Kwalitee Issues

has_license_in_source_file

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

no_pax_headers

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.31292/GenOO-1.5.0,./PaxHeaders.31292/GenOO-1.5.0,GenOO-1.5.0/PaxHeaders.31292/t,GenOO-1.5.0/PaxHeaders.31292/t,GenOO-1.5.0/t/PaxHeaders.31292/lib_for_test_class,GenOO-1.5.0/t/PaxHeaders.31292/lib_for_test_class,GenOO-1.5.0/t/lib_for_test_class/PaxHeaders.31292/Test,GenOO-1.5.0/t/lib_for_test_class/PaxHeaders.31292/Test,GenOO-1.5.0/t/lib_for_test_class/Test/PaxHeaders.31292/GenOO,GenOO-1.5.0/t/lib_for_test_class/Test/PaxHeaders.31292/GenOO,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/PaxHeaders.31292/Gene.pm,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/PaxHeaders.31292/Gene.pm,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/PaxHeaders.31292/Transcript,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/PaxHeaders.31292/Transcript,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/Transcript/PaxHeaders.31292/UTR3.pm,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/Transcript/PaxHeaders.31292/UTR3.pm,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/Transcript/PaxHeaders.31292/UTR5.pm,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/Transcript/PaxHeaders.31292/UTR5.pm,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/Transcript/PaxHeaders.31292/CDS.pm,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/Transcript/PaxHeaders.31292/CDS.pm,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/Transcript/PaxHeaders.31292/Part.pm,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/Transcript/PaxHeaders.31292/Part.pm,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/PaxHeaders.31292/Intron.pm,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/PaxHeaders.31292/Intron.pm,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/PaxHeaders.31292/Transcript.pm,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/PaxHeaders.31292/Transcript.pm,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/PaxHeaders.31292/TranscriptCollection.pm,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/PaxHeaders.31292/TranscriptCollection.pm,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/PaxHeaders.31292/RegionCollection,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/PaxHeaders.31292/RegionCollection,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/RegionCollection/PaxHeaders.31292/Type,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/RegionCollection/PaxHeaders.31292/Type,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/RegionCollection/Type/PaxHeaders.31292/DoubleHashArray.p,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/RegionCollection/Type/PaxHeaders.31292/DoubleHashArray.p,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/RegionCollection/PaxHeaders.31292/Factory,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/RegionCollection/PaxHeaders.31292/Factory,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/RegionCollection/Factory/PaxHeaders.31292/SAM.pm,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/RegionCollection/Factory/PaxHeaders.31292/SAM.pm,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/RegionCollection/Factory/PaxHeaders.31292/RegionArray.pm,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/RegionCollection/Factory/PaxHeaders.31292/RegionArray.pm,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/RegionCollection/Factory/PaxHeaders.31292/BED.pm,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/RegionCollection/Factory/PaxHeaders.31292/BED.pm,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/RegionCollection/PaxHeaders.31292/Factory.pm,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/RegionCollection/PaxHeaders.31292/Factory.pm,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/PaxHeaders.31292/Exon.pm,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/PaxHeaders.31292/Exon.pm,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/PaxHeaders.31292/GeneCollection,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/PaxHeaders.31292/GeneCollection,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/GeneCollection