8a7fe87bf9ffd7fc1038c9d85984955afb82f0dc gperez2 Thu Feb 20 17:06:31 2025 -0800 Updating the bedToBigBed help message and error output for the new sort option, refs #29104 diff --git src/lib/bbiWrite.c src/lib/bbiWrite.c index 23e5e8eac44..4ad92924fef 100644 --- src/lib/bbiWrite.c +++ src/lib/bbiWrite.c @@ -239,31 +239,31 @@ usage->name = cloneString(chrom); usage->id = id++; 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.", + errAbort("%s is not sorted at line %d. Please use the -sort option to sort the input file.", lf->fileName, lf->lineIx); minDiff = diff; } } lastStart = start; } slReverse(&usageList); double aveSize = 0; if (bedCount > 0) aveSize = (double)totalBases/bedCount; *retMinDiff = minDiff; *retAveSize = aveSize; *retBedCount = bedCount; return usageList; }