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Diff for: ‎.gitignore

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/tmp
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/lib/Bio/BPWrapper/pod2htmd.tmp
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Bio-BPWrapper-*.tar.gz
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META.json
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META.yml
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ChangeLog
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Makefile.PL
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t/check-data/*.err

Diff for: ‎.travis.yml

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@@ -5,7 +5,7 @@ sudo: true
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dist: bionic
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env:
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- PREREQS="Module::Build rlib Test::More Bio::Restriction::Analysis"
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- PREREQS="Module::Build rlib XML::DOM::XPath Test::More Bio::Restriction::Analysis"
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after_failure:
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- cat /home/travis/.cpanm/work/*/build.log
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- perl Build.PL && ./Build && ./Build test
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perl:
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# - "5.30"
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- "5.30"
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- "5.26"
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# - "5.26"
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# - "5.24"
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# - "5.22"
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# - "5.20"
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# - "5.18"
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# - "5.16"
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# - "5.14"
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- "5.26"
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- "5.24"
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- "5.22"
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- "5.20"
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- "5.18"
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- "5.16"
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- "5.14"

Diff for: ‎MANIFEST

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bin/bioaln
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bin/biodb
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bin/biopop
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bin/bioseq
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bin/biotree
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test-files/test-bioaln-pep2dna.aln
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test-files/test-bioaln-pep2dna.nuc
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test-files/test-bioaln.aln
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test-files/test-bioaln.aln.slice-142.aln
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test-files/test-bioaln.aln.slice-239.aln
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test-files/test-bioaln.aln.slice-258.aln
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test-files/test-bioaln.aln.slice-31.aln
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test-files/test-bioaln.aln.slice-67.aln
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test-files/test-bioaln.aln.slice-91.aln
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test-files/test-bioaln.cds
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test-files/test-biopop.fas
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test-files/test-bioseq-leadgap.fas
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test-files/test-biotree.dnd
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TODO.md
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META.json
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META.yml
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Makefile.PL
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META.json

Diff for: ‎MANIFEST.SKIP

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# We use Build.PL; having Makefile.PL messes things up
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Makefile.PL
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codon-info-sim.pl
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codon-info.pl
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Dockerfile
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test-files/BbB31.cutg
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test-files/blast.output
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test-files/test-bioseq.embl
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test-files/test-biotree.nhx

Diff for: ‎META.json

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{
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"abstract" : "wrappers of popular BioPerl classes (`Bio::SeqIO`, `Bio::Seq`, `Bio::AlignIO`, `Bio::SimpleAlign",
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"author" : [
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"Y. Hernandez",
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"P. Pagan",
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"G. Ramrattan",
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"W.-G. Qiu",
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"R. Bernstein"
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],
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"dynamic_config" : 1,
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"generated_by" : "Module::Build version 0.4231",
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"license" : [
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"perl_5"
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],
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"meta-spec" : {
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"url" : "http://search.cpan.org/perldoc?CPAN::Meta::Spec",
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"version" : 2
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},
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"name" : "Bio-BPWrapper",
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"prereqs" : {
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"build" : {
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"requires" : {
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"rlib" : "0.02"
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}
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},
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"configure" : {
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"requires" : {
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"Module::Build" : "0.4214"
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}
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},
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"runtime" : {
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"requires" : {
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"Bio::DB::GenBank" : "0",
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"Bio::Restriction::Analysis" : "0",
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"XML::DOM::XPath" : "0.14",
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"perl" : "v5.14.0",
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"rlib" : "0.02"
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}
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},
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"test" : {
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"requires" : {
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"Test::More" : "0.81",
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"rlib" : "0.02"
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}
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}
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},
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"provides" : {
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"Bio::BPWrapper" : {
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"file" : "lib/Bio/BPWrapper.pm",
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"version" : "1.13"
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},
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"Bio::BPWrapper::AlnManipulations" : {
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"file" : "lib/Bio/BPWrapper/AlnManipulations.pm"
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},
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"Bio::BPWrapper::PopManipulations" : {
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"file" : "lib/Bio/BPWrapper/PopManipulations.pm"
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},
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"Bio::BPWrapper::SeqManipulations" : {
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"file" : "lib/Bio/BPWrapper/SeqManipulations.pm",
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"version" : "1.0"
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},
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"Bio::BPWrapper::TreeManipulations" : {
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"file" : "lib/Bio/BPWrapper/TreeManipulations.pm"
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}
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},
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"release_status" : "stable",
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"resources" : {
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"bugtracker" : {
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"web" : "https://github.com/bioperl/bp-utils/issues"
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},
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"repository" : {
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"url" : "https://github.com/bioperl/bp-utils"
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}
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},
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"version" : "1.13",
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"x_serialization_backend" : "JSON::PP version 4.02"
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}

Diff for: ‎META.yml

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---
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abstract: 'wrappers of popular BioPerl classes (`Bio::SeqIO`, `Bio::Seq`, `Bio::AlignIO`, `Bio::SimpleAlign'
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author:
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- 'Y. Hernandez'
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- 'P. Pagan'
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- 'G. Ramrattan'
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- 'W.-G. Qiu'
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- 'R. Bernstein'
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build_requires:
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Test::More: '0.81'
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rlib: '0.02'
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configure_requires:
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Module::Build: '0.4214'
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dynamic_config: 1
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generated_by: 'Module::Build version 0.4231, CPAN::Meta::Converter version 2.150010'
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license: perl
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meta-spec:
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url: http://module-build.sourceforge.net/META-spec-v1.4.html
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version: '1.4'
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name: Bio-BPWrapper
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provides:
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Bio::BPWrapper:
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file: lib/Bio/BPWrapper.pm
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version: '1.13'
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Bio::BPWrapper::AlnManipulations:
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file: lib/Bio/BPWrapper/AlnManipulations.pm
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Bio::BPWrapper::PopManipulations:
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file: lib/Bio/BPWrapper/PopManipulations.pm
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Bio::BPWrapper::SeqManipulations:
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file: lib/Bio/BPWrapper/SeqManipulations.pm
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version: '1.0'
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Bio::BPWrapper::TreeManipulations:
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file: lib/Bio/BPWrapper/TreeManipulations.pm
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requires:
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Bio::DB::GenBank: '0'
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Bio::Restriction::Analysis: '0'
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XML::DOM::XPath: '0.14'
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perl: v5.14.0
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rlib: '0.02'
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resources:
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bugtracker: https://github.com/bioperl/bp-utils/issues
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repository: https://github.com/bioperl/bp-utils
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version: '1.13'
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x_serialization_backend: 'CPAN::Meta::YAML version 0.018'

Diff for: ‎lib/Bio/BPWrapper.pm

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package Bio::BPWrapper;
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our $VERSION = '1.12';
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our $VERSION = '1.13';
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use strict; use warnings;
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use 5.010;
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