dev-perl/Bio-SamTools: Cleanup old

Package-Manager: Portage-2.3.24, Repoman-2.3.6

diff --git a/dev-perl/Bio-SamTools/Bio-SamTools-1.420.0.ebuild b/dev-perl/Bio-SamTools/Bio-SamTools-1.420.0.ebuild
deleted file mode 100644 (file)
index 2688bc9..0000000
--- a/dev-perl/Bio-SamTools/Bio-SamTools-1.420.0.ebuild
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-DIST_AUTHOR=LDS
-DIST_VERSION=1.42
-inherit perl-module toolchain-funcs
-
-DESCRIPTION="Read SAM/BAM database files"
-
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-LICENSE="|| ( Apache-2.0 Artistic-2 GPL-1+ )"
-
-RDEPEND="
-       >=sci-biology/bioperl-1.6.9
-       >=sci-biology/samtools-1:0
-"
-DEPEND="${RDEPEND}
-       virtual/perl-ExtUtils-CBuilder
-       >=dev-perl/Module-Build-0.420.0
-"
-
-DIST_TEST=skip
-# cannot load its own library, fundamentally b0rken
-
-PATCHES=(
-       "${FILESDIR}"/${PN}-1.390.0-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";|' \
-               -i Build.PL || die
-       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 "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/Manifest b/dev-perl/Bio-SamTools/Manifest
index fe5383d88ca8eb2124a2ef25b0c2c620a708dd9d..e3b87c7144edadd38ccf9d80a9947533532d1013 100644 (file)
--- a/dev-perl/Bio-SamTools/Manifest
+++ b/dev-perl/Bio-SamTools/Manifest
@@ -1,2 +1 @@
-DIST Bio-SamTools-1.42.tar.gz 337821 BLAKE2B 21d18bdf8cd3f101dc07cf1bd0d978d949f3dc35ebc5b78cdb3aafff50d8be2a0d2e5999301cb51b5a2314ee6fa93a14f4d6c46431dfdc130f0dd8b0e1a03969 SHA512 6a1f95104ce91a800a314c304915af9d6e1cc477c7d5f42b640d0a27b18cd32c4ad9e261cac5556f4863652570a3c573d34245963fc4b9ade067981b2a329271
 DIST Bio-SamTools-1.43.tar.gz 340833 BLAKE2B 2b488667b86ef1bedb7cf74dfdcb3abc0302d9f309c1fc3077682bb400c8307f3b7d8fb1a9015a26f9a17f9e9955845d160512aa3273c368b720fe51b4392458 SHA512 cd5bc6213c093f5105399c95278803afcc537bb3d191686cda0193b82fda2580749bf7533791899939a78963fcc0d6b36eabe9c309c9c6816a9849e3c892c41b

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
deleted file mode 100644 (file)
index 8e7250c..0000000
--- a/dev-perl/Bio-SamTools/files/Bio-SamTools-1.390.0-samtools-1.patch
+++ /dev/null
@@ -1,59 +0,0 @@
- 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
-