New upstream version 3.01 (d52b1f31) · Commits · Debian Med / libbio-db-hts-perl

.gitignore

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		/blib/
		blib/
		*.bs
		_build/
		/.build/
		Build
		!Build/
		Build.bat
		cover_db/
		/_eumm/
		inc/
		.last_cover_stats
		lib/Bio/DB/HTS.c
		lib/Bio/DB/HTS/Faidx.c
		lib/Bio/DB/HTS/Faidx.o
		lib/Bio/DB/HTS.o
		/Makefile
		/Makefile.old
		/MANIFEST.bak
		/META.json
		/META.yml
		/MYMETA.*
		MYMETA.*
		nytprof.out
		*.o
		/pm_to_blib
		t/data/*ai
		t/data/*.gzi
		t/data/write_test_07.cram
		t/data/write_test_08.bam

.travis.yml

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		language: "perl"

		perl:
		- "5.26"
		- "5.14"
		- "5.10"

		env:
		matrix:
		- HTSLIB_VERSION=1.3.1
		- HTSLIB_VERSION=1.5
		- HTSLIB_VERSION=1.7
		- HTSLIB_VERSION=1.8
		- HTSLIB_VERSION=1.9

		sudo: false

		addons:
		apt:
		packages:
		- unzip
		- liblzma-dev
		- libbz2-dev

		before_install:
		- git clone -b BioPerl-v1.7.4 --depth 1 https://github.com/bioperl/bioperl-live.git
		- git clone --branch master --depth 1 https://github.com/Ensembl/ensembl-test.git

		install:
		- git clone --branch $HTSLIB_VERSION --depth=1 https://github.com/samtools/htslib.git
		- cd htslib
		- make prefix=~/biodbhts install
		- export HTSLIB_DIR=
		- cd ..
		# manually install items listed from cpanfile so we can skip BioPerl
		- cpanm -f -n Carp
		- cpanm -f -n Test::Most
		- cpanm -f -n Test::LeakTrace
		- cpanm -f -n Module::Build
		- cpanm -f -n Log::Log4perl
		- cpanm -f -n Try::Tiny
		# - cpanm -v --installdeps --notest .
		# install the modules just used here
		- cpanm --notest Perl::Tidy
		- cpanm --notest Test::Code::TidyAll
		- export PERL5LIB=$PERL5LIB:$PWD/bioperl-live/lib
		- perl Build.PL --prefix=~/biodbhts
		- ./Build
		- ./Build test

		script: "./travisci/harness.sh"


		notifications:
		email:
		on_success: always
		on_failure: always

Build.PL

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		#!/usr/bin/perl

		# Copyright [2015-2019] EMBL-European Bioinformatics Institute
		# Copyright [2015-2018] EMBL-European Bioinformatics Institute
		#
		# Licensed under the Apache License, Version 2.0 (the "License");
		# you may not use this file except in compliance with the License.
		@@ -75,15 +75,7 @@ sub find_hts {
		# If either of these are set, we expect to find the htslib files there:
		# (They're explicitly set by the user, so we shouldn't fall back to
		# finding another copy somewhere else.)
		my $incdir = $self->args('htslib-includedir');
		my $libdir = $self->args('htslib-libdir');
		if ($incdir && $libdir) {
		return 1 if $self->find_hts_in_split_install_dirs($incdir, $libdir);
		$self->die_hts_not_found(
		"--htslib-includedir '$incdir' or --htslib-libdir '$libdir' command line parameters do not contain expected files\n"
		);
		}
		elsif (my $dir = $self->args('htslib')) {
		if (my $dir = $self->args('htslib')) {
		return 1 if $self->find_hts_in_build_dir($dir);
		return 1 if $self->find_hts_in_install_dir($dir);
		$self->die_hts_not_found(
		@@ -113,9 +105,6 @@ sub find_hts {
		}
		return 1 if $found;

		# Try pkgconfig again but this time trust whatever it returns, without extra verification
		return 1 if $self->find_hts_with_pkgconfig();

		$self->die_hts_not_found();
		}

		@@ -125,15 +114,12 @@ sub set_include_and_compiler_flags {
		my $hts_include = $self->config_data('hts_include');
		my $hts_lib = $self->config_data('hts_lib');
		my $static = $self->args('static');

