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