.gitignore

-/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

-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

 #!/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

 #!/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

@@ -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.

MANIFEST.SKIP

-# Avoid version control files.
-\bRCS\b
-\bCVS\b
-,v$
-\B\.svn\b
-\B\.cvsignore$
-
-# Avoid Makemaker generated and utility files.
-\bMakefile$
-\bblib
-\bMakeMaker-\d
-\bpm_to_blib$
-\bblibdirs$
-^MANIFEST\.SKIP$
-
-# Avoid VMS specific Makmaker generated files
-\bDescrip.MMS$
-\bDESCRIP.MMS$
-\bdescrip.mms$
-
-# Avoid Module::Build generated and utility files.
-\bBuild$
-\bBuild.bat$
-\b_build
-\bBuild.COM$
-\bBUILD.COM$
-\bbuild.com$
-
-# Avoid Devel::Cover generated files
-\bcover_db
-
-# Avoid temp and backup files.
-~$
-\.tmp$
-\.old$
-\.bak$
-\#$
-\.#
-\.rej$
-\.orig$
-\.out$
-\.patch$
-
-# Avoid OS-specific files/dirs
-#   Mac OSX metadata
-\B\.DS_Store
-#   Mac OSX SMB mount metadata files
-\B\._
-# Avoid archives of this distribution
-\bBio-BigFile-[\d\.\_]+
-
-# avoid .c and .o files
-^lib/.+\.c$
-\.o$
-
-# avoid .pl files in the top level directory
-^[^/]+\.pl
-
-# avoid test files
-\btest\b
-
-# avoid cores
-\bcore\b
-
-# No tar files
-tar\.gz$
-
-# avoid these directories
-^test_gbrowse_db
-^timing_tests
-
-# avoid top level fa, bam, bed and fai files
-^[^/]+\.(?:bam|fa|sam|fai|bed)
-
-# avoid compiled files in c_bin
-c_bin/bam2bedgraph$
-
-\.bai
-\.fai
-^MYMETA.yml$
-^MYMETA\.json$
-

