CPANTS

GenOO 1.4.9

Kwalitee Issues

This is not the latest release. The following issues may have already been fixed in the newer releases.

If you use Mac OS X >= 10.6, use gnu tar (/usr/bin/gnutar) to avoid PAX headers. It's also important to rename (shorten) long file names (>= 100 characters) in the distribution.

Error: ./PaxHeaders.16960/GenOO-1.4.9,./PaxHeaders.16960/GenOO-1.4.9,GenOO-1.4.9/PaxHeaders.16960/t,GenOO-1.4.9/PaxHeaders.16960/t,GenOO-1.4.9/t/PaxHeaders.16960/lib_for_test_class,GenOO-1.4.9/t/PaxHeaders.16960/lib_for_test_class,GenOO-1.4.9/t/lib_for_test_class/PaxHeaders.16960/Test,GenOO-1.4.9/t/lib_for_test_class/PaxHeaders.16960/Test,GenOO-1.4.9/t/lib_for_test_class/Test/PaxHeaders.16960/GenOO,GenOO-1.4.9/t/lib_for_test_class/Test/PaxHeaders.16960/GenOO,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/PaxHeaders.16960/Gene.pm,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/PaxHeaders.16960/Gene.pm,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/PaxHeaders.16960/Transcript,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/PaxHeaders.16960/Transcript,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/Transcript/PaxHeaders.16960/UTR3.pm,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/Transcript/PaxHeaders.16960/UTR3.pm,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/Transcript/PaxHeaders.16960/UTR5.pm,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/Transcript/PaxHeaders.16960/UTR5.pm,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/Transcript/PaxHeaders.16960/CDS.pm,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/Transcript/PaxHeaders.16960/CDS.pm,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/Transcript/PaxHeaders.16960/Part.pm,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/Transcript/PaxHeaders.16960/Part.pm,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/PaxHeaders.16960/Intron.pm,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/PaxHeaders.16960/Intron.pm,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/PaxHeaders.16960/Transcript.pm,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/PaxHeaders.16960/Transcript.pm,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/PaxHeaders.16960/TranscriptCollection.pm,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/PaxHeaders.16960/TranscriptCollection.pm,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/PaxHeaders.16960/RegionCollection,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/PaxHeaders.16960/RegionCollection,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/RegionCollection/PaxHeaders.16960/Type,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/RegionCollection/PaxHeaders.16960/Type,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/RegionCollection/Type/PaxHeaders.16960/DoubleHashArray.p,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/RegionCollection/Type/PaxHeaders.16960/DoubleHashArray.p,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/RegionCollection/PaxHeaders.16960/Factory,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/RegionCollection/PaxHeaders.16960/Factory,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/RegionCollection/Factory/PaxHeaders.16960/SAM.pm,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/RegionCollection/Factory/PaxHeaders.16960/SAM.pm,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/RegionCollection/Factory/PaxHeaders.16960/RegionArray.pm,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/RegionCollection/Factory/PaxHeaders.16960/RegionArray.pm,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/RegionCollection/Factory/PaxHeaders.16960/BED.pm,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/RegionCollection/Factory/PaxHeaders.16960/BED.pm,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/RegionCollection/PaxHeaders.16960/Factory.pm,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/RegionCollection/PaxHeaders.16960/Factory.pm,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/PaxHeaders.16960/Exon.pm,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/PaxHeaders.16960/Exon.pm,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/PaxHeaders.16960/GeneCollection,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/PaxHeaders.16