improve large file support in compilation

diff --git a/Makefile.generic b/Makefile.generic
index 002c71af0757f4fe8f30d84983491f607b06be63..80bd9e76c0286de9427c96b3fb84e44b22e42184 100644 (file)
--- a/Makefile.generic
+++ b/Makefile.generic
@@ -2,7 +2,7 @@ CC=                     gcc
 CXX=           g++
 CFLAGS=                -g -Wall -O2 -m64 #-arch ppc
 CXXFLAGS=      $(CFLAGS)
-DFLAGS=                -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 #-D_NO_RAZF #-D_NO_CURSES
+DFLAGS=                -D_IOLIB=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 #-D_NO_RAZF #-D_NO_CURSES
 OBJS=          bam.o bam_import.o bam_pileup.o bam_lpileup.o bam_sort.o bam_index.o \
                        razf.o bgzf.o faidx.o bam_tview.o bam_maqcns.o bam_aux.o bam_plcmd.o \
                        bam_mate.o bam_rmdup.o glf.o bam_stat.o kstring.o bam_md.o

diff --git a/Makefile.lite b/Makefile.lite
index 5ddb284d9022165ca0e8800d56e3d0a181246615..a539d1eb4e21cc635f25a8d693b8a6c78e3f8e54 100644 (file)
--- a/Makefile.lite
+++ b/Makefile.lite
@@ -2,7 +2,7 @@ CC=                     gcc
 CXX=           g++
 CFLAGS=                -g -Wall -O2 -m64 #-arch ppc
 CXXFLAGS=      $(CFLAGS)
-DFLAGS=                -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -D_NO_CURSES -D_NO_RAZF
+DFLAGS=                -D_IOLIB=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_NO_CURSES -D_NO_RAZF
 OBJS=          bam.o bam_import.o bam_pileup.o bam_lpileup.o bam_sort.o bam_index.o \
                        bgzf.o faidx.o bam_tview.o bam_maqcns.o bam_aux.o bam_plcmd.o \
                        bam_mate.o bam_rmdup.o glf.o bam_stat.o kstring.o bam_md.o

diff --git a/configure.ac b/configure.ac
index d8d25e1d7e261592a75c9ced045703038db78efd..eace603adfaecfebf994f6f1de6243e873a4cd7d 100644 (file)
--- a/configure.ac
+++ b/configure.ac
@@ -8,7 +8,7 @@ AC_PROG_INSTALL
 AC_PROG_CC
 
 # set CFLAGS and CXXFLAGS
-user_CFLAGS="${CFLAGS} -D_IOLIB=2 -D_FILE_OFFSET_BITS=64"
+user_CFLAGS="${CFLAGS} -D_IOLIB=2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE"
 generic_CFLAGS="-Wall -L."
 
 AC_ARG_ENABLE(norazf, [  --disable-razf          disable razf support],

diff --git a/misc/Makefile.generic b/misc/Makefile.generic
index 0f65881232e2e9d6558dafb45b7dbfcbc5790ce2..6d69292fa19109e3f8bc1ec550377a7e4661d239 100644 (file)
--- a/misc/Makefile.generic
+++ b/misc/Makefile.generic
@@ -2,7 +2,7 @@ CC=                     gcc
 CXX=           g++
 CFLAGS=                -g -Wall -O2 -m64 #-arch ppc
 CXXFLAGS=      $(CFLAGS)
-DFLAGS=                #-D_FILE_OFFSET_BITS=64
+DFLAGS=                -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
 OBJS=          
 PROG=          faidx md5sum-lite md5fa maq2sam-short maq2sam-long wgsim
 INCLUDES=      -I..