From c63935337ec92edb5510ad061c296a9773790c8f Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Wed, 31 Aug 2011 18:16:48 -0400
Subject: [PATCH] fifo support add'l
---
src/utils/bedFilePE/bedFilePE.cpp | 43 ++++++-------------------
src/utils/bedGraphFile/bedGraphFile.cpp | 41 +++++------------------
2 files changed, 17 insertions(+), 67 deletions(-)
diff --git a/src/utils/bedFilePE/bedFilePE.cpp b/src/utils/bedFilePE/bedFilePE.cpp
index e1b84b3f..adc447cd 100644
--- a/src/utils/bedFilePE/bedFilePE.cpp
+++ b/src/utils/bedFilePE/bedFilePE.cpp
@@ -29,41 +29,16 @@ void BedFilePE::Open(void) {
_bedStream = &cin;
}
else {
- size_t foundPos;
- foundPos = bedFile.find_last_of(".gz");
- // is this a GZIPPED BED file?
- if (foundPos == bedFile.size() - 1) {
- igzstream beds(bedFile.c_str(), ios::in);
- if ( !beds ) {
- cerr << "Error: The requested bedpe file (" << bedFile << ") could not be opened. Exiting!" << endl;
- exit (1);
- }
- else {
- // if so, close it (this was just a test)
- beds.close();
- // now set a pointer to the stream so that we
- // can read the file later on.
- // Thank God for Josuttis, p. 631!
- _bedStream = new igzstream(bedFile.c_str(), ios::in);
- }
- }
- // not GZIPPED.
- else {
+ _bedStream = new ifstream(bedFile.c_str(), ios::in);
- ifstream beds(bedFile.c_str(), ios::in);
- // can we open the file?
- if ( !beds ) {
- cerr << "Error: The requested bed file (" << bedFile << ") could not be opened. Exiting!" << endl;
- exit (1);
- }
- else {
- // if so, close it (this was just a test)
- beds.close();
- // now set a pointer to the stream so that we
- // can read the file later on.
- // Thank God for Josuttis, p. 631!
- _bedStream = new ifstream(bedFile.c_str(), ios::in);
- }
+ if (isGzipFile(_bedStream) == true) {
+ delete _bedStream;
+ _bedStream = new igzstream(bedFile.c_str(), ios::in);
+ }
+ // can we open the file?
+ if ( !(_bedStream->good()) ) {
+ cerr << "Error: The requested bed file (" << bedFile << ") could not be opened. Exiting!" << endl;
+ exit (1);
}
}
}
diff --git a/src/utils/bedGraphFile/bedGraphFile.cpp b/src/utils/bedGraphFile/bedGraphFile.cpp
index df73d8c5..f3df5402 100644
--- a/src/utils/bedGraphFile/bedGraphFile.cpp
+++ b/src/utils/bedGraphFile/bedGraphFile.cpp
@@ -29,45 +29,20 @@ BedGraphFile::~BedGraphFile() {
void BedGraphFile::Open() {
if (bedGraphFile == "stdin" || bedGraphFile == "-") {
_bedGraphStream = &cin;
- return;
}
- // unzipped, regular
- else if ((isGzipFile(bedGraphFile) == false) && (isRegularFile(bedGraphFile) == true)) {
+ else {
_bedGraphStream = new ifstream(bedGraphFile.c_str(), ios::in);
- // open an ifstream
- ifstream bedg(bedGraphFile.c_str(), ios::in);
-
+ if (isGzipFile(_bedGraphStream) == true) {
+ delete _bedGraphStream;
+ _bedGraphStream = new igzstream(bedGraphFile.c_str(), ios::in);
+ }
// can we open the file?
- if ( !bedg ) {
- cerr << "Error: The requested bedgraph file (" << bedGraphFile << ") could not be opened. Exiting!" << endl;
- exit (1);
- }
- else {
- // if so, close it (this was just a test)
- bedg.close();
- // now set a pointer to the stream so that we
- _bedGraphStream = new ifstream(bedGraphFile.c_str(), ios::in);
- }
- }
- else if ((isGzipFile(bedGraphFile) == true) && (isRegularFile(bedGraphFile) == true)) {
-
- igzstream bedg(bedGraphFile.c_str(), ios::in);
- if ( !bedg ) {
- cerr << "Error: The requested bedgraph file (" << bedGraphFile << ") could not be opened. Exiting!" << endl;
+ if ( !(_bedGraphStream->good()) ) {
+ cerr << "Error: The requested bed file (" << bedGraphFile << ") could not be opened. Exiting!" << endl;
exit (1);
}
- else {
- // if so, close it (this was just a test)
- bedg.close();
- // now set a pointer to the stream so that we
- _bedGraphStream = new igzstream(bedGraphFile.c_str(), ios::in);
- }
- }
- else {
- cerr << "Error: Unexpected file type (" << bedGraphFile << "). Exiting!" << endl;
- exit(1);
- }
+ }
}
--
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