From f79903413907b542b16b3fee2eb238e6bf50fbd0 Mon Sep 17 00:00:00 2001
From: Aaron <aaronquinlan@gmail.com>
Date: Wed, 31 Aug 2011 15:31:55 -0400
Subject: [PATCH] BEDTools now supports FIFOs and named pipes. Many thanks Nate
Weeks and Michael Hoffman for the suggestions.
---
src/utils/bedFile/bedFile.cpp | 37 +++-----------
src/utils/fileType/fileType.cpp | 91 ++++++++++++++++-----------------
src/utils/fileType/fileType.h | 2 +-
3 files changed, 53 insertions(+), 77 deletions(-)
diff --git a/src/utils/bedFile/bedFile.cpp b/src/utils/bedFile/bedFile.cpp
index 43ca3de2..4b7bdc63 100644
--- a/src/utils/bedFile/bedFile.cpp
+++ b/src/utils/bedFile/bedFile.cpp
@@ -132,39 +132,18 @@ void BedFile::Open(void) {
if (bedFile == "stdin" || bedFile == "-") {
_bedStream = &cin;
}
- // New method thanks to Assaf Gordon
- else if ((isGzipFile(bedFile) == false) && (isRegularFile(bedFile) == true)) {
- // open an ifstream
- 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
- _bedStream = new ifstream(bedFile.c_str(), ios::in);
+ else {
+ _bedStream = new ifstream(bedFile.c_str(), ios::in);
+
+ if (isGzipFile(_bedStream) == true) {
+ delete _bedStream;
+ _bedStream = new igzstream(bedFile.c_str(), ios::in);
}
- }
- else if ((isGzipFile(bedFile) == true) && (isRegularFile(bedFile) == true)) {
- igzstream beds(bedFile.c_str(), ios::in);
- if ( !beds ) {
+ // can we open the file?
+ if ( !(_bedStream->good()) ) {
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
- _bedStream = new igzstream(bedFile.c_str(), ios::in);
- }
- }
- else {
- cerr << "Error: Unexpected file type (" << bedFile << "). Exiting!" << endl;
- exit(1);
}
}
diff --git a/src/utils/fileType/fileType.cpp b/src/utils/fileType/fileType.cpp
index 5aa05b88..bda6d582 100644
--- a/src/utils/fileType/fileType.cpp
+++ b/src/utils/fileType/fileType.cpp
@@ -1,64 +1,61 @@
/*****************************************************************************
- fileType.cpp
+fileType.cpp
- (c) 2009 - Aaron Quinlan
- Hall Laboratory
- Department of Biochemistry and Molecular Genetics
- University of Virginia
- aaronquinlan@gmail.com
+(c) 2009 - Aaron Quinlan
+Hall Laboratory
+Department of Biochemistry and Molecular Genetics
+University of Virginia
+aaronquinlan@gmail.com
- Licensed under the GNU General Public License 2.0 license.
+Licensed under the GNU General Public License 2.0 license.
******************************************************************************/
#include "fileType.h"
/*
- returns TRUE if the file is a regular file:
- not a pipe/device.
+returns TRUE if the file is a regular file:
+not a pipe/device.
- This implies that the file can be opened/closed/seek'd multiple times without losing information
- */
+This implies that the file can be opened/closed/seek'd multiple times without losing information
+*/
bool isRegularFile(const string& filename) {
- struct stat buf ;
- int i;
-
- i = stat(filename.c_str(), &buf);
- if (i!=0) {
- cerr << "Error: can't determine file type of '" << filename << "': " << strerror(errno) << endl;
- exit(1);
- }
- if (S_ISREG(buf.st_mode))
- return true;
-
- return false;
+ struct stat buf ;
+ int i;
+
+ i = stat(filename.c_str(), &buf);
+ if (i!=0) {
+ cerr << "Error: can't determine file type of '" << filename << "': " << strerror(errno) << endl;
+ exit(1);
+ }
+ if (S_ISREG(buf.st_mode))
+ return true;
+
+ return false;
}
/*
- returns TRUE if the file has a GZIP header.
- Should only be run on regular files.
- */
-bool isGzipFile(const string& filename) {
+returns TRUE if the file has a GZIP header.
+Should only be run on regular files.
+*/
+bool isGzipFile(istream *file) {
//see http://www.gzip.org/zlib/rfc-gzip.html#file-format
- struct {
- unsigned char id1;
- unsigned char id2;
- unsigned char cm;
- } gzip_header;
- ifstream f(filename.c_str(), ios::in|ios::binary);
- if (!f)
- return false;
-
- if (!f.read((char*)&gzip_header, sizeof(gzip_header)))
- return false;
-
- if ( gzip_header.id1 == 0x1f
- &&
- gzip_header.id2 == 0x8b
- &&
- gzip_header.cm == 8 )
- return true;
-
- return false;
+ struct {
+ unsigned char id1;
+ unsigned char id2;
+ unsigned char cm;
+ } gzip_header;
+
+ if (!file->read((char*)&gzip_header, sizeof(gzip_header)))
+ return false;
+
+ if ( gzip_header.id1 == 0x1f
+ &&
+ gzip_header.id2 == 0x8b
+ &&
+ gzip_header.cm == 8 )
+ return true;
+
+ return false;
}
diff --git a/src/utils/fileType/fileType.h b/src/utils/fileType/fileType.h
index adf2d621..b1d42244 100644
--- a/src/utils/fileType/fileType.h
+++ b/src/utils/fileType/fileType.h
@@ -33,6 +33,6 @@ using namespace std;
******************************************************************************/
string string_error(int errnum);
bool isRegularFile(const string& filename);
-bool isGzipFile(const string& filename);
+bool isGzipFile(istream *file);
#endif /* FILETYPE_H */
--
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