CVS commit: pkgsrc/biology/bioperl

["Wen Heping" <wen%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   wen
Date:           Thu Jul 17 12:12:26 UTC 2014

Modified Files:
        pkgsrc/biology/bioperl: Makefile distinfo

Log Message:
Update to 1.6.924

Upstream changes:
1.6.924

    [Significant changes]

    * Bug/feature issue tracking has moved to GitHub Issues:
          https://github.com/bioperl/bioperl-live/issues
    * DB_File has been demoted from "required" to "recommended",
      which should make easier for Windows users to install BioPerl
      if they don't need that module.

    [New features]

    * Bio::Search::HSP::GenericHSP
        - Bug #3370, added a "posterior_string" method to retrieve the
          posterior probability lines (PP) from HMMER3 reports [fjossandon]
        - Added a "consensus_string" method to retrieve the consensus
          structure lines (CS|RF) from HMMER2 and HMMER3 reports when available 
[fjossandon]
    * Bio::SearchIO::hmmer2
        - The number of identical and conserved residues are now calculated
          directly from the homology line [fjossandon]
        - Now the Query Length and Hit Length are reported when the alignment
          runs until the end of the sequence/model ('.]' or '[]') [fjossandon]
        - Implemented the capture of the consensus structure lines [fjossandon]
    * Bio::SearchIO::hmmer3
        - The number of identical and conserved residues are now calculated
          directly from the homology line [fjossandon]
        - Now the Hit Length is reported when the alignment runs until the end
          of the sequence/model ('.]' or '[]') [fjossandon]
        - Implemented the capture of the consensus structure lines [fjossandon]
        - Implemented the capture of the posterior probability lines 
[fjossandon]
        - Completed the development of NHMMER parsing, including alignments 
[fjossandon]
    * Bio::SearchIO::SearchResultEventBuilder & 
Bio::SearchIO::IteratedSearchResultEventBuilder
        - Feature #2615, moved "_init_parse_params", "max_significance, 
"signif",
          "min_score", "min_bits, and "hit_filter" methods from
          'IteratedSearchResultEventBuilder' to parent 
'SearchResultEventBuilder'.
          This means that the Bio::SearchIO->new() parameters '-signif', 
'-score',
          '-bits' and '-hit_filter' will now work with other Bio::SearchIO 
formats
          besides Blast, instead of being ignored. Added tests for all moved 
methods
          using HMMER outputs and run the full test suite and everything pass 
[fjossandon]
    * Bio::SeqIO::MultiFile
        - Autodetection of file format [fangly]
    * Bio::Tools::GuessSeqFormat:
        - Format detection from non-seekable filehandles such as STDIN [fangly]

    [Bug fixes]

    * Fix problems when using Storable as backend for cloning [v1.6.x branch, 
tsibley]
    * Fix potential problems with Storable in Bio::DB::SeqFeature::Store 
[tsibley]
    * SeqFeature::Lite: Fixed wrong strand when using "+", "-", or "." 
[nathanweeks]
    * Abstract: Fixed ActivePerl incapability of removing temporary files
      because of problems closing tied filehandles [fjossandon]
    * IndexedBase: For Windows' ActivePerl, several LocalDB tests were failing
      because ActivePerl were producing a ".index.pag" and ".index.dir"
      files instead of a single ".index" file (like Strawberry Perl).
      Now those temporary files are correctly considered and deleted. 
[fjossandon]
    * Test files: Added missing module requirements (DB_File and Data::Stag)
      to several tests files that were failing because those modules were
      not present. Now those test files are correctly skipped instead. 
[fjossandon]
    * Blast: Added support to changes in bl2seq from BLAST+ output, which
      now uses "Subject=" instead of ">" to start hit lines [yschensandiego]
    * Phylip: Return undef in "next_aln" at file end to avoid
      an infinite loop [yschensandiego]
    * HMMER3: When a hit description is too long, it is truncated in
      the Scores table. In those cases, the more complete description from
      the Annotation line (>>) will be used [fjossandon]
    * GenericHSP: Added '.' to gap symbols in "_pre_gaps" (except for ERPIN),
      since it is now used by HMMER3 format in alignments [fjossandon]
    * GenericHit: Changed "frac_aligned_query" and "frac_aligned_hit"
      to return undef if the query/hit length is unknown (like in some
      HMMER outputs), to avoid division by 0 crashes. Also "query_length"
      now is set to 0 if its undefined, to be consistent with hit "length" 
[fjossandon]
    * HMMER: fixed many bugs in the parsing of Hmmer2 and Hmmer3 outputs,
      added support to multi-query reports, reduced code redundancy,
      and eliminated the automatic removal of hits below "inclusion threshold" 
[fjossandon]
    * [3369] - Fixed reported bugs in parse from HMMSEARCH3 reports [fjossandon]
    * [3446] - Fixed wrong marker position in Bio::Map::Physical [fjossandon]
    * [3455] - Fixed wrong print of DBLink in Genbank file [bosborne]
    * Fixed some Bio::Root::Utilities subroutines [fjossandon]
    * Double-quotes on paths are needed in some places [fjossandon]
    * [3453] - Allow multiple homologies and products in Entrezgene [fjossandon]
    * Use "NUL" instead of"/dev/null" when running in Windows [fjossandon]
    * Updated all files from Bio-Root, Bio-Coordinate and Bio-SearchIO-blastxml
      with the latest changes made in their own repositories [fjossandon]
    * General synching of files with the master branch [fjossandon]
    * Fixed tests failing in Windows because of using Linux commands 
[fjossandon]
    * Closed many open filehandles that prevented temporary files deletion 
[fjossandon]
    * Fixed broken MeSH parser [fjossandon]
    * Fixed missing detection of format in SeqIO when given a -string [fangly]


To generate a diff of this commit:
cvs rdiff -u -r1.28 -r1.29 pkgsrc/biology/bioperl/Makefile
cvs rdiff -u -r1.5 -r1.6 pkgsrc/biology/bioperl/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.