META.json

 {
    "abstract" : "Perl interface to HTS library for DNA sequencing",
    "author" : [
-      "Rishi Nag"
+      "Alessandro Vullo"
    ],
    "dynamic_config" : 1,
    "generated_by" : "Module::Build version 0.4224",
@@ -26,7 +26,7 @@
       },
       "runtime" : {
          "requires" : {
-            "Bio::Root::Version" : "1.006001",
+            "Bio::SeqFeature::Lite" : "0",
             "perl" : "5.008"
          }
       }
@@ -34,114 +34,118 @@
    "provides" : {
       "Bio::DB::HTS" : {
          "file" : "lib/Bio/DB/HTS.pm",
-         "version" : "2.11"
+         "version" : "3.01"
       },
       "Bio::DB::HTS::AlignWrapper" : {
          "file" : "lib/Bio/DB/HTS/AlignWrapper.pm",
-         "version" : "2.11"
+         "version" : "3.01"
       },
       "Bio::DB::HTS::Alignment" : {
          "file" : "lib/Bio/DB/HTS/Alignment.pm",
-         "version" : "2.11"
+         "version" : "3.01"
       },
       "Bio::DB::HTS::Constants" : {
          "file" : "lib/Bio/DB/HTS/Constants.pm",
-         "version" : "2.11"
+         "version" : "3.01"
       },
       "Bio::DB::HTS::Fai" : {
          "file" : "lib/Bio/DB/HTS.pm",
-         "version" : "2.11"
+         "version" : "3.01"
       },
       "Bio::DB::HTS::Faidx" : {
          "file" : "lib/Bio/DB/HTS/Faidx.pm",
-         "version" : "2.11"
+         "version" : "3.01"
       },
       "Bio::DB::HTS::FetchIterator" : {
          "file" : "lib/Bio/DB/HTS/FetchIterator.pm",
-         "version" : "2.11"
+         "version" : "3.01"
+      },
+      "Bio::DB::HTS::HTSfile" : {
+         "file" : "lib/Bio/DB/HTS.pm",
+         "version" : "3.01"
       },
       "Bio::DB::HTS::Kseq" : {
          "file" : "lib/Bio/DB/HTS/Kseq.pm",
-         "version" : "2.11"
+         "version" : "3.01"
       },
       "Bio::DB::HTS::Kseq::Record" : {
          "file" : "lib/Bio/DB/HTS/Kseq/Record.pm",
-         "version" : "2.11"
+         "version" : "3.01"
       },
       "Bio::DB::HTS::Pileup" : {
          "file" : "lib/Bio/DB/HTS/Pileup.pm",
-         "version" : "2.11"
+         "version" : "3.01"
       },
       "Bio::DB::HTS::PileupWrapper" : {
          "file" : "lib/Bio/DB/HTS/PileupWrapper.pm",
-         "version" : "2.11"
+         "version" : "3.01"
       },
       "Bio::DB::HTS::Query" : {
          "file" : "lib/Bio/DB/HTS/Query.pm",
-         "version" : "2.11"
+         "version" : "3.01"
       },
       "Bio::DB::HTS::ReadIterator" : {
          "file" : "lib/Bio/DB/HTS/ReadIterator.pm",
-         "version" : "2.11"
+         "version" : "3.01"
       },
       "Bio::DB::HTS::Segment" : {
          "file" : "lib/Bio/DB/HTS/Segment.pm",
-         "version" : "2.11"
+         "version" : "3.01"
       },
       "Bio::DB::HTS::Segment::Iterator" : {
          "file" : "lib/Bio/DB/HTS/Segment.pm",
-         "version" : "2.11"
+         "version" : "3.01"
       },
       "Bio::DB::HTS::SplitAlignmentPart" : {
          "file" : "lib/Bio/DB/HTS/AlignWrapper.pm",
-         "version" : "2.11"
+         "version" : "3.01"
       },
       "Bio::DB::HTS::Tabix" : {
          "file" : "lib/Bio/DB/HTS/Tabix.pm",
-         "version" : "2.11"
+         "version" : "3.01"
       },
       "Bio::DB::HTS::Tabix::Iterator" : {
          "file" : "lib/Bio/DB/HTS/Tabix/Iterator.pm",
-         "version" : "2.11"
+         "version" : "3.01"
       },
       "Bio::DB::HTS::Target" : {
          "file" : "lib/Bio/DB/HTS/Target.pm",
-         "version" : "2.11"
+         "version" : "3.01"
       },
       "Bio::DB::HTS::VCF" : {
          "file" : "lib/Bio/DB/HTS/VCF.pm",
-         "version" : "2.11"
+         "version" : "3.01"
       },
       "Bio::DB::HTS::VCF::Header" : {
          "file" : "lib/Bio/DB/HTS/VCF/Header.pm",
-         "version" : "2.11"
+         "version" : "3.01"
       },
       "Bio::DB::HTS::VCF::HeaderPtr" : {
          "file" : "lib/Bio/DB/HTS/VCF/HeaderPtr.pm",
-         "version" : "2.11"
+         "version" : "3.01"
       },
       "Bio::DB::HTS::VCF::Iterator" : {
          "file" : "lib/Bio/DB/HTS/VCF/Iterator.pm",
-         "version" : "2.11"
+         "version" : "3.01"
       },
       "Bio::DB::HTS::VCF::Row" : {
          "file" : "lib/Bio/DB/HTS/VCF/Row.pm",
-         "version" : "2.11"
+         "version" : "3.01"
       },
       "Bio::DB::HTS::VCF::RowPtr" : {
          "file" : "lib/Bio/DB/HTS/VCF/RowPtr.pm",
-         "version" : "2.11"
+         "version" : "3.01"
       },
       "Bio::DB::HTS::VCF::Sweep" : {
          "file" : "lib/Bio/DB/HTS/VCF.pm",
-         "version" : "2.11"
+         "version" : "3.01"
       },
       "Bio::DB::HTSfile" : {
          "file" : "lib/Bio/DB/HTS.pm"
       },
       "Bio::SeqFeature::HTSCoverage" : {
          "file" : "lib/Bio/DB/HTS.pm",
-         "version" : "2.11"
+         "version" : "3.01"
       }
    },
    "release_status" : "stable",
@@ -150,6 +154,5 @@
          "url" : "https://github.com/Ensembl/Bio-DB-HTS"
       }
    },
-   "version" : "2.11",
-   "x_serialization_backend" : "JSON::PP version 2.27400_02"
+   "version" : "3.01"
 }

