From dbae600ab161ad49df6117414445611f07be3dd0 Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Fri, 30 Sep 2011 15:42:44 -0400
Subject: [PATCH] Minor updates.
---
src/tagBam/tagBam.cpp | 3 ++-
src/utils/bedFile/bedFile.cpp | 1 -
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/src/tagBam/tagBam.cpp b/src/tagBam/tagBam.cpp
index 36a2c4d1..f8d1d7ea 100644
--- a/src/tagBam/tagBam.cpp
+++ b/src/tagBam/tagBam.cpp
@@ -77,6 +77,7 @@ void TagBam::Tag() {
// rip through the BAM file and test for overlaps with each annotation file.
BamAlignment al;
vector<BED> hits;
+
while (reader.GetNextAlignment(al)) {
if (al.IsMapped() == true) {
BED a;
@@ -95,7 +96,7 @@ void TagBam::Tag() {
if (!_useNames && !_useScores) {
// add the label for this annotation file to tag if there is overlap
- if (anno->FindOneOrMoreOverlapsPerBin(a.chrom, a.start, a.end, a.strand, _sameStrand, _diffStrand, _overlapFraction))
+ if (anno->FindOneOrMoreOverlapsPerBin(a.chrom, a.start, a.end, a.strand, _sameStrand, _diffStrand, _overlapFraction))
{
annotations << _annoLabels[i] << ";";
}
diff --git a/src/utils/bedFile/bedFile.cpp b/src/utils/bedFile/bedFile.cpp
index 5542bed7..e225541b 100644
--- a/src/utils/bedFile/bedFile.cpp
+++ b/src/utils/bedFile/bedFile.cpp
@@ -270,7 +270,6 @@ bool BedFile::FindOneOrMoreOverlapsPerBin(string chrom, CHRPOS start, CHRPOS end
if ( (float) overlapBases / (float) aLength >= overlapFraction) {
bool strands_are_same = (strand == bedItr->strand);
-
// test for necessary strandedness
if ( (sameStrand == false && diffStrand == false)
||
--
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