From d65489703b0129f7da7e36762ac672cb9d24b146 Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Wed, 31 Aug 2011 22:39:21 -0400
Subject: [PATCH] Need to rewind to start of file after Gzip check.
---
src/utils/Fasta/Fasta.cpp | 4 ++--
src/utils/Fasta/Fasta.h | 4 ++--
src/utils/bedFile/bedFile.cpp | 3 +++
src/utils/bedFilePE/bedFilePE.cpp | 4 ++++
src/utils/bedGraphFile/bedGraphFile.cpp | 4 ++++
5 files changed, 15 insertions(+), 4 deletions(-)
diff --git a/src/utils/Fasta/Fasta.cpp b/src/utils/Fasta/Fasta.cpp
index 447eab8b..bd0c7009 100644
--- a/src/utils/Fasta/Fasta.cpp
+++ b/src/utils/Fasta/Fasta.cpp
@@ -286,7 +286,7 @@ string FastaReference::sequenceNameStartingWith(string seqnameStart) {
}
}
-string FastaReference::getSubSequence(const string &seqname, int start, int length) {
+string FastaReference::getSubSequence(string seqname, int start, int length) {
FastaIndexEntry entry = index->entry(seqname);
if (start < 0 || length < 1) {
cerr << "Error: cannot construct subsequence with negative offset or length < 1" << endl;
@@ -318,7 +318,7 @@ string FastaReference::getSubSequence(const string &seqname, int start, int leng
return s;
}
-long unsigned int FastaReference::sequenceLength(const string &seqname) {
+long unsigned int FastaReference::sequenceLength(string seqname) {
FastaIndexEntry entry = index->entry(seqname);
return entry.length;
}
diff --git a/src/utils/Fasta/Fasta.h b/src/utils/Fasta/Fasta.h
index 9bebae04..f9e3a7f5 100644
--- a/src/utils/Fasta/Fasta.h
+++ b/src/utils/Fasta/Fasta.h
@@ -70,9 +70,9 @@ class FastaReference {
string getSequence(string seqname);
// potentially useful for performance, investigate
// void getSequence(string seqname, string& sequence);
- string getSubSequence(const string &seqname, int start, int length);
+ string getSubSequence(string seqname, int start, int length);
string sequenceNameStartingWith(string seqnameStart);
- long unsigned int sequenceLength(const string &seqname);
+ long unsigned int sequenceLength(string seqname);
};
#endif
diff --git a/src/utils/bedFile/bedFile.cpp b/src/utils/bedFile/bedFile.cpp
index 4b7bdc63..f296b429 100644
--- a/src/utils/bedFile/bedFile.cpp
+++ b/src/utils/bedFile/bedFile.cpp
@@ -139,6 +139,9 @@ void BedFile::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;
diff --git a/src/utils/bedFilePE/bedFilePE.cpp b/src/utils/bedFilePE/bedFilePE.cpp
index adc447cd..08f8a456 100644
--- a/src/utils/bedFilePE/bedFilePE.cpp
+++ b/src/utils/bedFilePE/bedFilePE.cpp
@@ -35,6 +35,10 @@ 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;
diff --git a/src/utils/bedGraphFile/bedGraphFile.cpp b/src/utils/bedGraphFile/bedGraphFile.cpp
index f3df5402..d9e618f7 100644
--- a/src/utils/bedGraphFile/bedGraphFile.cpp
+++ b/src/utils/bedGraphFile/bedGraphFile.cpp
@@ -37,6 +37,10 @@ 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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