META.yml

 ---
 abstract: 'Perl interface to HTS library for DNA sequencing'
 author:
-  - 'Rishi Nag'
+  - 'Alessandro Vullo'
 build_requires:
   ExtUtils::CBuilder: '0'
 configure_requires:
   Module::Build: '0.38'
 dynamic_config: 1
-generated_by: 'Module::Build version 0.4224, CPAN::Meta::Converter version 2.150010'
+generated_by: 'Module::Build version 0.4224, CPAN::Meta::Converter version 2.150001'
 license: apache
 meta-spec:
   url: http://module-build.sourceforge.net/META-spec-v1.4.html
@@ -16,91 +16,93 @@ name: Bio-DB-HTS
 provides:
   Bio::DB::HTS:
     file: lib/Bio/DB/HTS.pm
-    version: '2.11'
+    version: '3.01'
   Bio::DB::HTS::AlignWrapper:
     file: lib/Bio/DB/HTS/AlignWrapper.pm
-    version: '2.11'
+    version: '3.01'
   Bio::DB::HTS::Alignment:
     file: lib/Bio/DB/HTS/Alignment.pm
-    version: '2.11'
+    version: '3.01'
   Bio::DB::HTS::Constants:
     file: lib/Bio/DB/HTS/Constants.pm
-    version: '2.11'
+    version: '3.01'
   Bio::DB::HTS::Fai:
     file: lib/Bio/DB/HTS.pm
-    version: '2.11'
+    version: '3.01'
   Bio::DB::HTS::Faidx:
     file: lib/Bio/DB/HTS/Faidx.pm
-    version: '2.11'
+    version: '3.01'
   Bio::DB::HTS::FetchIterator:
     file: lib/Bio/DB/HTS/FetchIterator.pm
-    version: '2.11'
+    version: '3.01'
+  Bio::DB::HTS::HTSfile:
+    file: lib/Bio/DB/HTS.pm
+    version: '3.01'
   Bio::DB::HTS::Kseq:
     file: lib/Bio/DB/HTS/Kseq.pm
-    version: '2.11'
+    version: '3.01'
   Bio::DB::HTS::Kseq::Record:
     file: lib/Bio/DB/HTS/Kseq/Record.pm
-    version: '2.11'
+    version: '3.01'
   Bio::DB::HTS::Pileup:
     file: lib/Bio/DB/HTS/Pileup.pm
-    version: '2.11'
+    version: '3.01'
   Bio::DB::HTS::PileupWrapper:
     file: lib/Bio/DB/HTS/PileupWrapper.pm
-    version: '2.11'
+    version: '3.01'
   Bio::DB::HTS::Query:
     file: lib/Bio/DB/HTS/Query.pm
-    version: '2.11'
+    version: '3.01'
   Bio::DB::HTS::ReadIterator:
     file: lib/Bio/DB/HTS/ReadIterator.pm
-    version: '2.11'
+    version: '3.01'
   Bio::DB::HTS::Segment:
     file: lib/Bio/DB/HTS/Segment.pm
-    version: '2.11'
+    version: '3.01'
   Bio::DB::HTS::Segment::Iterator:
     file: lib/Bio/DB/HTS/Segment.pm
-    version: '2.11'
+    version: '3.01'
   Bio::DB::HTS::SplitAlignmentPart:
     file: lib/Bio/DB/HTS/AlignWrapper.pm
-    version: '2.11'
+    version: '3.01'
   Bio::DB::HTS::Tabix:
     file: lib/Bio/DB/HTS/Tabix.pm
-    version: '2.11'
+    version: '3.01'
   Bio::DB::HTS::Tabix::Iterator:
     file: lib/Bio/DB/HTS/Tabix/Iterator.pm
-    version: '2.11'
+    version: '3.01'
   Bio::DB::HTS::Target:
     file: lib/Bio/DB/HTS/Target.pm
-    version: '2.11'
+    version: '3.01'
   Bio::DB::HTS::VCF:
     file: lib/Bio/DB/HTS/VCF.pm
-    version: '2.11'
+    version: '3.01'
   Bio::DB::HTS::VCF::Header:
     file: lib/Bio/DB/HTS/VCF/Header.pm
-    version: '2.11'
+    version: '3.01'
   Bio::DB::HTS::VCF::HeaderPtr:
     file: lib/Bio/DB/HTS/VCF/HeaderPtr.pm
-    version: '2.11'
+    version: '3.01'
   Bio::DB::HTS::VCF::Iterator:
     file: lib/Bio/DB/HTS/VCF/Iterator.pm
-    version: '2.11'
+    version: '3.01'
   Bio::DB::HTS::VCF::Row:
     file: lib/Bio/DB/HTS/VCF/Row.pm
-    version: '2.11'
+    version: '3.01'
   Bio::DB::HTS::VCF::RowPtr:
     file: lib/Bio/DB/HTS/VCF/RowPtr.pm
-    version: '2.11'
+    version: '3.01'
   Bio::DB::HTS::VCF::Sweep:
     file: lib/Bio/DB/HTS/VCF.pm
-    version: '2.11'
+    version: '3.01'
   Bio::DB::HTSfile:
     file: lib/Bio/DB/HTS.pm
   Bio::SeqFeature::HTSCoverage:
     file: lib/Bio/DB/HTS.pm
-    version: '2.11'
+    version: '3.01'
 requires:
-  Bio::Root::Version: '1.006001'
+  Bio::SeqFeature::Lite: '0'
   perl: '5.008'
 resources:
   repository: https://github.com/Ensembl/Bio-DB-HTS
-version: '2.11'
-x_serialization_backend: 'CPAN::Meta::YAML version 0.018'
+version: '3.01'

