1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
|
From 82942523b2db5143a9da0f9d2f8ec83a26c8d5b0 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 | 14 +++++++-------
c_bin/bam2bedgraph.c | 2 +-
c_bin/makefile | 6 +++---
lib/Bio/DB/Sam.xs | 6 +++---
4 files changed, 14 insertions(+), 14 deletions(-)
diff --git a/Build.PL b/Build.PL
index 685815f..882f231 100644
--- a/Build.PL
+++ b/Build.PL
@@ -4,11 +4,10 @@ use strict;
use Module::Build;
use Module::Load::Conditional qw(can_load);
-my $HeaderFile = "bam.h";
-my $LibFile = "libbam.a";
-my $ReadLine;
-
-my ($sam_include,$sam_lib) = find_sam(); # may exit with error here
+my ($sam_include,$sam_lib) = do {
+ ($ENV{"SAM_INCLUDE"} || die "SAM_INCLUDE not set"),
+ ($ENV{"SAM_LIB"} || die "SAM_LIB not set")
+};
my $class = Module::Build->subclass(code=><<EOF);
sub process_c_bin_files {
@@ -39,7 +38,7 @@ 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=>[
@@ -67,7 +66,7 @@ $build->add_build_element('c_bin');
$build->create_build_script;
exit 0;
-
+=for non-gentoo
sub find_sam {
my ($sam_include,$sam_lib);
@@ -162,6 +161,7 @@ sub prompt {
$ReadLine->addhistory($in) if $in =~ /\S/;
return $in;
}
+=cut
sub _samtools {
$ENV{SAMTOOLS} ||
diff --git a/c_bin/bam2bedgraph.c b/c_bin/bam2bedgraph.c
index 298e9a8..91218fa 100644
--- a/c_bin/bam2bedgraph.c
+++ b/c_bin/bam2bedgraph.c
@@ -1,5 +1,5 @@
#include <stdio.h>
-#include "sam.h"
+#include "bam-0.1-legacy/sam.h"
typedef struct {
uint32_t ltid;
diff --git a/c_bin/makefile b/c_bin/makefile
index 9aef917..0abbb4c 100644
--- a/c_bin/makefile
+++ b/c_bin/makefile
@@ -1,5 +1,5 @@
-CC= gcc
-CFLAGS= -g -Wall -O2 -fPIC
+CC?= gcc
+CFLAGS?= -g -Wall -O2 -fPIC
DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1
INCLUDES=
LIBPATH=
@@ -14,7 +14,7 @@ PROG= bam2bedgraph
all:$(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
--
2.26.2
|
