From 18b0b3ce037705ba5d5e6e5847c2f9264d96302e Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Wed, 14 Apr 2010 20:26:01 -0400
Subject: [PATCH] Added gzstream to bedFile.
---
src/utils/bedFile/bedFile.cpp | 18 +-----------------
src/utils/bedFile/bedFile.h | 5 ++++-
2 files changed, 5 insertions(+), 18 deletions(-)
diff --git a/src/utils/bedFile/bedFile.cpp b/src/utils/bedFile/bedFile.cpp
index cb5b8fde..fc5ec7d7 100755
--- a/src/utils/bedFile/bedFile.cpp
+++ b/src/utils/bedFile/bedFile.cpp
@@ -181,8 +181,8 @@ bool BedFile::GetNextBed (BED &bed, int &lineNum) {
if (parseLine(bed, bedFields, lineNum)) {
return true;
}
- return false;
}
+ return false;
}
@@ -355,22 +355,6 @@ void BedFile::countHits(const BED &a, bool forceStrand) {
}
-
-
-/*******************************************
-Class methods
-*******************************************/
-
-// Constructor
-BedFile::BedFile(string &bedFile) {
- this->bedFile = bedFile;
-}
-
-// Destructor
-BedFile::~BedFile(void) {
-}
-
-
void BedFile::setGff (bool gff) {
if (gff == true) this->isGff = true;
else this->isGff = false;
diff --git a/src/utils/bedFile/bedFile.h b/src/utils/bedFile/bedFile.h
index 960dfc60..e0cc18d8 100755
--- a/src/utils/bedFile/bedFile.h
+++ b/src/utils/bedFile/bedFile.h
@@ -12,6 +12,7 @@
#ifndef BEDFILE_H
#define BEDFILE_H
+#include "gzstream.h"
#include <vector>
#include <map>
#include <string>
@@ -22,7 +23,7 @@
#include <algorithm>
#include <limits.h>
#include <cstdio>
-//#include <tr1/unordered_map>
+
using namespace std;
//*************************************************
@@ -207,6 +208,8 @@ private:
bool parseGffLine (BED &bed, const vector<string> &lineVector, int lineNum);
void setGff (bool isGff);
+
+ istream *bedStream;
};
#endif /* BEDFILE_H */
--
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