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From 74b38ded97f7a1940c3a37b9aec9b3287a3a78bd Mon Sep 17 00:00:00 2001
From: Kent Fredric <kentfredric@gmail.com>
Date: Sun, 10 Sep 2017 13:33:32 +1200
Subject: Fix linking/compiling for bam-0.1-legacy
---
Build.PL | 6 +++---
c_bin/bam2bedgraph.c | 2 +-
c_bin/makefile | 6 +++---
lib/Bio/DB/Sam.xs | 6 +++---
4 files changed, 10 insertions(+), 10 deletions(-)
diff --git a/Build.PL b/Build.PL
index 685815f..2611759 100644
--- a/Build.PL
+++ b/Build.PL
@@ -4,8 +4,8 @@ use strict;
use Module::Build;
use Module::Load::Conditional qw(can_load);
-my $HeaderFile = "bam.h";
-my $LibFile = "libbam.a";
+my $HeaderFile = "bam-0.1-legacy/bam.h";
+my $LibFile = "libbam-0.1-legacy.so";
my $ReadLine;
my ($sam_include,$sam_lib) = find_sam(); # may exit with error here
@@ -39,7 +39,7 @@ my $build = $class->new(
dist_abstract => 'Perl interface to SamTools library for DNA sequencing',
license => 'perl',
include_dirs => [$sam_include],
- extra_linker_flags => ["-L$sam_lib",'-lbam','-lpthread','-lz'],
+ extra_linker_flags => ["-L$sam_lib",'-lbam-0.1-legacy','-lpthread','-lz'],
extra_compiler_flags=>[
diff --git a/c_bin/bam2bedgraph.c b/c_bin/bam2bedgraph.c
index 298e9a8..91218fa 100644
--- a/c_bin/bam2bedgraph.c
+++ b/c_bin/bam2bedgraph.c
@@ -1,5 +1,5 @@
#include <stdio.h>
-#include "sam.h"
+#include "bam-0.1-legacy/sam.h"
typedef struct {
uint32_t ltid;
diff --git a/c_bin/makefile b/c_bin/makefile
index 9aef917..0abbb4c 100644
--- a/c_bin/makefile
+++ b/c_bin/makefile
@@ -1,5 +1,5 @@
-CC= gcc
-CFLAGS= -g -Wall -O2 -fPIC
+CC?= gcc
+CFLAGS?= -g -Wall -O2 -fPIC
DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1
INCLUDES=
LIBPATH=
@@ -14,7 +14,7 @@ PROG= bam2bedgraph
all:$(PROG)
bam2bedgraph: bam2bedgraph.o
- $(CC) $(CFLAGS) -o $@ $< $(LDFLAGS) $(LIBPATH) -lbam -lpthread -lm -lz
+ $(CC) $(CFLAGS) -o $@ $< $(LDFLAGS) $(LIBPATH) -lbam-0.1-legacy -lpthread -lm -lz
clean:
rm -f *.o $(PROG)
diff --git a/lib/Bio/DB/Sam.xs b/lib/Bio/DB/Sam.xs
index 023f655..86410fb 100644
--- a/lib/Bio/DB/Sam.xs
+++ b/lib/Bio/DB/Sam.xs
@@ -25,9 +25,9 @@
#include <unistd.h>
#include <math.h>
-#include "bam.h"
-#include "khash.h"
-#include "faidx.h"
+#include "bam-0.1-legacy/bam.h"
+#include "bam-0.1-legacy/khash.h"
+#include "bam-0.1-legacy/faidx.h"
/* stolen from bam_aux.c */
#define MAX_REGION 1<<29
--
2.14.1
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