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Merge pull request #27 from ICGC-TCGA-PanCancer/dev
Dev - merge 1.0.0 into master ready for release
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@@ -2,8 +2,6 @@ | |
| /blib | ||
| /docs | ||
| /pm_to_blib | ||
| /MYMETA.yml | ||
| /MYMETA.json | ||
| /MANIFEST.bak | ||
| /install_tmp | ||
| /setup.log | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,57 @@ | ||
| { | ||
| "abstract" : "unknown", | ||
| "author" : [ | ||
| "unknown" | ||
| ], | ||
| "dynamic_config" : 0, | ||
| "generated_by" : "ExtUtils::MakeMaker version 6.68, CPAN::Meta::Converter version 2.131560", | ||
| "license" : [ | ||
| "unknown" | ||
| ], | ||
| "meta-spec" : { | ||
| "url" : "http://search.cpan.org/perldoc?CPAN::Meta::Spec", | ||
| "version" : "2" | ||
| }, | ||
| "name" : "PCAP", | ||
| "no_index" : { | ||
| "directory" : [ | ||
| "t", | ||
| "inc" | ||
| ] | ||
| }, | ||
| "prereqs" : { | ||
| "build" : { | ||
| "requires" : { | ||
| "ExtUtils::MakeMaker" : "0" | ||
| } | ||
| }, | ||
| "configure" : { | ||
| "requires" : { | ||
| "ExtUtils::MakeMaker" : "0" | ||
| } | ||
| }, | ||
| "runtime" : { | ||
| "requires" : { | ||
| "Bio::DB::Sam" : "1.39", | ||
| "Bio::Root::Version" : "1.006923", | ||
| "Capture::Tiny" : "0.24", | ||
| "Const::Fast" : "0.014", | ||
| "Data::UUID" : "1.219", | ||
| "Devel::Cover" : "1.09", | ||
| "File::Which" : "0.05", | ||
| "GD" : "2.52", | ||
| "IPC::System::Simple" : "1.25", | ||
| "List::Util" : "1.38", | ||
| "Math::Gradient" : "0.04", | ||
| "Module::Build" : "0.42", | ||
| "Pod::Coverage" : "0.23", | ||
| "Proc::ProcessTable" : "0.5", | ||
| "Term::UI" : "0.42", | ||
| "Test::Fatal" : "0.013", | ||
| "Try::Tiny" : "0.19" | ||
| } | ||
| } | ||
| }, | ||
| "release_status" : "stable", | ||
| "version" : "v1.0.0" | ||
| } |
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| --- | ||
| abstract: unknown | ||
| author: | ||
| - unknown | ||
| build_requires: | ||
| ExtUtils::MakeMaker: 0 | ||
| configure_requires: | ||
| ExtUtils::MakeMaker: 0 | ||
| dynamic_config: 0 | ||
| generated_by: 'ExtUtils::MakeMaker version 6.68, CPAN::Meta::Converter version 2.131560' | ||
| license: unknown | ||
| meta-spec: | ||
| url: http://module-build.sourceforge.net/META-spec-v1.4.html | ||
| version: 1.4 | ||
| name: PCAP | ||
| no_index: | ||
| directory: | ||
| - t | ||
| - inc | ||
| requires: | ||
| Bio::DB::Sam: 1.39 | ||
| Bio::Root::Version: 1.006923 | ||
| Capture::Tiny: 0.24 | ||
| Const::Fast: 0.014 | ||
| Data::UUID: 1.219 | ||
| Devel::Cover: 1.09 | ||
| File::Which: 0.05 | ||
| GD: 2.52 | ||
| IPC::System::Simple: 1.25 | ||
| List::Util: 1.38 | ||
| Math::Gradient: 0.04 | ||
| Module::Build: 0.42 | ||
| Pod::Coverage: 0.23 | ||
| Proc::ProcessTable: 0.5 | ||
| Term::UI: 0.42 | ||
| Test::Fatal: 0.013 | ||
| Try::Tiny: 0.19 | ||
| version: v1.0.0 |
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| Original file line number | Diff line number | Diff line change |
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| package PCAP::Bam::Bas; | ||
|
|
||
| ##########LICENCE########## | ||
| # PCAP - NGS reference implementations and helper code for the ICGC/TCGA Pan-Cancer Analysis Project | ||
