dev-perl/Bio-SamTools: Make it build with samtools-1, #523568

(Portage version: 2.2.14_rc1/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!)

3 files changed, 77 insertions, 7 deletions

diff --git a/dev-perl/Bio-SamTools/Bio-SamTools-1.390.0-r1.ebuild b/dev-perl/Bio-SamTools/Bio-SamTools-1.390.0-r1.ebuild
index 4ea422c499a0..cde1aa75c77b 100644
--- a/dev-perl/Bio-SamTools/Bio-SamTools-1.390.0-r1.ebuild
+++ b/dev-perl/Bio-SamTools/Bio-SamTools-1.390.0-r1.ebuild
@@ -1,12 +1,13 @@
 # Copyright 1999-2014 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/dev-perl/Bio-SamTools/Bio-SamTools-1.390.0-r1.ebuild,v 1.2 2014/09/24 07:52:53 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/dev-perl/Bio-SamTools/Bio-SamTools-1.390.0-r1.ebuild,v 1.3 2014/10/02 10:25:34 jlec Exp $
 
 EAPI=5
 
 MODULE_AUTHOR=LDS
 MODULE_VERSION=1.39
-inherit perl-module
+
+inherit perl-module toolchain-funcs
 
 DESCRIPTION="Read SAM/BAM database files"
 
@@ -16,8 +17,7 @@ IUSE=""
 
 RDEPEND="
 	sci-biology/bioperl
-	>=sci-biology/samtools-0.1.16
-	<sci-biology/samtools-1
+	>=sci-biology/samtools-1
 "
 DEPEND="${RDEPEND}
 	virtual/perl-ExtUtils-CBuilder
@@ -26,7 +26,12 @@ DEPEND="${RDEPEND}
 
 SRC_TEST=do
 
+PATCHES=(
+	"${FILESDIR}"/${P}-samtools-1.patch
+)
+
 src_prepare() {
+	find . -type f -exec chmod +w '{}' + || die
 	sed \
 		-e 's|my $HeaderFile = "bam.h";|my $HeaderFile = "bam/bam.h";|' \
 		-e 's|my $LibFile    = "libbam.a";|my $LibFile    = "libbam.so";|' \
@@ -34,9 +39,11 @@ src_prepare() {
 	sed \
 		-e 's|#include "bam.h"|#include "bam/bam.h"|' \
 		-e 's|#include "sam.h"|#include "bam/sam.h"|' \
-		-e 's|#include "khash.h"|#include "bam/khash.h"|' \
-		-e 's|#include "faidx.h"|#include "bam/faidx.h"|' \
+		-e 's|#include "khash.h"|#include "htslib/khash.h"|' \
+		-e 's|#include "faidx.h"|#include "htslib/faidx.h"|' \
 		-i lib/Bio/DB/Sam.xs c_bin/bam2bedgraph.c || die
 
 	perl-module_src_prepare
+
+	tc-export CC
 }
diff --git a/dev-perl/Bio-SamTools/ChangeLog b/dev-perl/Bio-SamTools/ChangeLog
index fdc3e45e8c3f..a2e48a0349cf 100644
--- a/dev-perl/Bio-SamTools/ChangeLog
+++ b/dev-perl/Bio-SamTools/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for dev-perl/Bio-SamTools
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/dev-perl/Bio-SamTools/ChangeLog,v 1.15 2014/09/24 07:52:53 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/dev-perl/Bio-SamTools/ChangeLog,v 1.16 2014/10/02 10:25:34 jlec Exp $
+
+  02 Oct 2014; Justin Lecher <jlec@gentoo.org> Bio-SamTools-1.390.0-r1.ebuild,
+  +files/Bio-SamTools-1.390.0-samtools-1.patch:
+  Make it build with samtools-1, #523568
 
   24 Sep 2014; Justin Lecher <jlec@gentoo.org> -Bio-SamTools-1.330.0.ebuild,
   -Bio-SamTools-1.370.0-r1.ebuild, -Bio-SamTools-1.380.0.ebuild,
diff --git a/dev-perl/Bio-SamTools/files/Bio-SamTools-1.390.0-samtools-1.patch b/dev-perl/Bio-SamTools/files/Bio-SamTools-1.390.0-samtools-1.patch
new file mode 100644
index 000000000000..8e7250c51736
--- /dev/null
+++ b/dev-perl/Bio-SamTools/files/Bio-SamTools-1.390.0-samtools-1.patch
@@ -0,0 +1,59 @@
+ Build.PL          | 2 +-
+ c_bin/makefile    | 6 +++---
+ lib/Bio/DB/Sam.xs | 9 ++++++---
+ 3 files changed, 10 insertions(+), 7 deletions(-)
+
+diff --git a/Build.PL b/Build.PL
+index 1393e03..cf97ad5 100644
+--- a/Build.PL
++++ b/Build.PL
+@@ -38,7 +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','-lhts','-lpthread','-lz'],
+ 
+     extra_compiler_flags=>[
+ 
+diff --git a/c_bin/makefile b/c_bin/makefile
+index 9aef917..96a30f2 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 -lhts -lpthread -lm -lz
+ 
+ clean:
+ 	rm -f *.o $(PROG)
+diff --git a/lib/Bio/DB/Sam.xs b/lib/Bio/DB/Sam.xs
+index 5ca303b..7f92860 100644
+--- a/lib/Bio/DB/Sam.xs
++++ b/lib/Bio/DB/Sam.xs
+@@ -571,9 +571,12 @@ bama_l_aux(b,...)
+     Bio::DB::Bam::Alignment b
+ PROTOTYPE: $;$
+ CODE:
+-    if (items > 1)
+-      b->l_aux = SvIV(ST(1));
+-    RETVAL=b->l_aux;
++    if (items > 1) {
++      RETVAL = SvIV(ST(1));
++      }
++    else {
++      RETVAL=bam_get_l_aux(b);
++    }
+ OUTPUT:
+     RETVAL
+