960/GeneCollection,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/GeneCollection/PaxHeaders.16960/Factory,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/GeneCollection/PaxHeaders.16960/Factory,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/GeneCollection/Factory/PaxHeaders.16960/GTF.pm,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/GeneCollection/Factory/PaxHeaders.16960/GTF.pm,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/GeneCollection/Factory/PaxHeaders.16960/FromTranscriptCo,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/GeneCollection/Factory/PaxHeaders.16960/FromTranscriptCo,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/PaxHeaders.16960/TranscriptCollection,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/PaxHeaders.16960/TranscriptCollection,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/TranscriptCollection/PaxHeaders.16960/Factory,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/TranscriptCollection/PaxHeaders.16960/Factory,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/TranscriptCollection/Factory/PaxHeaders.16960/GTF.pm,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/TranscriptCollection/Factory/PaxHeaders.16960/GTF.pm,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/TranscriptCollection/Factory/PaxHeaders.16960/FromGeneCo,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/TranscriptCollection/Factory/PaxHeaders.16960/FromGeneCo,GenOO-1.4.9/t/lib_for_test_class/Test/GenOO/TranscriptCollection/PaxHeaders.16960/Factory.pm,GenOO-1.4.9/t/lib_for_test_class/Test/G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ders.16960/BED.pm,GenOO-1.4.9/lib/GenOO/Data/File/PaxHeaders.16960/BED.pm,GenOO-1.4.9/lib/GenOO/Data/PaxHeaders.16960/DB,GenOO-1.4.9/lib/GenOO/Data/PaxHeaders.16960/DB,GenOO-1.4.9/lib/GenOO/Data/DB/PaxHeaders.16960/Connector.pm,GenOO-1.4.9/lib/GenOO/Data/DB/PaxHeaders.16960/Connector.pm,GenOO-1.4.9/lib/GenOO/Data/DB/PaxHeaders.16960/DBIC,GenOO-1.4.9/lib/GenOO/Data/DB/PaxHeaders.16960/DBIC,GenOO-1.4.9/lib/GenOO/Data/DB/DBIC/PaxHeaders.16960/Species,GenOO-1.4.9/lib/GenOO/Data/DB/DBIC/PaxHeaders.16960/Species,GenOO-1.4.9/lib/GenOO/Data/DB/DBIC/Species/PaxHeaders.16960/Schema.pm,GenOO-1.4.9/lib/GenOO/Data/DB/DBIC/Species/PaxHeaders.16960/Schema.pm,GenOO-1.4.9/lib/GenOO/Data/DB/DBIC/Species/PaxHeaders.16960/Schema,GenOO-1.4.9/lib/GenOO/Data/DB/DBIC/Species/PaxHeaders.16960/Schema,GenOO-1.4.9/lib/GenOO/Data/DB/DBIC/Species/Schema/PaxHeaders.16960/SampleResultBase,GenOO-1.4.9/lib/GenOO/Data/DB/DBIC/Species/Schema/PaxHeaders.16960/SampleResultBase,GenOO-1.4.9/lib/GenOO/Data/DB/DBIC/Species/Schema/SampleResultBase/PaxHeaders.16960/v3.pm,GenOO-1.4.9/lib/GenOO/Data/DB/DBIC/Species/Schema/SampleResultBase/PaxHeaders.16960/v3.pm,GenOO-1.4.9/lib/GenOO/Data/DB/DBIC/Species/Schema/SampleResultBase/PaxHeaders.16960/v1.pm,GenOO-1.4.9/lib/GenOO/Data/DB/DBIC/Species/Schema/SampleResultBase/PaxHeaders.16960/v1.pm,GenOO-1.4.9/lib/GenOO/Data/DB/DBIC/Species/Schema/SampleResultBase/PaxHeaders.16960/v2.pm,GenOO-1.4.9/lib/GenOO/Data/DB/DBIC/Species/Schema/SampleResultBase/PaxHeaders.16960/v2.pm,GenOO-1.4.9/lib/GenOO/PaxHeaders.16960/Junction.pm,GenOO-1.4.9/lib/GenOO/PaxHeaders.16960/Junction.pm,GenOO-1.4.9/lib/GenOO/PaxHeaders.16960/RegionCollection.pm,GenOO-1.4.9/lib/GenOO/PaxHeaders.16960/RegionCollection.pm,GenOO-1.4.9/lib/GenOO/PaxHeaders.16960/GenomicRegion.pm,GenOO-1.4.9/lib/GenOO/PaxHeaders.16960/GenomicRegion.pm,GenOO-1.4.9/lib/GenOO/PaxHeaders.16960/Module,GenOO-1.4.9/lib/GenOO/PaxHeaders.16960/Module,GenOO-1.4.9/lib/GenOO/Module/PaxHeaders.16960/Search,GenOO-1.4.9/lib/GenOO/Module/PaxHeaders.16960/Search,GenOO-1.4.9/lib/GenOO/Module/Search/PaxHeaders.16960/Binary.pm,GenOO-1.4.9/lib/GenOO/Module/Search/PaxHeaders.16960/Binary.pm,GenOO-1.4.9/lib/PaxHeaders.16960/GenOO.pm,GenOO-1.4.9/lib/PaxHeaders.16960/GenOO.pm,GenOO-1.4.9/PaxHeaders.16960/CHANGES.md,GenOO-1.4.9/PaxHeaders.16960/CHANGES.md,GenOO-1.4.9/PaxHeaders.16960/Makefile.PL,GenOO-1.4.9/PaxHeaders.16960/Makefile.PL,GenOO-1.4.9/PaxHeaders.16960/README.md,GenOO-1.4.9/PaxHeaders.16960/README.md,GenOO-1.4.9/PaxHeaders.16960/META.json,GenOO-1.4.9/PaxHeaders.16960/META.json,GenOO-1.4.9/PaxHeaders.16960/MANIFEST,GenOO-1.4.9/PaxHeaders.16960/MANIFEST

