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pkgsrc/biology/bioperl/PLIST
wen 1538be2122 Update to 1.007001 
Upstream changes:
1.7.1 - "Election"

    [Bugs]

    * Minor release to incorporate fix for CPAN indexing, which
      prevented proper updates [cjfields]
    * Fix problem in managing Target attribute for gff3 [Jukes34]
    * Minor bug fixes related to NCBI HTTPS support [cjfields]

1.7.0 - "Disney"

    [New site]

    * We have migrated to Github Pages. This was actually planned, but the
      recent OBF server compromise forced our hand.

      Brian Osborne [bosborne] took this under his wing to move docs and has
      done a tremendous amount of work formatting the site and working out some
      of the idiosyncracies with the new Jekyll-based design.  Mark Jensen, Paul
      Cantalupo and Franscison Ossandon also helped.  Kudos!!

    * Similarly, the official issue tracker is now Github Issues.  This has
      been updated in the relevant documentation bits (we hope!)

    [Code changes]

    * Previously deprecated modules removed
      * Bio::Tools::Infernal, Bio::Tools::ERPIN, Bio::Tools::RNAMotif
    * Bio::DB::SeqHound has been removed due to the service no longer being
      available
    * Bio::Tools::Analysis::Protein::Mitoprot has been removed for security
      reasons due to the server no longer having a valid cert
    * Bio::EUtilities, Bio::Biblio are now separate releases on CPAN
    * Bio::Coordinate, Bio::SearchIO::blastxml,
      Bio::SearchIO::Writer::BSMLResultWriter are now separate releases to be
      added on CPAN

    [New features]

    * Docker instances of tagged releases are available! [hlapp]
    * NCBI HTTPS support [mjohnson and others]
    * Bio::SearchIO::infernal
      - Issue #131: added CMSEARCH parsing support for Infernal 1.1 [pcantalupo]
    * Bio::Search::HSP::ModelHSP
      - Added a 'noncanonical_string' method to retrieve the NC line from CMSEARCH
        reports [pcantalupo]
    * Bio::Search::Result::INFERNALResult
      - Added new module to represent features of Infernal reports [pcantalupo]
    * Bio::DB::Taxonomy SQLite option [cjfields]
    * WrapperBase quoted option values [majensen]
    * Various documentation fixes and updates [bosborne]

   [Bug Fixes]

    * Fixes in Bio::Root::Build to deal with META.json/yml for CPAN indexing [cjfields]
    * Bio::SeqFeature::Generic spliced_seq() bug fix [Eric Snyder, via bosborne]
    * NeXML parser fixes [fjossandon]
    * Bug fix for Bio::DB::SeqFeature memory adapter [lstein]
    * RT 103272 : SeqFeature database deletion skipped features with a decimal -
      Joshua Fortriede (Xenbase)
    * RT 98374: AlignIO issues with sequence names not correctly parsing - Xiaoyu Zhuo
    * Issue #70: CONTIG parsing in GenBank output fixed [fjossandon]
    * Issue #76: Circular genome fixes with Bio::Location::Split [fjossandon]
    * Issue #80: Fix lack of caching issue with Bio::DB::Taxonomy [fjossandon]
    * Issue #81: Small updates to make sure possible memory leaks are detected [cjfields]
    * Issue #84: EMBL format wrapping problem [nyamned]
    * Issue #90: Missing entries for translation tables 24 and 25 [fjossandon]
    * Issue #95: Speed up of Bio::DB::Fasta::subseq by using a compiled regex
      or compiled C code (when Inline::C is installed) [rocky]
    * Fix various Bio::Tools::Analysis remote server config problems [cjfields]
    * Added several missing 'Data::Stag' and 'LWP::UserAgent' requirements [fjossandon]
    * Added a workaround in Bio::DB::Registry to get Username in Windows [fjossandon]
    * For HMMer report parsing, changed "$hsp->bits" to return 0 instead of undef
      to be consistent with "$hit->bits" behaviour [fjossandon]
    * Fixed a bug in HMMer3 parsing, where an homology line ending in CS or RF
      aminoacids made "next_seq" confused and broke the parser [fjossandon]
    * Adjusted FTLocationFactory.pm to comply with current GenBank Feature Table
      Definition, so now "join(complement(C..D),complement(A..B))" is equivalent
      to "complement(join(A..B,C..D))" [fjossandon]
    * For the many many many fixes that weren't mentioned - blame the release guy!
2016-11-06 08:05:24 +00:00

