diff --git a/src/pairToBed/pairToBed.cpp b/src/pairToBed/pairToBed.cpp index 5640791d0f78bfd613f400e348a12ed1c2be0e24..4e5349485963479b21990e11b661e8b49e274b14 100644 --- a/src/pairToBed/pairToBed.cpp +++ b/src/pairToBed/pairToBed.cpp @@ -32,6 +32,7 @@ bool IsCorrectMappingForBEDPE (const BamAlignment &bam) { Constructor */ + BedIntersectPE::BedIntersectPE(string bedAFilePE, string bedBFile, float overlapFraction, string searchType, bool sameStrand, bool diffStrand, bool bamInput, bool bamOutput, bool uncompressedBam, bool useEditDistance) { @@ -419,7 +420,7 @@ void BedIntersectPE::IntersectBamPE(string bamFile) { ProcessBamBlock(bam1, bam2, refs, writer); } else { - cerr << "*****ERROR: -bedpe requires BAM to be sorted or grouped by query name. " << endl; + cerr << "*****ERROR: BAM must be sorted by query name. " << endl; exit(1); } }