From 48d2065e4b74e0796dad3f0cbd80885e7304cf85 Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Thu, 1 Sep 2011 10:49:23 -0400
Subject: [PATCH] Proper Gzip check
---
src/utils/bedFile/bedFile.cpp | 2 +-
src/utils/bedFilePE/bedFilePE.cpp | 5 +----
src/utils/bedGraphFile/bedGraphFile.cpp | 4 ----
3 files changed, 2 insertions(+), 9 deletions(-)
diff --git a/src/utils/bedFile/bedFile.cpp b/src/utils/bedFile/bedFile.cpp
index 2d6104d9..c43969c3 100644
--- a/src/utils/bedFile/bedFile.cpp
+++ b/src/utils/bedFile/bedFile.cpp
@@ -135,7 +135,7 @@ void BedFile::Open(void) {
else {
_bedStream = new ifstream(bedFile.c_str(), ios::in);
- if(bedFile.substr(bedFile.find_last_of(".") + 1) == "gz") {
+ if( isGzipFile(_bedStream) ) {
delete _bedStream;
_bedStream = new igzstream(bedFile.c_str(), ios::in);
}
diff --git a/src/utils/bedFilePE/bedFilePE.cpp b/src/utils/bedFilePE/bedFilePE.cpp
index 08f8a456..19ab2b1a 100644
--- a/src/utils/bedFilePE/bedFilePE.cpp
+++ b/src/utils/bedFilePE/bedFilePE.cpp
@@ -35,10 +35,6 @@ void BedFilePE::Open(void) {
delete _bedStream;
_bedStream = new igzstream(bedFile.c_str(), ios::in);
}
-
- // bytes were consumed. rewind.
- _bedStream->seekg(0);
-
// can we open the file?
if ( !(_bedStream->good()) ) {
cerr << "Error: The requested bed file (" << bedFile << ") could not be opened. Exiting!" << endl;
@@ -48,6 +44,7 @@ void BedFilePE::Open(void) {
}
+
// Close the BEDPE file
void BedFilePE::Close(void) {
if (bedFile != "stdin") delete _bedStream;
diff --git a/src/utils/bedGraphFile/bedGraphFile.cpp b/src/utils/bedGraphFile/bedGraphFile.cpp
index d9e618f7..f3df5402 100644
--- a/src/utils/bedGraphFile/bedGraphFile.cpp
+++ b/src/utils/bedGraphFile/bedGraphFile.cpp
@@ -37,10 +37,6 @@ void BedGraphFile::Open() {
delete _bedGraphStream;
_bedGraphStream = new igzstream(bedGraphFile.c_str(), ios::in);
}
-
- // bytes were consumed. rewind.
- _bedGraphStream->seekg(0);
-
// can we open the file?
if ( !(_bedGraphStream->good()) ) {
cerr << "Error: The requested bed file (" << bedGraphFile << ") could not be opened. Exiting!" << endl;
--
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