fefdc562bc014756f3c22f53dce16126ada37b56 hiram Wed Sep 8 11:09:33 2021 -0700 update bad blocks message to read as documentation refs #28131 diff --git src/lib/basicBed.c src/lib/basicBed.c index 1fd9843..d14d464 100644 --- src/lib/basicBed.c +++ src/lib/basicBed.c @@ -1573,34 +1573,31 @@ "in chromStarts."); else lineFileAbort(lf, "BED chromStarts[i]+chromStart must be less than chromEnd."); } // chrom blocks must ascend without overlap int fudge = 0; if (allow1bpOverlap) fudge = -1; if (!(chromStarts[i] >= chromStarts[i-1] + blockSizes[i-1] + fudge)) lineFileAbort(lf, "BED blocks must be in ascending order without overlap. Blocks %d and %d overlap.", i-1, i); } // last block-end must match chromEnd i = bed->blockCount-1; if ((bed->chromStart + chromStarts[i] + blockSizes[i]) != bed->chromEnd) - { - lineFileAbort(lf, "BED blocks must span chromStart to chromEnd. (chromStart + " - "chromStarts[last] + blockSizes[last]) must equal chromEnd."); - } + lineFileAbort(lf, BAD_BLOCKS); } if (bedFieldCount > 12) // get the microarray/colored-exon fields { lineFileAllInts(lf, row, 12, &bed->expCount, TRUE, 4, "integer", TRUE); if (!(bed->expCount >= 1)) lineFileAbort(lf, "Expecting expCount (%d) to be 1 or more.", bed->expCount); if (isCt) { AllocArray(bed->expIds,bed->expCount+1); // having +1 allows us to detect incorrect size count = lineFileAllIntsArray(lf, row, 13, bed->expIds, bed->expCount+1, TRUE, 4, "integer", TRUE); } else {