From bd91cd68348f887a0ec0252e69de50d19c78e965 Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Tue, 21 Sep 2010 13:19:38 -0400
Subject: [PATCH] windowBed supports -ubam.
---
src/windowBed/windowBed.cpp | 24 +++++++++++++-----------
src/windowBed/windowBed.h | 6 ++++--
2 files changed, 17 insertions(+), 13 deletions(-)
diff --git a/src/windowBed/windowBed.cpp b/src/windowBed/windowBed.cpp
index e993a81d..dfd56226 100644
--- a/src/windowBed/windowBed.cpp
+++ b/src/windowBed/windowBed.cpp
@@ -16,8 +16,9 @@
/*
Constructor
*/
-BedWindow::BedWindow(string bedAFile, string bedBFile, int leftSlop, int rightSlop, bool anyHit, bool noHit,
- bool writeCount, bool strandWindows, bool matchOnStrand, bool bamInput, bool bamOutput) {
+BedWindow::BedWindow(string bedAFile, string bedBFile, int leftSlop, int rightSlop,
+ bool anyHit, bool noHit, bool writeCount, bool strandWindows,
+ bool matchOnStrand, bool bamInput, bool bamOutput, bool isUncompressedBam) {
_bedAFile = bedAFile;
_bedBFile = bedBFile;
@@ -25,14 +26,15 @@ BedWindow::BedWindow(string bedAFile, string bedBFile, int leftSlop, int rightSl
_leftSlop = leftSlop;
_rightSlop = rightSlop;
- _anyHit = anyHit;
- _noHit = noHit;
- _writeCount = writeCount;
- _strandWindows = strandWindows;
- _matchOnStrand = matchOnStrand;
- _bamInput = bamInput;
- _bamOutput = bamOutput;
-
+ _anyHit = anyHit;
+ _noHit = noHit;
+ _writeCount = writeCount;
+ _strandWindows = strandWindows;
+ _matchOnStrand = matchOnStrand;
+ _bamInput = bamInput;
+ _bamOutput = bamOutput;
+ _isUncompressedBam = isUncompressedBam;
+
_bedA = new BedFile(bedAFile);
_bedB = new BedFile(bedBFile);
@@ -169,7 +171,7 @@ 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", header, refs);
+ writer.Open("stdout", header, refs, _isUncompressedBam);
}
vector<BED> hits; // vector of potential hits
diff --git a/src/windowBed/windowBed.h b/src/windowBed/windowBed.h
index b1af9111..5da5cb02 100644
--- a/src/windowBed/windowBed.h
+++ b/src/windowBed/windowBed.h
@@ -32,8 +32,9 @@ class BedWindow {
public:
// constructor
- BedWindow(string bedAFile, string bedBFile, int leftSlop, int rightSlop, bool anyHit, bool noHit,
- bool writeCount, bool strandWindows, bool matchOnStrand, bool bamInput, bool bamOutput);
+ BedWindow(string bedAFile, string bedBFile, int leftSlop, int rightSlop,
+ bool anyHit, bool noHit, bool writeCount, bool strandWindows,
+ bool matchOnStrand, bool bamInput, bool bamOutput, bool isUncompressedBam);
// destructor
~BedWindow(void);
@@ -51,6 +52,7 @@ private:
bool _matchOnStrand;
bool _bamInput;
bool _bamOutput;
+ bool _isUncompressedBam;
// instance of a bed file class.
BedFile *_bedA, *_bedB;
--
GitLab