From c24686535855db49071752d174384362df77042c Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Wed, 14 Apr 2010 15:07:16 -0400
Subject: [PATCH] Updated bamToBed to include new AlignmentEnd method.
---
src/bamToBed/bamToBed.cpp | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/src/bamToBed/bamToBed.cpp b/src/bamToBed/bamToBed.cpp
index dc2ccb5a..d082f86e 100755
--- a/src/bamToBed/bamToBed.cpp
+++ b/src/bamToBed/bamToBed.cpp
@@ -201,6 +201,7 @@ void ParseCigarBed(const vector<CigarOp> cigar, unsigned int &alignmentEnd) {
}
+
void ParseCigarBed12(const vector<CigarOp> cigar, vector<int> &blockStarts, vector<int> &blockLengths, unsigned int &alignmentEnd) {
int currPosition = 0;
@@ -245,9 +246,9 @@ void PrintBed(const BamAlignment &bam, const RefVector &refs, bool useEditDista
if (bam.IsSecondMate()) name += "/2";
// rip through the CIGAR string and reconstruct the alignment coordinates
- unsigned int alignmentEnd;
- ParseCigarBed(bam.CigarData, alignmentEnd);
- alignmentEnd += bam.Position;
+ unsigned int alignmentEnd = bam.GetAlignmentEnd();
+ //ParseCigarBed(bam.CigarData, alignmentEnd);
+ //alignmentEnd += bam.Position;
// report the alignment in BED6 format.
if (useEditDistance == false) {
--
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