Bio-HTS

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Build.PL  view on Meta::CPAN

    include_dirs         => [$hts_include],
    extra_linker_flags   => ["-L$hts_lib", '-lhts', '-lz'],
    extra_compiler_flags => [
        # must match DFLAGS in Samtools Makefile
        '-D_FILE_OFFSET_BITS=64', 
        # allow everything to work on files from the internet
        '-D_USE_KNETFILE',
    ],
    requires             => {
        'perl'          => '5.008',
        'Try::Tiny'     => '0.22',
        'Mouse'         => '2.4.2',
        'Log::Log4perl' => '1.46',
    },
    verbose              => 1,
    create_makefile_pl   => 'traditional',
);

$build->create_build_script;

sub find_hts {

META.json  view on Meta::CPAN

      },
      "configure" : {
         "requires" : {
            "Module::Build" : "0.42"
         }
      },
      "runtime" : {
         "requires" : {
            "Log::Log4perl" : "1.46",
            "Mouse" : "2.004002",
            "Try::Tiny" : "0.22",
            "perl" : "5.008"
         }
      }
   },
   "provides" : {
      "Bio::HTS" : {
         "file" : "lib/Bio/HTS.pm",
         "version" : "v0.0.1"
      },
      "Bio::HTS::File" : {

META.yml  view on Meta::CPAN

    file: lib/Bio/HTS/Logger.pm
  Bio::HTS::Tabix:
    file: lib/Bio/HTS/Tabix.pm
  Bio::HTS::Tabix::Iterator:
    file: lib/Bio/HTS/Tabix/Iterator.pm
  Bio::HTS::VCF:
    file: lib/Bio/HTS/VCF.pm
requires:
  Log::Log4perl: '1.46'
  Mouse: '2.004002'
  Try::Tiny: '0.22'
  perl: '5.008'
version: v0.0.1
x_serialization_backend: 'CPAN::Meta::YAML version 0.012'

Makefile.PL  view on Meta::CPAN

# Note: this file was auto-generated by Module::Build::Compat version 0.4214
require 5.008;
use ExtUtils::MakeMaker;
WriteMakefile
(
  'INSTALLDIRS' => 'site',
  'VERSION_FROM' => 'lib/Bio/HTS.pm',
  'NAME' => 'Bio::HTS',
  'PREREQ_PM' => {
                   'Try::Tiny' => '0.22',
                   'Mouse' => '2.004002',
                   'Log::Log4perl' => '1.46',
                   'ExtUtils::CBuilder' => 0
                 },
  'EXE_FILES' => [
                   'bin/performance_test.pl'
                 ],
  'PL_FILES' => {}
)
;

bin/performance_test.pl  view on Meta::CPAN

#!/usr/bin/env perl

use strict;
use warnings;

use Bio::HTS::Tabix;
use Data::Dumper;
use feature qw(say);
use Try::Tiny;
use Benchmark qw/cmpthese timethese/;

use Sapientia::Util::Bed;

die "File " . $ARGV[0] . " doesn't exist" unless -e $ARGV[0];

my @chroms = (1..22, 'X', 'Y', 'M');
my $num_lookups = 20;

cpanfile  view on Meta::CPAN

requires 'Mouse';
requires 'Log::Log4perl';
requires 'Try::Tiny';

lib/Bio/HTS.pm  view on Meta::CPAN

package Bio::HTS;

our $VERSION = 0.0.1;

use Try::Tiny;
use Log::Log4perl qw( :easy );

BEGIN {
    #if there's no logger already make our own
    if ( ! Log::Log4perl->initialized() ) {
        Log::Log4perl->easy_init( { level => $DEBUG, layout => "%F{1} - %p - %m%n" });
    }
};

require XSLoader;