Added +1 to start reporting for GFF features.

338bc1fd · Aaron · 204128fd · 338bc1fd · 338bc1fd · 338bc1fd
Commit 338bc1fd authored 15 years ago by Aaron
--- a/bin/closestBed
+++ b/bin/closestBed
--- a/bin/complementBed
+++ b/bin/complementBed
--- a/bin/coverageBed
+++ b/bin/coverageBed
--- a/bin/fastaFromBed
+++ b/bin/fastaFromBed
--- a/bin/genomeCoverageBed
+++ b/bin/genomeCoverageBed
--- a/bin/intersectBed
+++ b/bin/intersectBed
--- a/bin/linksBed
+++ b/bin/linksBed
--- a/bin/maskFastaFromBed
+++ b/bin/maskFastaFromBed
--- a/bin/mergeBed
+++ b/bin/mergeBed
--- a/bin/pairToBed
+++ b/bin/pairToBed
--- a/bin/pairToPair
+++ b/bin/pairToPair
--- a/bin/shuffleBed
+++ b/bin/shuffleBed
--- a/bin/slopBed
+++ b/bin/slopBed
--- a/bin/sortBed
+++ b/bin/sortBed
--- a/bin/subtractBed
+++ b/bin/subtractBed
--- a/bin/windowBed
+++ b/bin/windowBed
--- a/obj/bedFile.o
+++ b/obj/bedFile.o
--- a/src/utils/bedFile/bedFile.cpp
+++ b/src/utils/bedFile/bedFile.cpp
@@ -696,7 +696,7 @@ void BedFile::reportBedRangeTab(const BED &bed, int start, int end) {
 	}
 	else if (this->bedType == 9) {
 		printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\t%s\t", bed.chrom.c_str(), bed.otherFields[0].c_str(),
-														 bed.name.c_str(), start, end, 
+														 bed.name.c_str(), start+1, end, 
 														 bed.score.c_str(), bed.strand.c_str(),
 														 bed.otherFields[1].c_str(), bed.otherFields[2].c_str());

@@ -740,9 +740,9 @@ void BedFile::reportBedRangeNewLine(const BED &bed, int start, int end) {
 		}
 		printf("\n");
 	}
-	else if (this->bedType == 9) {
+	else if (this->bedType == 9) {	// add 1 to the start for GFF
 		printf ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\t%s\n", bed.chrom.c_str(), bed.otherFields[0].c_str(),
-														 bed.name.c_str(), start, end, 
+														 bed.name.c_str(), start+1, end, 
 														 bed.score.c_str(), bed.strand.c_str(),
 														 bed.otherFields[1].c_str(), bed.otherFields[2].c_str());