6a0341e94481208d74b44d8d0b710fb8282ade47 angie Wed Oct 3 14:32:11 2012 -0700 Bug #9265 (bigBed with columns containing spaces is mangled in hgTables schema and output):chop by tabs, not spaces, in bigBedIntervalToRow. bedToBigBed always stores tab-sep. diff --git src/lib/bigBed.c src/lib/bigBed.c index 5875373..f58d145 100644 --- src/lib/bigBed.c +++ src/lib/bigBed.c @@ -1,253 +1,253 @@ /* 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"); } boolean bigBedFileCheckSigs(char *fileName) /* check file signatures at beginning and end of file */ { return bbiFileCheckSigs(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); + int wordCount = chopByChar(interval->rest, '\t', row+3, rowSize-3); fieldCount += wordCount; } return fieldCount; } 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 evenly 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; } struct asObject *bigBedAsOrDefault(struct bbiFile *bbi) // Get asObject associated with bigBed - if none exists in file make it up from field counts. { struct asObject *as = bigBedAs(bbi); if (as == NULL) as = asParseText(bedAsDef(bbi->definedFieldCount, bbi->fieldCount)); return as; } struct asObject *bigBedFileAsObjOrDefault(char *fileName) // Get asObject associated with bigBed file, or the default. { struct bbiFile *bbi = bigBedFileOpen(fileName); if (bbi) { struct asObject *as = bigBedAsOrDefault(bbi); bbiFileClose(&bbi); return as; } return NULL; } bits64 bigBedItemCount(struct bbiFile *bbi) /* Return total items in file. */ { udcSeek(bbi->udc, bbi->unzoomedDataOffset); return udcReadBits64(bbi->udc, bbi->isSwapped); }