From: Derek <derekwbarnett@gmail.com>
Date: Fri, 9 Jul 2010 16:04:07 +0000 (-0400)
Subject: Enforced proper handling of large files (>4Gb) on 32-bit systems.
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=78a223dbe7949c65cfc16d972ef84f4a62351fc7;p=bamtools.git

Enforced proper handling of large files (>4Gb) on 32-bit systems.
---

diff --git a/BGZF.cpp b/BGZF.cpp
index 5aeb26a..1d185ba 100644
--- a/BGZF.cpp
+++ b/BGZF.cpp
@@ -3,7 +3,7 @@
 // Marth Lab, Department of Biology, Boston College
 // All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 11 January 2010 (DB)
+// Last modified: 9 July 2010 (DB)
 // ---------------------------------------------------------------------------
 // BGZF routines were adapted from the bgzf.c code developed at the Broad
 // Institute.
@@ -232,15 +232,15 @@ 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 = fopen(filename.c_str(), mode);
+        Stream = fopen64(filename.c_str(), mode);
     }
     else if ( (filename == "stdin") && (strcmp(mode, "rb") == 0 ) ) { 
         // read BGZF data from stdin
-        Stream = freopen(NULL, mode, stdin);
+        Stream = freopen64(NULL, mode, stdin);
     }
     else if ( (filename == "stdout") && (strcmp(mode, "wb") == 0) ) { 
         // write BGZF data to stdout
-        Stream = freopen(NULL, mode, stdout);
+        Stream = freopen64(NULL, mode, stdout);
     }
 
     if(!Stream) {
@@ -279,7 +279,7 @@ int BgzfData::Read(char* data, const unsigned int dataLength) {
    }
 
    if ( BlockOffset == BlockLength ) {
-       BlockAddress = ftell(Stream);
+       BlockAddress = ftello(Stream);
        BlockOffset  = 0;
        BlockLength  = 0;
    }
@@ -291,8 +291,8 @@ int BgzfData::Read(char* data, const unsigned int dataLength) {
 bool BgzfData::ReadBlock(void) {
 
     char    header[BLOCK_HEADER_LENGTH];
-    int64_t blockAddress = ftell(Stream);
-
+    int64_t blockAddress = ftello(Stream);
+    
     int count = fread(header, 1, sizeof(header), Stream);
     if (count == 0) {
         BlockLength = 0;
@@ -340,7 +340,7 @@ bool BgzfData::Seek(int64_t position) {
     int     blockOffset  = (position & 0xFFFF);
     int64_t blockAddress = (position >> 16) & 0xFFFFFFFFFFFFLL;
 
-    if (fseek(Stream, blockAddress, SEEK_SET) != 0) {
+    if (fseeko(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 29d6d14..5904fe5 100644
--- a/BGZF.h
+++ b/BGZF.h
@@ -3,7 +3,7 @@
 // Marth Lab, Department of Biology, Boston College
 // All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 22 June 2010 (DB)
+// Last modified: 9 July 2010 (DB)
 // ---------------------------------------------------------------------------
 // BGZF routines were adapted from the bgzf.c code developed at the Broad
 // Institute.
@@ -90,7 +90,7 @@ struct BgzfData {
     
     // closes BGZF file
     void Close(void);
-    // opens the BGZF file for reading (mode is either "rb" for reading, or "wb" for writing
+    // opens the BGZF file (mode is either "rb" for reading, or "wb" for writing)
     bool Open(const std::string& filename, const char* mode);
     // reads BGZF data into a byte buffer
     int Read(char* data, const unsigned int dataLength);
diff --git a/Makefile b/Makefile
index ee9be97..01405ca 100644
--- a/Makefile
+++ b/Makefile
@@ -1,9 +1,23 @@
 CXX=		g++
-CXXFLAGS=	-Wall -O3
+CXXFLAGS=	-Wall -O3 -D_FILE_OFFSET_BITS=64
 PROG= 		bamtools
-API=		BGZF.o BamReader.o BamWriter.o BamMultiReader.o
-UTILS=		bamtools_options.o bamtools_utilities.o
-TOOLKIT=	bamtools_convert.o bamtools_count.o bamtools_coverage.o bamtools_filter.o bamtools_header.o bamtools_index.o bamtools_merge.o bamtools_sam.o bamtools_sort.o bamtools_stats.o
+API=		BGZF.o \
+		BamIndex.o \
+		BamReader.o \
+		BamWriter.o \
+		BamMultiReader.o
+UTILS=		bamtools_options.o \
+		bamtools_utilities.o
+TOOLKIT=	bamtools_convert.o \
+		bamtools_count.o \
+		bamtools_coverage.o \
+		bamtools_filter.o \
+		bamtools_header.o \
+		bamtools_index.o \
+		bamtools_merge.o \
+		bamtools_sam.o \
+		bamtools_sort.o \
+		bamtools_stats.o
 MAIN=		bamtools.o
 OBJS=		$(API) $(UTILS) $(TOOLKIT) $(MAIN)
 LIBS=		-lz
@@ -11,7 +25,7 @@ LIBS=		-lz
 all: $(PROG)
 
 bamtools: $(OBJS)
-	$(CXX) $(CXXFLAGS) -o $@ $(OBJS) $(LIBS)
+	$(CXX) $(CXXFLAGS) -o $@ $(OBJS) $(LIBS)
 
 clean:
 	rm -fr gmon.out *.o *.a a.out *~