From e200d064f3812489e89a8b6cbb4fc02aac74cd90 Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Sat, 3 Jul 2010 22:02:10 -0400
Subject: [PATCH] Fixed string references for strand (i.e. '+' to "+") in
windowBed and pairToBed.
---
src/pairToBed/pairToBed.h | 8 ++++----
src/utils/bedFile/bedFile.cpp | 2 ++
src/windowBed/windowBed.cpp | 2 +-
3 files changed, 7 insertions(+), 5 deletions(-)
diff --git a/src/pairToBed/pairToBed.h b/src/pairToBed/pairToBed.h
index 66a26eb8..420426f8 100755
--- a/src/pairToBed/pairToBed.h
+++ b/src/pairToBed/pairToBed.h
@@ -95,8 +95,8 @@ private:
a.chrom1 = refs.at(bam1.RefID).RefName;
a.start1 = bam1.Position;
a.end1 = bam1.GetEndPosition();
- a.strand1 = '+';
- if (bam1.IsReverseStrand()) a.strand1 = '-';
+ a.strand1 = "+";
+ if (bam1.IsReverseStrand()) a.strand1 = "-";
// extract the edit distance from the NM tag
// if possible. otherwise, complain.
@@ -113,8 +113,8 @@ private:
a.chrom2 = refs.at(bam2.RefID).RefName;
a.start2 = bam2.Position;
a.end2 = bam2.GetEndPosition();
- a.strand2 = '+';
- if (bam2.IsReverseStrand()) a.strand2 = '-';
+ a.strand2 = "+";
+ if (bam2.IsReverseStrand()) a.strand2 = "-";
// extract the edit distance from the NM tag
// if possible. otherwise, complain.
diff --git a/src/utils/bedFile/bedFile.cpp b/src/utils/bedFile/bedFile.cpp
index 4ffe3e70..b97c404a 100755
--- a/src/utils/bedFile/bedFile.cpp
+++ b/src/utils/bedFile/bedFile.cpp
@@ -422,6 +422,8 @@ void BedFile::countSplitHits(const vector<BED> &bedBlocks, bool forceStrand) {
set< vector<BEDCOV>::iterator >::iterator validHitsItr = validHits.begin();
set< vector<BEDCOV>::iterator >::iterator validHitsEnd = validHits.end();
for (; validHitsItr != validHitsEnd; ++validHitsItr)
+ // the validHitsItr points to another itr, hence the (*itr)-> dereferencing.
+ // ugly, but that's C++.
(*validHitsItr)->count++;
}
diff --git a/src/windowBed/windowBed.cpp b/src/windowBed/windowBed.cpp
index e1809f79..e993a81d 100755
--- a/src/windowBed/windowBed.cpp
+++ b/src/windowBed/windowBed.cpp
@@ -194,7 +194,7 @@ void BedWindow::WindowIntersectBam(string bamFile) {
if (bam.IsSecondMate()) a.name += "/2";
a.score = ToString(bam.MapQuality);
- a.strand = '+'; if (bam.IsReverseStrand()) a.strand = '-';
+ a.strand = "+"; if (bam.IsReverseStrand()) a.strand = "-";
if (_bamOutput == true) {
overlapsFound = FindOneOrMoreWindowOverlaps(a);
--
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