App-RecordStream-Bio

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Changes  view on Meta::CPAN

Revision history for App-RecordStream-Bio

0.24  2017-08-04 10:44:18 PDT
    - New command togff3, complementing fromgff3

0.23  2017-07-21 10:30:24 PDT
    - Fixing the release process, no functional changes!

0.22  2017-07-21 10:25:50 PDT
    - Testing release process, no functional changes (but hey, version numbers
      are cheap!)

0.20  2017-07-21 10:08:10 PDT
    - Better fatpacking of the standalone bio.pm download

0.19  2017-07-20 13:33:09 PDT

META.json  view on Meta::CPAN

      "bugtracker" : {
         "web" : "https://github.com/MullinsLab/App-RecordStream-Bio/issues"
      },
      "homepage" : "https://github.com/MullinsLab/App-RecordStream-Bio",
      "repository" : {
         "type" : "git",
         "url" : "https://github.com/MullinsLab/App-RecordStream-Bio.git",
         "web" : "https://github.com/MullinsLab/App-RecordStream-Bio"
      }
   },
   "version" : "0.24"
}

META.yml  view on Meta::CPAN

    - t
    - xt
requires:
  App::RecordStream::Operation: v4.0.0
  Bio::GFF3::LowLevel: '0'
  perl: '5.010'
resources:
  bugtracker: https://github.com/MullinsLab/App-RecordStream-Bio/issues
  homepage: https://github.com/MullinsLab/App-RecordStream-Bio
  repository: https://github.com/MullinsLab/App-RecordStream-Bio.git
version: '0.24'

Makefile.PL  view on Meta::CPAN

    "App::RecordStream::Operation" => "4.0.0",
    "Bio::GFF3::LowLevel" => 0
  },
  "TEST_REQUIRES" => {
    "App::RecordStream::Test::OperationHelper" => "4.0.0",
    "App::RecordStream::Test::Tester" => "4.0.0",
    "File::Temp" => 0,
    "JSON" => 0,
    "Test::More" => "0.88"
  },
  "VERSION" => "0.24",
  "test" => {
    "TESTS" => "t/*.t"
  }
);


my %FallbackPrereqs = (
  "App::RecordStream::Operation" => "4.0.0",
  "App::RecordStream::Test::OperationHelper" => "4.0.0",
  "App::RecordStream::Test::Tester" => "4.0.0",

lib/App/RecordStream/Bio.pm  view on Meta::CPAN

package App::RecordStream::Bio;

use strict;
use 5.010;
our $VERSION = '0.24';

# For informational purposes only in the fatpacked file, so it's OK to fail.
# For now, classes are still under the App::RecordStream::Operation namespace
# instead of ::Bio::Operation.
eval {
    require App::RecordStream::Site;
    App::RecordStream::Site->register_site(
        name => __PACKAGE__,
        path => __PACKAGE__,
    );

t/data/fromsam-output-extra  view on Meta::CPAN

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{"tlen":"0","pnext":"0","rnext":"*","quals":[34,34,34,34,34,38,35,38,38,38,38,37,38,37,38,38,35,36,38,38,38,38,38,38,38,38,38,38,38,38,38,38,38,38,38,38,37,38,38,35,37,37,38,38,37,36,38,37,38,38,38,38,38,27,35,35,37,37,34,36,38,35,38,38,38,38,38,38,3...
{"tlen":"0","rnext":"*","quals":[34,34,27,27,33,37,27,31,24,31,36,37,38,27,11,37,37,23,37,32,37,34,38,31,32,36,37,37,35,37,37,34,11,27,11,34,36,32,34,37,37,23,27,37,24,34,37,23,26,21,36,38,34,31,34,36,36,34,37,38,38,35,35,23,37,23,21,27,37,34,24,23,3...
{"tag":{"XA":{"type":"Z","value":"refname,+9300,7M1D2M1D1M1D2M2D104M,13;"},"MD":{"type":"Z","value":"0A0G1A3^G2^G1^A2^TC10G19G11G39A14G6"},"AS":{"value":"94","type":"i"},"RG":{"type":"Z","value":"1"},"NM":{"type":"i","value":"13"},"XS":{"type":"i","v...
{"tag":{"AS":{"type":"i","value":"0"},"RG":{"value":"1","type":"Z"},"XS":{"value":"0","type":"i"}},"qual":"CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGAFGGGGGGGGGGGFGGGGGGGGGFGGGGGGGGGGGGEGGFFGGGGGGGGGGFDGGGFGGGGFGGGGGGGGD...