has_license_in_source_file

Add =head1 LICENSE and the text of the license to the main module in your code.

use_strict

Add 'use strict' (or its equivalents) to all modules, or convince us that your favorite module is well-known enough and people can easily see the modules are strictly written.

Error: GenOO::GeneCollection::Factory, GenOO::RegionCollection::Factory, GenOO::TranscriptCollection::Factory

3 Extra Issues

meta_yml_declares_perl_version

If you are using Build.PL define the {requires}{perl} = VERSION field. If you are using MakeMaker (Makefile.PL) you should upgrade ExtUtils::MakeMaker to 6.48 and use MIN_PERL_VERSION parameter. Perl::MinimumVersion can help you determine which version of Perl your module needs.

has_known_license_in_source_file

Add =head1 LICENSE and/or the proper text of the well-known license to the main module in your code.

use_warnings

Add 'use warnings' (or its equivalents) to all modules, or convince us that your favorite module is well-known enough and people can easily see the modules warn when something bad happens.

Error: GenOO::GeneCollection::Factory, GenOO::RegionCollection::Factory, GenOO::TranscriptCollection::Factory

1 Experimental Issue

meta_yml_has_provides: Add all modules contained in this distribution to the META.yml field 'provides'. Module::Build or Dist::Zilla::Plugin::MetaProvides do this automatically for you.

