diff --git a/src/mergeBed/mergeBed.cpp b/src/mergeBed/mergeBed.cpp index b5c20c699a66c12212015a9faccdbb46d3c5e030..7e6159698b25e07feccb50fd9c0ea5a81949f39b 100755 --- a/src/mergeBed/mergeBed.cpp +++ b/src/mergeBed/mergeBed.cpp @@ -209,8 +209,7 @@ void BedMerge::MergeBedStranded() { } continue; } - - + if ( overlaps(bedList[prev].start, bedList[prev].end, bedList[curr].start, bedList[curr].end) >= this->maxDistance) { @@ -243,7 +242,7 @@ void BedMerge::MergeBedStranded() { if (n < (names.size() - 1)) {cout << names[n] << ";";} else {cout << names[n];} } - cout << endl; + cout << "\t" << strands[s] << endl; } else { cout << bedList[prev].chrom << "\t" << minStart << "\t" << maxEnd << "\t" << strands[s] << endl; @@ -254,7 +253,7 @@ void BedMerge::MergeBedStranded() { cout << bedList[prev].chrom << "\t" << bedList[prev].start << "\t" << bedList[prev].end << "\t" << mergeCount << "\t" << strands[s] << endl; } else if (this->reportNames) { - cout << bedList[prev].chrom << "\t" << bedList[prev].start << "\t" << bedList[prev].end << "\t" << bedList[prev].name << endl; + cout << bedList[prev].chrom << "\t" << bedList[prev].start << "\t" << bedList[prev].end << "\t" << bedList[prev].name << "\t" << strands[s] << endl; } else if (numOnStrand > 0) { cout << bedList[prev].chrom << "\t" << bedList[prev].start << "\t" << bedList[prev].end << "\t" << strands[s] << endl; @@ -285,7 +284,7 @@ void BedMerge::MergeBedStranded() { if (n < (names.size() - 1)) {cout << names[n] << ";";} else {cout << names[n];} } - cout << endl; + cout << "\t" << strands[s] << endl; } else { cout << bedList[prev].chrom << "\t" << minStart << "\t" << maxEnd << "\t" << strands[s] << endl; @@ -295,8 +294,8 @@ void BedMerge::MergeBedStranded() { if ((this->numEntries) && (numOnStrand > 0)) { cout << bedList[prev].chrom << "\t" << bedList[prev].start << "\t" << bedList[prev].end << "\t" << mergeCount << "\t" << strands[s] << endl; } - else if (this->reportNames) { - cout << bedList[prev].chrom << "\t" << bedList[prev].start << "\t" << bedList[prev].end << "\t" << bedList[prev].name << endl; + else if ((this->reportNames) && (numOnStrand > 0)) { + cout << bedList[prev].chrom << "\t" << bedList[prev].start << "\t" << bedList[prev].end << "\t" << bedList[prev].name << "\t" << strands[s] << endl; } else if (numOnStrand > 0) { cout << bedList[prev].chrom << "\t" << bedList[prev].start << "\t" << bedList[prev].end << "\t" << strands[s] << endl;