/PaxHeaders.31292/Factory,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/GeneCollection/PaxHeaders.31292/Factory,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/GeneCollection/Factory/PaxHeaders.31292/GTF.pm,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/GeneCollection/Factory/PaxHeaders.31292/GTF.pm,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/GeneCollection/Factory/PaxHeaders.31292/FromTranscriptCo,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/GeneCollection/Factory/PaxHeaders.31292/FromTranscriptCo,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/PaxHeaders.31292/TranscriptCollection,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/PaxHeaders.31292/TranscriptCollection,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/TranscriptCollection/PaxHeaders.31292/Factory,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/TranscriptCollection/PaxHeaders.31292/Factory,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/TranscriptCollection/Factory/PaxHeaders.31292/GTF.pm,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/TranscriptCollection/Factory/PaxHeaders.31292/GTF.pm,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/TranscriptCollection/Factory/PaxHeaders.31292/FromGeneCo,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/TranscriptCollection/Factory/PaxHeaders.31292/FromGeneCo,GenOO-1.5.0/t/lib_for_test_class/Test/GenOO/TranscriptCollection/PaxHeaders.31292/Factory.pm,GenOO-1.5.0/t/lib_for_test_class/Test/G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ders.31292/BED.pm,GenOO-1.5.0/lib/GenOO/Data/File/PaxHeaders.31292/BED.pm,GenOO-1.5.0/lib/GenOO/Data/PaxHeaders.31292/DB,GenOO-1.5.0/lib/GenOO/Data/PaxHeaders.31292/DB,GenOO-1.5.0/lib/GenOO/Data/DB/PaxHeaders.31292/Connector.pm,GenOO-1.5.0/lib/GenOO/Data/DB/PaxHeaders.31292/Connector.pm,GenOO-1.5.0/lib/GenOO/Data/DB/PaxHeaders.31292/DBIC,GenOO-1.5.0/lib/GenOO/Data/DB/PaxHeaders.31292/DBIC,GenOO-1.5.0/lib/GenOO/Data/DB/DBIC/PaxHeaders.31292/Species,GenOO-1.5.0/lib/GenOO/Data/DB/DBIC/PaxHeaders.31292/Species,GenOO-1.5.0/lib/GenOO/Data/DB/DBIC/Species/PaxHeaders.31292/Schema.pm,GenOO-1.5.0/lib/GenOO/Data/DB/DBIC/Species/PaxHeaders.31292/Schema.pm,GenOO-1.5.0/lib/GenOO/Data/DB/DBIC/Species/PaxHeaders.31292/Schema,GenOO-1.5.0/lib/GenOO/Data/DB/DBIC/Species/PaxHeaders.31292/Schema,GenOO-1.5.0/lib/GenOO/Data/DB/DBIC/Species/Schema/PaxHeaders.31292/SampleResultBase,GenOO-1.5.0/lib/GenOO/Data/DB/DBIC/Species/Schema/PaxHeaders.31292/SampleResultBase,GenOO-1.5.0/lib/GenOO/Data/DB/DBIC/Species/Schema/SampleResultBase/PaxHeaders.31292/v3.pm,GenOO-1.5.0/lib/GenOO/Data/DB/DBIC/Species/Schema/SampleResultBase/PaxHeaders.31292/v3.pm,GenOO-1.5.0/lib/GenOO/Data/DB/DBIC/Species/Schema/SampleResultBase/PaxHeaders.31292/v1.pm,GenOO-1.5.0/lib/GenOO/Data/DB/DBIC/Species/Schema/SampleResultBase/PaxHeaders.31292/v1.pm,GenOO-1.5.0/lib/GenOO/Data/DB/DBIC/Species/Schema/SampleResultBase/PaxHeaders.31292/v2.pm,GenOO-1.5.0/lib/GenOO/Data/DB/DBIC/Species/Schema/SampleResultBase/PaxHeaders.31292/v2.pm,GenOO-1.5.0/lib/GenOO/PaxHeaders.31292/Junction.pm,GenOO-1.5.0/lib/GenOO/PaxHeaders.31292/Junction.pm,GenOO-1.5.0/lib/GenOO/PaxHeaders.31292/RegionCollection.pm,GenOO-1.5.0/lib/GenOO/PaxHeaders.31292/RegionCollection.pm,GenOO-1.5.0/lib/GenOO/PaxHeaders.31292/GenomicRegion.pm,GenOO-1.5.0/lib/GenOO/PaxHeaders.31292/GenomicRegion.pm,GenOO-1.5.0/lib/GenOO/PaxHeaders.31292/Module,GenOO-1.5.0/lib/GenOO/PaxHeaders.31292/Module,GenOO-1.5.0/lib/GenOO/Module/PaxHeaders.31292/Search,GenOO-1.5.0/lib/GenOO/Module/PaxHeaders.31292/Search,GenOO-1.5.0/lib/GenOO/Module/Search/PaxHeaders.31292/Binary.pm,GenOO-1.5.0/lib/GenOO/Module/Search/PaxHeaders.31292/Binary.pm,GenOO-1.5.0/lib/PaxHeaders.31292/GenOO.pm,GenOO-1.5.0/lib/PaxHeaders.31292/GenOO.pm,GenOO-1.5.0/PaxHeaders.31292/CHANGES.md,GenOO-1.5.0/PaxHeaders.31292/CHANGES.md,GenOO-1.5.0/PaxHeaders.31292/Makefile.PL,GenOO-1.5.0/PaxHeaders.31292/Makefile.PL,GenOO-1.5.0/PaxHeaders.31292/README.md,GenOO-1.5.0/PaxHeaders.31292/README.md,GenOO-1.5.0/PaxHeaders.31292/META.json,GenOO-1.5.0/PaxHeaders.31292/META.json,GenOO-1.5.0/PaxHeaders.31292/MANIFEST,GenOO-1.5.0/PaxHeaders.31292/MANIFEST

