiBoundsArray **pBoundsPt, 
 	struct bbiBoundsArray *boundsEnd, bits32 chromSize, struct lm *lm, 
 	struct bbiSumOutStream *stream)
 /* Write out sum to file, keeping track of minimal info on it in *pBoundsPt, and also adding
  * it to second level summary. */
 {
 /* Get place to store file offset etc and make sure we have not gone off end. */
 struct bbiBoundsArray *bounds = *pBoundsPt;
 assert(bounds < boundsEnd);
 *pBoundsPt += 1;
 
 /* Fill in bounds info. */
 bounds->offset = ftell(stream->f);
 bounds->range.chromIx = sum->chromId;
 bounds->range.start = sum->start;
 bounds->range.end = sum->end;
 
 /* Write out summary info. */
 bbiSumOutStreamWrite(stream, sum);
 
 /* Fold summary info into pTwiceReducedList. */
 struct bbiSummary *twiceReduced = *pTwiceReducedList;
 if (twiceReduced == NULL || twiceReduced->chromId != sum->chromId 
 	|| twiceReduced->start + doubleReductionSize < sum->end)
     {
     lmAllocVar(lm, twiceReduced);
     *twiceReduced = *sum;
     slAddHead(pTwiceReducedList, twiceReduced);
     }
 else
     {
     twiceReduced->end = sum->end;
     twiceReduced->validCount += sum->validCount;
     if (sum->minVal < twiceReduced->minVal) twiceReduced->minVal = sum->minVal;
     if (sum->maxVal > twiceReduced->maxVal) twiceReduced->maxVal = sum->maxVal;
     twiceReduced->sumData += sum->sumData;
     twiceReduced->sumSquares += sum->sumSquares;
     }
 }
 
 struct bbiSummary *bbiSummarySimpleReduce(struct bbiSummary *list, int reduction, struct lm *lm)
 /* Do a simple reduction - where among other things the reduction level is an integral
  * multiple of the previous reduction level, and the list is sorted. Allocate result out of lm. */
 {
 struct bbiSummary *newList = NULL, *sum, *newSum = NULL;
 for (sum = list; sum != NULL; sum = sum->next)
     {
     if (newSum == NULL || newSum->chromId != sum->chromId || sum->end > newSum->start + reduction)
         {
 	lmAllocVar(lm, newSum);
 	*newSum = *sum;
 	slAddHead(&newList, newSum);
 	}
     else
         {
 	assert(newSum->end < sum->end);	// check sorted input assumption
 	newSum->end = sum->end;
 	newSum->validCount += sum->validCount;
 	if (newSum->minVal > sum->minVal) newSum->minVal = sum->minVal;
 	if (newSum->maxVal < sum->maxVal) newSum->maxVal = sum->maxVal;
 	newSum->sumData += sum->sumData;
 	newSum->sumSquares += sum->sumSquares;
 	}
     }
 slReverse(&newList);
 return newList;
 }
 