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@comment $NetBSD: PLIST,v 1.4 2016/11/06 08:05:24 wen Exp $
share/examples/bioperl/Bio-DB-GFF/load_ucsc.pl
share/examples/bioperl/align/FastAlign.pl
share/examples/bioperl/align/align_on_codons.pl
share/examples/bioperl/align/aligntutorial.pl
share/examples/bioperl/align/clustalw.pl
share/examples/bioperl/align/simplealign.pl
share/examples/bioperl/bioperl.pl
share/examples/bioperl/cluster/dbsnp.pl
share/examples/bioperl/contributed/nmrpdb_parse.pl
share/examples/bioperl/contributed/prosite2perl.pl
share/examples/bioperl/contributed/rebase2list.pl
share/examples/bioperl/db/dbfetch
share/examples/bioperl/db/est_tissue_query.pl
share/examples/bioperl/db/gb2features.pl
share/examples/bioperl/db/getGenBank.pl
share/examples/bioperl/db/get_seqs.pl
share/examples/bioperl/db/rfetch.pl
share/examples/bioperl/db/use_registry.pl
share/examples/bioperl/generate_random_seq.pl
share/examples/bioperl/liveseq/change_gene.pl
share/examples/bioperl/longorf.pl
share/examples/bioperl/make_primers.pl
share/examples/bioperl/popgen/parse_calc_stats.pl
share/examples/bioperl/quality/svgtrace.pl
share/examples/bioperl/rev_and_trans.pl
share/examples/bioperl/revcom_dir.pl
share/examples/bioperl/root/README
share/examples/bioperl/root/exceptions1.pl
share/examples/bioperl/root/exceptions2.pl
share/examples/bioperl/root/exceptions3.pl
share/examples/bioperl/root/exceptions4.pl
share/examples/bioperl/searchio/blast_example.pl
share/examples/bioperl/searchio/custom_writer.pl
share/examples/bioperl/searchio/hitwriter.pl
share/examples/bioperl/searchio/hspwriter.pl
share/examples/bioperl/searchio/htmlwriter.pl
share/examples/bioperl/searchio/psiblast_features.pl
share/examples/bioperl/searchio/psiblast_iterations.pl
share/examples/bioperl/searchio/rawwriter.pl
share/examples/bioperl/searchio/resultwriter.pl
share/examples/bioperl/searchio/waba2gff.pl
share/examples/bioperl/searchio/waba2gff3.pl
share/examples/bioperl/sirna/TAG
share/examples/bioperl/sirna/rnai_finder.cgi
share/examples/bioperl/structure/structure-io.pl
share/examples/bioperl/subsequence.cgi
share/examples/bioperl/tk/gsequence.pl
share/examples/bioperl/tk/hitdisplay.pl
share/examples/bioperl/tools/extract_genes.pl
share/examples/bioperl/tools/gb_to_gff.pl
share/examples/bioperl/tools/gff2ps.pl
share/examples/bioperl/tools/parse_codeml.pl
share/examples/bioperl/tools/psw.pl
share/examples/bioperl/tools/reverse-translate.pl
share/examples/bioperl/tools/run_genscan.pl
share/examples/bioperl/tools/run_primer3.pl
share/examples/bioperl/tools/seq_pattern.pl
share/examples/bioperl/tools/standaloneblast.pl
share/examples/bioperl/tree/paup2phylip.pl
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