Kwalitee Issues

has_changelog

Add a Changelog (best named 'Changes') to the distribution. It should list at least major changes implemented in newer versions.

package_version_matches_dist_version

Fix the version(s).

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: Bio::Pipeline::Comparison::Exceptions

has_meta_json

Add a META.json to the distribution. Your buildtool should be able to autogenerate it.

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.

no_invalid_versions

Fix the version numbers so that version::is_lax($version) returns true.

Error:

  • lib/Vcf.pm: HASH(0x7bb64a0)

no_unauthorized_packages

Ask the owner of the distribution (the one who released it first, or the one who is designated in x_authority) to give you a (co-)maintainer's permission.

Error:

  • Vcf

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: Bio::Pipeline::Comparison::Exceptions

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
Bio::Pipeline::Comparison Comparative assesment of variant calling (CAVar) metacpan
Bio::Pipeline::Comparison::Exceptions Custom exceptions metacpan
Bio::Pipeline::Comparison::Generate::Evolve Take in a reference genome and evolve it. metacpan
Bio::Pipeline::Comparison::Generate::EvolvedSet Take in a reference genome and evolve it multiple times to produce multiple FASTA files and VCF files containing the differences to the original reference. metacpan
Bio::Pipeline::Comparison::Generate::VCFWriter Create a VCF with the differences between a reference and a single evolved genome. Outputs a gzipped VCF file and a tabix file. metacpan
Bio::Pipeline::Comparison::Report::InputParameters Take in a set of input parameters for the evalute pipeline functionality, validate them, then manipulate them into a usable set. metacpan
Bio::Pipeline::Comparison::Report::Overview Aggregate together the results of multiple VCF comparisons metacpan
Bio::Pipeline::Comparison::Report::ParseVCFCompare Take in the output of VCF compare and return details about intersection of variants. metacpan
Bio::Pipeline::Comparison::Types Moose types to use for validation metacpan
Bio::Pipeline::Comparison::Validate::Executable Validates the executable is available in the path before running it metacpan
FaSlice FaSlice.pm from VCFTools metacpan
Vcf Vcf.pm from VCFTools metacpan

Provides

Name File View
Vcf3_2 lib/Vcf.pm metacpan
Vcf3_3 lib/Vcf.pm metacpan
Vcf4_0 lib/Vcf.pm metacpan
Vcf4_1 lib/Vcf.pm metacpan
VcfReader lib/Vcf.pm metacpan

Other Files

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