README

@@ -91,7 +91,7 @@ based on Bio::DB::Sam by Lincoln Stein
 
 ### COPYRIGHT
 
-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.

debian/changelog

-libbio-db-hts-perl (98+git20190710.83c9327-1) UNRELEASED; urgency=medium
+libbio-db-hts-perl (3.01-1) UNRELEASED; urgency=medium
 
   * Initial release (Closes: #<bug>)
 

debian/patches/find_htslib.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: 2019-07-10
+Description: Take over changes in Build.PL from commit 83c9327 to make sure htslib will be found
+
+--- a/Build.PL
++++ b/Build.PL
+@@ -1,6 +1,6 @@
+ #!/usr/bin/perl
+ 
+-# Copyright [2015-2018] EMBL-European Bioinformatics Institute
++# Copyright [2015-2019] 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.
+@@ -75,7 +75,15 @@ 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.)
+-    if (my $dir = $self->args('htslib')) {
++    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')) {
+         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(
+@@ -105,6 +113,9 @@ 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();
+ }
+ 
+@@ -114,12 +125,15 @@ 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($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');
++
++    $self->include_dirs([$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;
+     }
++    $self->extra_linker_flags(@linker_dirflags, '-lhts', '-lpthread', '-lz');
+ }
+ 
+ sub hts_dev_files_exist {
+@@ -165,6 +179,48 @@ sub find_hts_in_install_dir {
+     }
+ }
+ 
++sub find_hts_in_split_install_dirs {
++    my ($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) = @_;
+ 
+@@ -177,12 +233,17 @@ Install it if you have not done so alrea
+ This script will attempt to locate HTSlib by looking for htslib/hts.h
+ and libhts.a / libhts.so in:
+ 
+-  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
++  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.
+ 
+ END
+ 

debian/patches/series

+find_htslib.patch

debian/rules

 #!/usr/bin/make -f
 
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
 %:
 	dh $@

debian/tests/control

-Tests: run-unit-test
-Depends: @
-Restrictions: allow-stderr

debian/tests/run-unit-test

-#!/bin/bash
-set -e
-
-pkg=#PACKAGENAME#
-
-export LC_ALL=C.UTF-8
-if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
-  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
-  # Double quote below to expand the temporary directory variable now versus
-  # later is on purpose.
-  # shellcheck disable=SC2064
-  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
-fi
-
-cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
-
-cd "${AUTOPKGTEST_TMP}"
-
-#do_stuff_to_test_package#

debian/watch

-version=3
-https://metacpan.org/release/Bio-DB-HTS \
-  .*/Bio-DB-HTS-v?(\d[\d.-]*)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip)$
+version=4
+
+https://metacpan.org/release/Bio-DB-HTS .*/Bio-DB-HTS-v?@ANY_VERSION@@ARCHIVE_EXT@

lib/Bio/DB/HTS.pm

 
 =head1 LICENSE
 
-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.

lib/Bio/DB/HTS.xs

 /*
-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.

lib/Bio/DB/HTS/AlignWrapper.pm

 
 =head1 LICENSE
 
-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.

lib/Bio/DB/HTS/Alignment.pm

 
 =head1 LICENSE
 
-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.