bamtools GetEndPosition() now defaults to unpadded, zero-based

src/genomeCoverageBed/genomeCoverageBed.cpp

@@ -228,7 +228,7 @@ void BedGenomeCoverage::CoverageBam(string bamFile) {
         // extract the chrom, start and end from the BAM alignment
         string chrom(refs.at(bam.RefID).RefName);
         CHRPOS start = bam.Position;
-        CHRPOS end = bam.GetEndPosition(false) - 1;
+        CHRPOS end = bam.GetEndPosition() - 1;
         
         // are we on a new chromosome?
         if ( chrom != _currChromName )

src/intersectBed/intersectBed.cpp

@@ -266,7 +266,7 @@ void BedIntersect::IntersectBam(string bamFile) {
             BED a;
             a.chrom = refs.at(bam.RefID).RefName;
             a.start = bam.Position;
-            a.end   = bam.GetEndPosition(false);
+            a.end   = bam.GetEndPosition();
 
             // build the name field from the BAM alignment.
             a.name = bam.Name;

src/windowBed/windowBed.cpp

@@ -182,7 +182,7 @@ void BedWindow::WindowIntersectBam(string bamFile) {
             BED a;
             a.chrom = refs.at(bam.RefID).RefName;
             a.start = bam.Position;
-            a.end   = bam.GetEndPosition(false);
+            a.end   = bam.GetEndPosition();
 
             // build the name field from the BAM alignment.
             a.name = bam.Name;