Bio-HTS
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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 {
},
"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" : {
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;
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;
( run in 0.304 second using v1.01-cache-2.11-cpan-05444aca049 )