From a446d2fb6948e7138febc219c92007d98c0b407b Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Fri, 17 Jun 2011 15:49:33 -0400
Subject: [PATCH] Set BAM compression mode before opening
---
src/bedToBam/bedToBam.cpp | 8 ++++----
src/intersectBed/intersectBed.cpp | 6 +++---
src/pairToBed/pairToBed.cpp | 4 ++--
src/windowBed/windowBed.cpp | 4 ++--
4 files changed, 11 insertions(+), 11 deletions(-)
diff --git a/src/bedToBam/bedToBam.cpp b/src/bedToBam/bedToBam.cpp
index 69a91e1f..41509d6f 100644
--- a/src/bedToBam/bedToBam.cpp
+++ b/src/bedToBam/bedToBam.cpp
@@ -175,12 +175,12 @@ void ProcessBed(istream &bedInput, BedFile *bed, GenomeFile *genome, bool isBED1
map<string, int, std::less<string> > chromToId;
MakeBamHeader(genome->getGenomeFileName(), refs, bamHeader, chromToId);
- // open a BAM and add the reference headers to the BAM file
- writer->Open("stdout", bamHeader, refs);
- // set compression mode
+ // set compression mode
BamWriter::CompressionMode compressionMode = BamWriter::Compressed;
if ( uncompressedBam ) compressionMode = BamWriter::Uncompressed;
- writer->SetCompressionMode(compressionMode);
+ writer->SetCompressionMode(compressionMode);
+ // open a BAM and add the reference headers to the BAM file
+ writer->Open("stdout", bamHeader, refs);
// process each BED entry and convert to BAM
diff --git a/src/intersectBed/intersectBed.cpp b/src/intersectBed/intersectBed.cpp
index 7a2ebbb3..e5ec453b 100644
--- a/src/intersectBed/intersectBed.cpp
+++ b/src/intersectBed/intersectBed.cpp
@@ -245,12 +245,12 @@ void BedIntersect::IntersectBam(string bamFile) {
// open a BAM output to stdout if we are writing BAM
if (_bamOutput == true) {
- // open our BAM writer
- writer.Open("stdout", bamHeader, refs);
// set compression mode
BamWriter::CompressionMode compressionMode = BamWriter::Compressed;
if ( _isUncompressedBam ) compressionMode = BamWriter::Uncompressed;
- writer.SetCompressionMode(compressionMode);
+ writer.SetCompressionMode(compressionMode);
+ // open our BAM writer
+ writer.Open("stdout", bamHeader, refs);
}
vector<BED> hits;
diff --git a/src/pairToBed/pairToBed.cpp b/src/pairToBed/pairToBed.cpp
index 7c7343df..5bfbe87e 100644
--- a/src/pairToBed/pairToBed.cpp
+++ b/src/pairToBed/pairToBed.cpp
@@ -386,12 +386,12 @@ void BedIntersectPE::IntersectBamPE(string bamFile) {
// open a BAM output to stdout if we are writing BAM
if (_bamOutput == true) {
- // open our BAM writer
- writer.Open("stdout", bamHeader, refs);
// set compression mode
BamWriter::CompressionMode compressionMode = BamWriter::Compressed;
if ( _isUncompressedBam ) compressionMode = BamWriter::Uncompressed;
writer.SetCompressionMode(compressionMode);
+ // open our BAM writer
+ writer.Open("stdout", bamHeader, refs);
}
// track the previous and current sequence
diff --git a/src/windowBed/windowBed.cpp b/src/windowBed/windowBed.cpp
index b8e1a1ea..2b0fad05 100644
--- a/src/windowBed/windowBed.cpp
+++ b/src/windowBed/windowBed.cpp
@@ -160,12 +160,12 @@ void BedWindow::WindowIntersectBam(string bamFile) {
// open a BAM output to stdout if we are writing BAM
if (_bamOutput == true) {
- // open our BAM writer
- writer.Open("stdout", bamHeader, refs);
// set compression mode
BamWriter::CompressionMode compressionMode = BamWriter::Compressed;
if ( _isUncompressedBam ) compressionMode = BamWriter::Uncompressed;
writer.SetCompressionMode(compressionMode);
+ // open our BAM writer
+ writer.Open("stdout", bamHeader, refs);
}
vector<BED> hits; // vector of potential hits
--
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