From aea2ee257728846a31535ba367da7e7d14a2fa7c Mon Sep 17 00:00:00 2001
From: Derek <derekwbarnett@gmail.com>
Date: Mon, 19 Jul 2010 19:05:51 -0400
Subject: [PATCH] Added cross-platform LFS for tell/seek. Removed
 fopen64/freopen64 - hopefully unecessary with -D_FILE_OFFSET_BITS=64 compiler
 flag

---
 BGZF.cpp | 17 ++++++++++-------
 BGZF.h   | 14 +++++++++++++-
 2 files changed, 23 insertions(+), 8 deletions(-)

diff --git a/BGZF.cpp b/BGZF.cpp
index 1d185ba..a9f2f56 100644
--- a/BGZF.cpp
+++ b/BGZF.cpp
@@ -3,7 +3,7 @@
 // Marth Lab, Department of Biology, Boston College
 // All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 9 July 2010 (DB)
+// Last modified: 19 July 2010 (DB)
 // ---------------------------------------------------------------------------
 // BGZF routines were adapted from the bgzf.c code developed at the Broad
 // Institute.
@@ -232,15 +232,18 @@ bool BgzfData::Open(const string& filename, const char* mode) {
     // stdin/stdout option contributed by Aaron Quinlan (2010-Jan-03)
     if ( (filename != "stdin") && (filename != "stdout") ) {
         // read/write BGZF data to/from a file
-        Stream = fopen64(filename.c_str(), mode);
+//         Stream = fopen64(filename.c_str(), mode);
+        Stream = fopen(filename.c_str(), mode);
     }
     else if ( (filename == "stdin") && (strcmp(mode, "rb") == 0 ) ) { 
         // read BGZF data from stdin
-        Stream = freopen64(NULL, mode, stdin);
+//         Stream = freopen64(NULL, mode, stdin);
+        Stream = freopen(NULL, mode, stdin);
     }
     else if ( (filename == "stdout") && (strcmp(mode, "wb") == 0) ) { 
         // write BGZF data to stdout
-        Stream = freopen64(NULL, mode, stdout);
+//         Stream = freopen64(NULL, mode, stdout);
+        Stream = freopen(NULL, mode, stdout);
     }
 
     if(!Stream) {
@@ -279,7 +282,7 @@ int BgzfData::Read(char* data, const unsigned int dataLength) {
    }
 
    if ( BlockOffset == BlockLength ) {
-       BlockAddress = ftello(Stream);
+       BlockAddress = ftell64(Stream);
        BlockOffset  = 0;
        BlockLength  = 0;
    }
@@ -291,7 +294,7 @@ int BgzfData::Read(char* data, const unsigned int dataLength) {
 bool BgzfData::ReadBlock(void) {
 
     char    header[BLOCK_HEADER_LENGTH];
-    int64_t blockAddress = ftello(Stream);
+    int64_t blockAddress = ftell64(Stream);
     
     int count = fread(header, 1, sizeof(header), Stream);
     if (count == 0) {
@@ -340,7 +343,7 @@ bool BgzfData::Seek(int64_t position) {
     int     blockOffset  = (position & 0xFFFF);
     int64_t blockAddress = (position >> 16) & 0xFFFFFFFFFFFFLL;
 
-    if (fseeko(Stream, blockAddress, SEEK_SET) != 0) {
+    if (fseek64(Stream, blockAddress, SEEK_SET) != 0) {
         printf("BGZF ERROR: unable to seek in file\n");
         return false;
     }
diff --git a/BGZF.h b/BGZF.h
index 5904fe5..303684e 100644
--- a/BGZF.h
+++ b/BGZF.h
@@ -3,7 +3,7 @@
 // Marth Lab, Department of Biology, Boston College
 // All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 9 July 2010 (DB)
+// Last modified: 19 July 2010 (DB)
 // ---------------------------------------------------------------------------
 // BGZF routines were adapted from the bgzf.c code developed at the Broad
 // Institute.
@@ -25,6 +25,18 @@
 // zlib includes
 #include "zlib.h"
 
+// Platform-specific large-file support
+#ifndef BAMTOOLS_LFS
+#define BAMTOOLS_LFS
+    #ifdef WIN32
+        #define ftell64(a)     _ftelli64(a)
+        #define fseek64(a,b,c) _fseeki64(a,b,c)
+    #else
+        #define ftell64(a)     ftello(a)
+        #define fseek64(a,b,c) fseeko(a,b,c) 
+    #endif
+#endif // BAMTOOLS_LFS
+
 // Platform-specific type definitions
 #ifndef BAMTOOLS_TYPES
 #define BAMTOOLS_TYPES
-- 
2.39.5