Bio-MUST-Apps-FortyTwo

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META.yml  view on Meta::CPAN

  IO::Prompter: '0'
  List::AllUtils: '0'
  Modern::Perl: '0'
  Moose: '0'
  Moose::Role: '0'
  Number::Interval: '0'
  POSIX: '0'
  Parallel::Batch: '0'
  Path::Class: '0'
  Smart::Comments: '0'
  Sort::Naturally: '0'
  Template: '0'
  Term::Completion::Path: '0'
  Test::Deep::NoTest: '0'
  Test::Most: '0'
  Tie::IxHash: '0'
  aliased: '0'
  autodie: '0'
  experimental: '0'
  feature: '0'
  namespace::autoclean: '0'

Makefile.PL  view on Meta::CPAN

    "IO::Prompter" => 0,
    "List::AllUtils" => 0,
    "Modern::Perl" => 0,
    "Moose" => 0,
    "Moose::Role" => 0,
    "Number::Interval" => 0,
    "POSIX" => 0,
    "Parallel::Batch" => 0,
    "Path::Class" => 0,
    "Smart::Comments" => 0,
    "Sort::Naturally" => 0,
    "Template" => 0,
    "Term::Completion::Path" => 0,
    "Test::Deep::NoTest" => 0,
    "Test::Most" => 0,
    "Tie::IxHash" => 0,
    "aliased" => 0,
    "autodie" => 0,
    "experimental" => 0,
    "feature" => 0,
    "namespace::autoclean" => 0

Makefile.PL  view on Meta::CPAN

  "IO::Prompter" => 0,
  "List::AllUtils" => 0,
  "Modern::Perl" => 0,
  "Moose" => 0,
  "Moose::Role" => 0,
  "Number::Interval" => 0,
  "POSIX" => 0,
  "Parallel::Batch" => 0,
  "Path::Class" => 0,
  "Smart::Comments" => 0,
  "Sort::Naturally" => 0,
  "Template" => 0,
  "Term::Completion::Path" => 0,
  "Test::Deep::NoTest" => 0,
  "Test::Files" => 0,
  "Test::Most" => 0,
  "Tie::IxHash" => 0,
  "aliased" => 0,
  "autodie" => 0,
  "experimental" => 0,
  "feature" => 0,

lib/Bio/MUST/Apps/FortyTwo/AliProcessor.pm  view on Meta::CPAN

use feature qw(say);

use Smart::Comments -ENV;

use Carp;
use Const::Fast;
use File::Basename;
use List::AllUtils qw(first part partition_by pairmap);
use Path::Class qw(file);
use POSIX;
use Sort::Naturally;
use Tie::IxHash;

use Bio::MUST::Core;
use Bio::MUST::Core::Utils qw(:filenames secure_outfile);
use Bio::MUST::Drivers;
use aliased 'Bio::MUST::Core::Ali';
use aliased 'Bio::MUST::Core::Ali::Temporary';
use aliased 'Bio::MUST::Core::IdList';
use aliased 'Bio::MUST::Core::Seq';
use aliased 'Bio::MUST::Core::SeqId';

lib/Bio/MUST/Apps/SlaveAligner/Local.pm  view on Meta::CPAN

use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say switch);
use experimental qw(smartmatch);        # to suppress warnings about 'when'

use Smart::Comments -ENV;

use List::AllUtils qw(max);
use Sort::Naturally;

use Bio::MUST::Core;
use aliased 'Bio::MUST::Core::Seq';


# _delayed_indels is a hash (site) of hashes (new_seq id)
# storing the number of insertions caused by each new_seq at each
# pos (as if each new_seq was added on its own to the Ali)

has 'ali' => (