Bio-Pipeline-Comparison 1.123050
- Released by
- AJPAGE
- Version
- Release Date
- 2012-10-31
- Kwalitee
- 134.38
- Core Kwalitee
- 90.62
- LINKS
Bio-Pipeline-Comparison 1.123050 Deleted
Kwalitee Issues
- has_changelog
-
Add a Changelog (best named 'Changes') to the distribution. It should list at least major changes implemented in newer versions.
- 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
- main_module_version_matches_dist_version
-
Make sure that the main module name and version are the same of the distribution.
- 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_meta_json
-
Add a META.json to the distribution. Your buildtool should be able to autogenerate it.
- 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: Bio::Pipeline::Comparison::Exceptions
- 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
- no_invalid_versions
-
Fix the version numbers so that version::is_lax($version) returns true.
Error:
- lib/Vcf.pm: HASH(0x5609d55e0f00)
- 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.
- has_security_doc
-
Add SECURITY(.pod|md). See Software::Security::Policy.
- security_doc_contains_contact
-
Add SECURITY(.pod|md) and add a contact address. See Software::Security::Policy.
- has_contributing_doc
-
Add CONTRIBUTING(.pod|md). See https://docs.github.com/en/communities/setting-up-your-project-for-healthy-contributions/setting-guidelines-for-repository-contributors.
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 |