diff options
Diffstat (limited to 'dev-perl/Bio-SamTools')
| -rw-r--r-- | dev-perl/Bio-SamTools/Bio-SamTools-1.420.0.ebuild | 49 | ||||
| -rw-r--r-- | dev-perl/Bio-SamTools/Manifest | 1 | ||||
| -rw-r--r-- | dev-perl/Bio-SamTools/files/Bio-SamTools-1.390.0-samtools-1.patch | 59 |
3 files changed, 0 insertions, 109 deletions
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 index 2688bc95030a..000000000000 --- 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 fe5383d88ca8..e3b87c7144ed 100644 --- 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 index 8e7250c51736..000000000000 --- 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 - |