Modules

Name	Abstract	Version	View
GenOO	A Modern Perl Framework for High Throughput Sequencing analysis	1.004009	metacpan
GenOO::Data::DB::Connector		1.004009	metacpan
GenOO::Data::DB::DBIC::Species::Schema	Schema object	1.004009	metacpan
GenOO::Data::DB::DBIC::Species::Schema::SampleResultBase::v1	DBIC Result class for sequenced reads	1.004009	metacpan
GenOO::Data::DB::DBIC::Species::Schema::SampleResultBase::v2	DBIC Result class for sequenced reads	1.004009	metacpan
GenOO::Data::DB::DBIC::Species::Schema::SampleResultBase::v3	DBIC Result class for sequenced reads	1.004009	metacpan
GenOO::Data::File::BED	Object implementing methods for accessing bed formatted files (http://genome.ucsc.edu/FAQ/FAQformat#format1)	1.004009	metacpan
GenOO::Data::File::BED::Record	Object representing a record of a bed file	1.004009	metacpan
GenOO::Data::File::FASTA	Object implementing methods for accessing fasta formatted files (http://genome.ucsc.edu/FAQ/FAQformat#format1)	1.004009	metacpan
GenOO::Data::File::FASTA::Record	Object representing a record of a fasta file	1.004009	metacpan
GenOO::Data::File::FASTQ	Object implementing methods for accessing fastq formatted files	1.004009	metacpan
GenOO::Data::File::FASTQ::Record	Object representing a record of a fastq file	1.004009	metacpan
GenOO::Data::File::GFF	Object implementing methods for accessing GFF formatted files (http://www.sanger.ac.uk/resources/software/gff/spec.html)	1.004009	metacpan
GenOO::Data::File::GFF::Record	Object representing a record of a gff file	1.004009	metacpan
GenOO::Data::File::SAM	Object implementing methods for accessing SAM formatted files	1.004009	metacpan
GenOO::Data::File::SAM::Cigar	Role that corresponds to the SAM file CIGAR string	1.004009	metacpan
GenOO::Data::File::SAM::CigarAndMDZ	Role that combines SAM CIGAR string with MD:Z tag	1.004009	metacpan
GenOO::Data::File::SAM::MDZ	Role - The MD:Z tag in a SAM file	1.004009	metacpan
GenOO::Data::File::SAM::Record	Object representing a record of a sam file	1.004009	metacpan
GenOO::Data::Structure::DoubleHashArray	Object for a data structure which corresponds of a 2D hash whose values are references to array	1.004009	metacpan
GenOO::Exon	Exon object	1.004009	metacpan
GenOO::Gene	Gene object	1.004009	metacpan
GenOO::GeneCollection::Factory	Factory for creating L<GenOO::RegionCollection> objects	1.004009	metacpan
GenOO::GeneCollection::Factory::FromTranscriptCollection	Factory for creating GenOO::GeneCollection object from a Transcript Collection and a hash{transcript_name} = genename	1.004009	metacpan
GenOO::GeneCollection::Factory::GTF	Factory to create GeneCollection from a GTF file	1.004009	metacpan
GenOO::GenomicRegion	Object that corresponds to a region on a genome	1.004009	metacpan
GenOO::Helper::MyMath	A collection of useful mathematical methods	1.004009	metacpan
GenOO::Intron	Intron object	1.004009	metacpan
GenOO::Junction	A junction (eg exon-exon) object with features	1.004009	metacpan
GenOO::Module::Search::Binary	Module that offers methods for searching in an array using binary search	1.004009	metacpan
GenOO::Region	Role that represents a region on a reference sequence	1.004009	metacpan
GenOO::RegionCollection	Role for a collection of GenOO::Region objects	1.004009	metacpan
GenOO::RegionCollection::Factory	Factory for creating L<GenOO::RegionCollection> objects	1.004009	metacpan
GenOO::RegionCollection::Factory::BED	Factory for creating GenOO::RegionCollection object from a BED file	1.004009	metacpan
GenOO::RegionCollection::Factory::DBIC		1.004009	metacpan
GenOO::RegionCollection::Factory::RegionArray	Factory for creating a RegionCollection from array of regions	1.004009	metacpan
GenOO::RegionCollection::Factory::Requires	Role for a concrete factory that creates GenOO::RegionCollection objects	1.004009	metacpan
GenOO::RegionCollection::Factory::SAM	Factory for creating GenOO::RegionCollection object from a SAM file	1.004009	metacpan
GenOO::RegionCollection::Type::DBIC	Class for a collection of GenOO::Region objects stored in a database.	1.004009	metacpan
GenOO::RegionCollection::Type::DoubleHashArray	Object for a collection of GenOO::Region objects, with features	1.004009	metacpan
GenOO::Spliceable	Role for a region that can be spliced	1.004009	metacpan
GenOO::Transcript	Corresponds to a gene transcript	1.004009	metacpan
GenOO::Transcript::CDS	Transcript part (coding sequence)	1.004009	metacpan
GenOO::Transcript::Part	A functional region within a transcript consisting of spliceable elements	1.004009	metacpan
GenOO::Transcript::UTR3	Transcript part (coding sequence)	1.004009	metacpan
GenOO::Transcript::UTR5		1.004009	metacpan
GenOO::TranscriptCollection	Role for a collection of GenOO::Transcript objects	1.004009	metacpan
GenOO::TranscriptCollection::Factory	Factory for creating L<GenOO::TranscriptCollection> objects	1.004009	metacpan
GenOO::TranscriptCollection::Factory::FromGeneCollection	Factory to create GenOO::TranscriptCollection object from a GeneCollection	1.004009	metacpan
GenOO::TranscriptCollection::Factory::GTF	Factory to create TranscriptCollection from a GTF file	1.004009	metacpan

Other Files


MANIFEST	metacpan
META.json	metacpan
META.yml	metacpan
Makefile.PL	metacpan
README.md	metacpan
dist.ini	metacpan