		$self->include_dirs([$hts_include]) if $hts_include;

		my @linker_dirflags;
		if ($hts_lib) {
		push @linker_dirflags, "-L$hts_lib";
		push @linker_dirflags, "-Wl,-rpath,$hts_lib" unless $static;
		$self->include_dirs([$hts_include]);
		if($static){
		$self->extra_linker_flags("-L$hts_lib", '-lhts', '-lpthread', '-lz');
		}else{
		$self->extra_linker_flags("-L$hts_lib", "-Wl,-rpath,$hts_lib", '-lhts', '-lpthread', '-lz');
		}
		$self->extra_linker_flags(@linker_dirflags, '-lhts', '-lpthread', '-lz');
		}

		sub hts_dev_files_exist {
		@@ -179,48 +165,6 @@ sub find_hts_in_install_dir {
		}
		}

		sub find_hts_in_split_install_dirs {
		my ($self, $hts_include, $hts_lib) = @_;

		chomp($hts_lib);
		chomp($hts_include);
		$hts_include =~ s{include/htslib$}{include};

		if (hts_dev_files_exist($hts_lib, $hts_include)) {
		$self->config_data('hts_lib' => $hts_lib);
		$self->config_data('hts_include' => $hts_include);
		return 1;
		}
		else {
		return 0;
		}
		}

		sub find_hts_with_pkgconfig {
		my ($self) = @_;

		return 0 unless can_load(
		modules => { 'ExtUtils::PkgConfig' => undef }
		);
		my $pkg_name = 'htslib';
		return 0 unless ExtUtils::PkgConfig->exists($pkg_name);

		if (my $libs_only_L = ExtUtils::PkgConfig->libs_only_L($pkg_name)) {
		# For compatibility with other htslib search methods. Note that this
		# assumes there will be at most one each of -I/-L directories, which
		# is true as of htslib-1.5 but might change in the future.
		$libs_only_L =~ s{^-L}{};
		$self->config_data('hts_lib' => $libs_only_L);
		}
		if (my $cflags_only_I = ExtUtils::PkgConfig->cflags_only_I($pkg_name)) {
		# See above
		$cflags_only_I =~ s{^-I}{};
		$self->config_data('hts_include' => $cflags_only_I);
		}

		return 1;
		}

		sub die_hts_not_found {
		my ($self, $msg) = @_;

		@@ -233,17 +177,12 @@ Install it if you have not done so already.
		This script will attempt to locate HTSlib by looking for htslib/hts.h
		and libhts.a / libhts.so in:

		1. --htslib-includedir and --htslib-libdir command line arguments
		2. --htslib command line argument
		3. HTSLIB_DIR environment variable
		4. --prefix command line argument (which also sets installation location)
		5. Alien::HTSlib dependency resolver
		6. pkg-config (extra directories can be set in PKG_CONFIG_PATH environment variable)
		7. common library locations: /usr /usr/local, /usr/share, /opt/local

		If none of the above succeeds but htslib is registered with pkg-config, the script
		will try using pkg-config paths (via ExtUtils::PkgConfig) without checking if header
		and library files exist.
		1. --htslib command line argument
		2. HTSLIB_DIR environment variable
		3. --prefix command line argument (which also sets installation location)
		4. Alien::HTSlib dependency resolver
		5. pkg-config (extra directories can be set in PKG_CONFIG_PATH environment variable)
		6. common library locations: /usr /usr/local, /usr/share, /opt/local

		END

INSTALL.pl

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		#!/usr/bin/perl

		# Copyright [2015-2019] EMBL-European Bioinformatics Institute
		# Copyright [2015-2018] EMBL-European Bioinformatics Institute
		#
		# Licensed under the Apache License, Version 2.0 (the "License");
		# you may not use this file except in compliance with the License.

LICENSE

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		@@ -186,7 +186,7 @@
		same "printed page" as the copyright notice for easier
		identification within third-party archives.

		Copyright [2015-2019] EMBL-European Bioinformatics Institute
		Copyright [2015-2018] EMBL-European Bioinformatics Institute

		Licensed under the Apache License, Version 2.0 (the "License");
		you may not use this file except in compliance with the License.