| # Copyright (C) 2014 ICGC PanCancer Project | ||
| # | ||
| # This program is free software; you can redistribute it and/or | ||
| # modify it under the terms of the GNU General Public License | ||
| # as published by the Free Software Foundation; either version 2 | ||
| # of the License, or (at your option) any later version. | ||
| # | ||
| # This program is distributed in the hope that it will be useful, | ||
| # but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| # GNU General Public License for more details. | ||
| # | ||
| # You should have received a copy of the GNU General Public License | ||
| # along with this program; if not see: | ||
| # http://www.gnu.org/licenses/gpl-2.0.html | ||
| ##########LICENCE########## | ||
|
|
||
| use PCAP; | ||
| our $VERSION = PCAP->VERSION; | ||
|
|
||
| use strict; | ||
| use English qw( -no_match_vars ); | ||
| use warnings FATAL=>'all'; | ||
| use autodie qw( :all ); | ||
| use Carp qw(croak carp); | ||
|
|
||
| sub new { | ||
| my ($class, $bas) = @_; | ||
| my $self = { }; | ||
| bless $self, $class; | ||
| $self->_init($bas); | ||
| return $self; | ||
| } | ||
|
|
||
| sub _init { | ||
| my ($self, $bas) = @_; | ||
| croak "No bas file defined" if(!defined $bas); | ||
| die "*.bas file: $bas does not exist" unless(-e $bas); | ||
| die "*.bas file: $bas is empty" unless(-s $bas); | ||
| open my $IN, '<', $bas; | ||
| $self->bas_keys($IN); | ||
| $self->_import_data($IN); | ||
| close $IN; | ||
| return 1; | ||
| } | ||
|
|
||
| sub _import_data { | ||
| my ($self, $fh) = @_; | ||
| while(my $line = <$fh>) { | ||
| chomp $line; | ||
| my @bits = split /\t/, $line; | ||
| my %rg; | ||
| for my $key(@{$self->bas_keys}) { | ||
| $rg{$key} = $bits[$self->{'key_pos_map'}->{$key}]; | ||
| } | ||
| $self->{'_data'}->{$rg{'readgroup'}} = \%rg; | ||
| } | ||
| return 1; | ||
| } | ||
|
|
||
| sub bas_keys { | ||
| my ($self, $key_fh) = @_; | ||
| croak "bas_keys should only be initialised once\n" if(exists $self->{'keys'} && defined $key_fh); | ||
| if(defined $key_fh) { | ||
| my $line = <$key_fh>; | ||
| chomp $line; | ||
| my @head = split /\t/, $line; | ||
| my %key_pos_map; | ||
| my $pos=0; | ||
| for my $key(@head) { | ||
| $key_pos_map{$key} = $pos++; | ||
| } | ||
| $self->{'keys'} = \@head; | ||
| $self->{'key_pos_map'} = \%key_pos_map; | ||
| } | ||
| return $self->{'keys'}; | ||
| } | ||
|
|
||
| sub get { | ||
| my ($self, $rg, $key) = @_; | ||
| die qq{Readgroup '$rg' does not exist\n} unless(exists $self->{'_data'}->{$rg}); | ||
| return exists $self->{'_data'}->{$rg}->{$key} ? $self->{'_data'}->{$rg}->{$key} : undef; | ||
| } | ||
|
|
||
| 1; | ||
|
|
||
| __END__ | ||
| =head1 PCAP::Bam::Bas | ||
| Convenience class for accessing data in a *.bas file. | ||
| =head2 METHODS | ||
| =over 2 | ||
| =item new | ||
| Construct an access object for BAM statistics file. | ||
| my $bas_ob = PCAP::Bam::Bas->new($bas); | ||
| =item bas_keys | ||
| Returns the list of available keys for this BAS file. | ||
| =item get | ||
| Retrieve a value by its readgroup and key: | ||
| $bas->($rg, 'median_insert_size'); | ||
| NOTE: Returns undef if a key is not available. | ||
| =back |
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