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

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.

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.

use_warnings

Add 'use warnings' (or its equivalents) to all modules (this will require perl > 5.6), 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

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 1.005000 metacpan
GenOO::Data::DB::Connector 1.005000 metacpan
GenOO::Data::DB::DBIC::Species::Schema Schema object 1.005000 metacpan
GenOO::Data::DB::DBIC::Species::Schema::SampleResultBase::v1 DBIC Result class for sequenced reads 1.005000 metacpan
GenOO::Data::DB::DBIC::Species::Schema::SampleResultBase::v2 DBIC Result class for sequenced reads 1.005000 metacpan
GenOO::Data::DB::DBIC::Species::Schema::SampleResultBase::v3 DBIC Result class for sequenced reads 1.005000 metacpan
GenOO::Data::File::BED Object implementing methods for accessing bed formatted files (http://genome.ucsc.edu/FAQ/FAQformat#format1) 1.005000 metacpan
GenOO::Data::File::BED::Record Object representing a record of a bed file 1.005000 metacpan
GenOO::Data::File::FASTA Object implementing methods for accessing fasta formatted files (http://genome.ucsc.edu/FAQ/FAQformat#format1) 1.005000 metacpan
GenOO::Data::File::FASTA::Record Object representing a record of a fasta file 1.005000 metacpan
GenOO::Data::File::FASTQ Object implementing methods for accessing fastq formatted files 1.005000 metacpan
GenOO::Data::File::FASTQ::Record Object representing a record of a fastq file 1.005000 metacpan
GenOO::Data::File::GFF Object implementing methods for accessing GFF formatted files (http://www.sanger.ac.uk/resources/software/gff/spec.html) 1.005000 metacpan
GenOO::Data::File::GFF::Record Object representing a record of a gff file 1.005000 metacpan
GenOO::Data::File::SAM Object implementing methods for accessing SAM formatted files 1.005000 metacpan
GenOO::Data::File::SAM::Cigar Role that corresponds to the SAM file CIGAR string 1.005000 metacpan
GenOO::Data::File::SAM::CigarAndMDZ Role that combines SAM CIGAR string with MD:Z tag 1.005000 metacpan
GenOO::Data::File::SAM::MDZ Role - The MD:Z tag in a SAM file 1.005000 metacpan
GenOO::Data::File::SAM::Record Object representing a record of a sam file 1.005000 metacpan
GenOO::Data::Structure::DoubleHashArray Object for a data structure which corresponds of a 2D hash whose values are references to array 1.005000 metacpan
GenOO::Exon Exon object 1.005000 metacpan
GenOO::Gene Gene object 1.005000 metacpan
GenOO::GeneCollection::Factory Factory for creating L<GenOO::RegionCollection> objects 1.005000 metacpan
GenOO::GeneCollection::Factory::FromTranscriptCollection Factory for creating GenOO::GeneCollection object from a Transcript Collection and a hash{transcript_name} = genename 1.005000 metacpan
GenOO::GeneCollection::Factory::GTF Factory to create GeneCollection from a GTF file 1.005000 metacpan
GenOO::GenomicRegion Object that corresponds to a region on a genome 1.005000 metacpan
GenOO::Helper::MyMath A collection of useful mathematical methods 1.005000 metacpan
GenOO::Intron Intron object 1.005000 metacpan
GenOO::Junction A junction (eg exon-exon) object with features 1.005000 metacpan
GenOO::Module::Search::Binary Module that offers methods for searching in an array using binary search 1.005000 metacpan
GenOO::Region Role that represents a region on a reference sequence 1.005000 metacpan
GenOO::RegionCollection Role for a collection of GenOO::Region objects 1.005000 metacpan
GenOO::RegionCollection::Factory Factory for creating L<GenOO::RegionCollection> objects 1.005000 metacpan
GenOO::RegionCollection::Factory::BED Factory for creating GenOO::RegionCollection object from a BED file 1.005000 metacpan
GenOO::RegionCollection::Factory::DBIC 1.005000 metacpan
GenOO::RegionCollection::Factory::RegionArray Factory for creating a RegionCollection from array of regions 1.005000 metacpan
GenOO::RegionCollection::Factory::Requires Role for a concrete factory that creates GenOO::RegionCollection objects 1.005000 metacpan
GenOO::RegionCollection::Factory::SAM Factory for creating GenOO::RegionCollection object from a SAM file 1.005000 metacpan
GenOO::RegionCollection::Type::DBIC Class for a collection of GenOO::Region objects stored in a database. 1.005000 metacpan
GenOO::RegionCollection::Type::DoubleHashArray Object for a collection of GenOO::Region objects, with features 1.005000 metacpan
GenOO::Spliceable Role for a region that can be spliced 1.005000 metacpan
GenOO::Transcript Corresponds to a gene transcript 1.005000 metacpan
GenOO::Transcript::CDS Transcript part (coding sequence) 1.005000 metacpan
GenOO::Transcript::Part A functional region within a transcript consisting of spliceable elements 1.005000 metacpan
GenOO::Transcript::UTR3 Transcript part (coding sequence) 1.005000 metacpan
GenOO::Transcript::UTR5 1.005000 metacpan
GenOO::TranscriptCollection Role for a collection of GenOO::Transcript objects 1.005000 metacpan
GenOO::TranscriptCollection::Factory Factory for creating L<GenOO::TranscriptCollection> objects 1.005000 metacpan
GenOO::TranscriptCollection::Factory::FromGeneCollection Factory to create GenOO::TranscriptCollection object from a GeneCollection 1.005000 metacpan
GenOO::TranscriptCollection::Factory::GTF Factory to create TranscriptCollection from a GTF file 1.005000 metacpan

Other Files

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