12d0f12bd304787c52cab0780e367d36b020f84e kent Tue Feb 26 12:11:18 2013 -0800 Adding name index to bigBed files. The write side I _think_ is working. Still developing read side. diff --git src/lib/bbiWrite.c src/lib/bbiWrite.c index fce4c04..811d116 100644 --- src/lib/bbiWrite.c +++ src/lib/bbiWrite.c @@ -120,53 +120,62 @@ } 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) +struct bbiChromUsage *bbiChromUsageFromBedFile(struct lineFile *lf, struct hash *chromSizesHash, + int *retMinDiff, double *retAveSize, bits64 *retBedCount, int *retMaxNameSize) /* Go through bed file and collect chromosomes and statistics. */ { -char *row[3]; +char *row[4]; +int maxRowSize = (retMaxNameSize != NULL ? 4 : 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; +int maxNameSize = 0; lineFileRemoveInitialCustomTrackLines(lf); for (;;) { - int rowSize = lineFileChopNext(lf, row, ArraySize(row)); + int rowSize = lineFileChopNext(lf, row, maxRowSize); if (rowSize == 0) break; - lineFileExpectWords(lf, 3, rowSize); + lineFileExpectAtLeast(lf, maxRowSize, rowSize); char *chrom = row[0]; int start = lineFileNeedNum(lf, row, 1); int end = lineFileNeedNum(lf, row, 2); + if (rowSize > 3) + { + char *name = row[3]; + int nameSize = strlen(name); + if (nameSize > maxNameSize) + maxNameSize = nameSize; + } if (start > end) { 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); @@ -189,30 +198,32 @@ 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; +if (retMaxNameSize != NULL) + *retMaxNameSize = maxNameSize; 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); }