From 6cfb163fb283627b76a6a9a557777e8896495455 Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Thu, 18 Mar 2010 17:14:23 -0400
Subject: [PATCH] Renamed end to alignmentEnd in bamToBed
---
src/bamToBed/bamToBed.cpp | 30 +++++++++++++++---------------
1 file changed, 15 insertions(+), 15 deletions(-)
diff --git a/src/bamToBed/bamToBed.cpp b/src/bamToBed/bamToBed.cpp
index eaed581d..777210b8 100755
--- a/src/bamToBed/bamToBed.cpp
+++ b/src/bamToBed/bamToBed.cpp
@@ -187,7 +187,7 @@ void ShowHelp(void) {
}
-void ParseCigarBed(const vector<CigarOp> cigar, unsigned int &end) {
+void ParseCigarBed(const vector<CigarOp> cigar, unsigned int &alignmentEnd) {
int currPosition = 0;
@@ -198,11 +198,11 @@ void ParseCigarBed(const vector<CigarOp> cigar, unsigned int &end) {
for (; cigItr != cigEnd; ++cigItr) {
if (cigItr->Type =='M') currPosition += cigItr->Length;
}
- end = currPosition;
+ alignmentEnd = currPosition;
}
-void ParseCigarBed12(const vector<CigarOp> cigar, vector<int> &blockStarts, vector<int> &blockLengths, unsigned int &end) {
+void ParseCigarBed12(const vector<CigarOp> cigar, vector<int> &blockStarts, vector<int> &blockLengths, unsigned int &alignmentEnd) {
int currPosition = 0;
int blockLength = 0;
@@ -232,13 +232,13 @@ void ParseCigarBed12(const vector<CigarOp> cigar, vector<int> &blockStarts, vect
}
blockLengths.push_back(blockLength);
- end = currPosition;
+ alignmentEnd = currPosition;
}
void PrintBed(const BamAlignment &bam, const RefVector &refs, bool useEditDistance) {
- unsigned int end;
+ unsigned int alignmentEnd;
string strand = "+";
if (bam.IsReverseStrand()) strand = "-";
@@ -247,18 +247,18 @@ 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
- ParseCigarBed(bam.CigarData, end);
- end += bam.Position;
+ ParseCigarBed(bam.CigarData, alignmentEnd);
+ alignmentEnd += bam.Position;
if (useEditDistance == false) {
printf("%s\t%d\t%d\t\%s\t%d\t%s\n", refs.at(bam.RefID).RefName.c_str(), bam.Position,
- end, name.c_str(), bam.MapQuality, strand.c_str());
+ alignmentEnd, name.c_str(), bam.MapQuality, strand.c_str());
}
else {
uint8_t editDistance;
if (bam.GetEditDistance(editDistance)) {
printf("%s\t%d\t%d\t\%s\t%u\t%s\n", refs.at(bam.RefID).RefName.c_str(), bam.Position,
- end, name.c_str(), editDistance, strand.c_str());
+ alignmentEnd, name.c_str(), editDistance, strand.c_str());
}
else {
cerr << "The edit distance tag (NM) was not found in the BAM file. Please disable -ed. Exiting\n";
@@ -276,25 +276,25 @@ void PrintBed12(const BamAlignment &bam, const RefVector &refs, bool useEditDist
if (bam.IsFirstMate()) name += "/1";
if (bam.IsSecondMate()) name += "/2";
- unsigned int end;
+ unsigned int alignmentEnd;
vector<int> blockLengths;
vector<int> blockStarts;
blockStarts.push_back(0); // by default, we have a block start at the start of the alignment.
// rip through the CIGAR string and reconstruct the alignment coordinates
- ParseCigarBed12(bam.CigarData, blockStarts, blockLengths, end);
- end += bam.Position;
+ ParseCigarBed12(bam.CigarData, blockStarts, blockLengths, alignmentEnd);
+ alignmentEnd += bam.Position;
// write BED6 portion
if (useEditDistance == false) {
printf("%s\t%d\t%d\t\%s\t%d\t%s\t", refs.at(bam.RefID).RefName.c_str(), bam.Position,
- end, name.c_str(), bam.MapQuality, strand.c_str());
+ alignmentEnd, name.c_str(), bam.MapQuality, strand.c_str());
}
else {
uint8_t editDistance;
if (bam.GetEditDistance(editDistance)) {
printf("%s\t%d\t%d\t\%s\t%u\t%s\t", refs.at(bam.RefID).RefName.c_str(), bam.Position,
- end, name.c_str(), editDistance, strand.c_str());
+ alignmentEnd, name.c_str(), editDistance, strand.c_str());
}
else {
cerr << "The edit distance tag (NM) was not found in the BAM file. Please disable -ed. Exiting\n";
@@ -303,7 +303,7 @@ void PrintBed12(const BamAlignment &bam, const RefVector &refs, bool useEditDist
}
// write the colors, etc.
- printf("%d\t%d\t%s\t%d\t", bam.Position, end, color.c_str(), (int) blockStarts.size());
+ printf("%d\t%d\t%s\t%d\t", bam.Position, alignmentEnd, color.c_str(), (int) blockStarts.size());
// now write the lengths portion
unsigned int b;
--
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