some more README tweaks

[bioperl-live.git] / Changes

---------------------------------------------------------
Revision history for BioPerl core modules
---------------------------------------------------------
The comprehensive history and ongoing development of BioPerl:

   http://github.com/bioperl/bioperl-live

Some of that history is also highlighted on our wiki:

   http://www.bioperl.org/wiki/Change_log
   http://www.bioperl.org/wiki/History_of_BioPerl

Bugs and requested features list:

   https://redmine.open-bio.org/projects/bioperl

CPAN releases are branched from 'master'.
---------------------------------------------------------

1.6.910

    [New features]

    * Hash randomization fixes for perl 5.18.x
      - Note: at least one module (Bio::Map::Physical) still has a failing test;
        this is documented in bug #3446 and has been TODO'd; we will be pulling
        Bio::Map and similar modules out of core into separate distributions in the
        1.7.x release series [cjfields]

    [New features]

    * Bio::Seq::SimulatedRead
        - New module to represent reads taken from other sequences [fangly]
    * Bio::Tools::IUPAC
        - New regexp() method to create regular expressions from IUPAC sequences
          [fangly]
    * Bio::SeqFeature::Primer and Bio::Seq::PrimedSeq:
        - Code refresh [fangly]
    * Bio::DB::Taxonomy
        - Added support for the Greengenes and Silva taxonomies [fangly]
    * Bio::Tree::TreeFunctionsI
        - get_lineage_string() represents a lineage as a string [fangly]
        - add_trait() returns instead of reporting an error when the column
          number is exceeded in add_trait() [fangly]
        - Option to support tree leaves without trait [fangly]
        - Allow ID of 0 in trait files [fangly]
    * Bio::DB::Taxonomy::list
        - Misc optimizations [fangly]
        - Option -names of get_taxon() to help with ambiguous taxa [fangly]
    * Bio::DB::Taxonomy::*
        - get_num_taxa() returns the number of taxa in the database [fangly]
    * Bio::DB::Fasta and Bio::DB::Qual
        - support indexing an arbitrary list of files [fangly]
        - user can supply an arbitrary index file name [fangly]
        - new option to remove index file at the end [fangly]
    * Bio::DB::Fasta
        - now handles IUPAC degenerate residues [fangly]
    * Bio::PrimarySeq and Bio::PrimarySeqI
        - speed improvements for large sequences [Ben Woodcroft, fangly]
    * Bio::PrimaryQual
        - tightened and optimized quality string validation [fangly]
    * Bio::SeqIO::fasta
        - new method and option 'block', to create FASTA output with space
          intervaled blocks (similar to genbank or EMBL) has been implemented.
        - package variables $WIDTH and $DEFAULT_SEQ_ID_TYPE have been removed
          in favour of the methods 'width' and 'preferred_id_type` respectively.
    * Bio::FeatureIO::*
        - moved from bioperl-live into the separate distribution Bio-FeatureIO
    * Bio::SeqFeature::Annotated
        - moved from bioperl-live into the separate distribution Bio-FeatureIO
    * Bio::Cluster::SequenceFamily
        - improved performance when using get_members with overlapping multiple
          criteria
    * Bio::SearchIO::hmmer3
        - now supports nhmmer [bosborne]

    [Bug fixes]

    * [3302] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse
      multi-query hmmer output [Francisco J. Ossandon, Paul Cantalupo]
    * [3421] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse an HSP
      with a line full of dashes [Francisco J. Ossandon, Paul Cantalupo]
    * [3298] Fix bug in Bio::SearchIO::blast.pm where algorithm version
      information was lost in a multi-result blast file [Paul Cantalupo]
    * [3343] Fix bug in Bio::SearchIO::blasttable.pm to correctly calculate
      total gaps [Paul Cantalupo]
    * [3375] Fix DBLINK parsing bug in Bio::SeqIO::genbank.pm [Paul Cantalupo]
    * [3376] Fix bug in Bio::SearchIO::hmmer2.pm to correctly handle case
      when end of domain indicator is split across lines [Paul Cantalupo]
    * [3240] Bio::AlignIO::stockholm now parses simple sequences [Bernd Web,
      cjfields]
    * [3237] Bio::DB::Fasta now allows blank lines between sequences, catches
      instances where blank lines are within sequences [cjfields]
    * Bio::DB::Fasta reports correct alphabet for files with multiple sequence
      types [fangly]
    * Bio::DB::Fasta rev-comps sequences other than DNA properly [fangly]
    * [3238] Fixes for Bio::DB::SeqFeature::Store::DBI::Pg [Thomas Burkhard,
      cjfields]
    * Various fixes for Stockholm file indexing and processing [bosborne]
    * Fix edge case in FASTQ parsing where sequence of length 1 and qual of 0
      breaks parsing [cjfields]
    * Fix case where Bio::Seq::Meta* objects with no meta information could not
      be reverse-complemented [fangly]
    * Fix bug for fields without aliases in Bio::DB::Query::HIVQuery [fangly]
    * Fix Bio::PopGen::IO::phase: sort values lexically instead of numerically
      when unsure that values will be numerical [fangly]
    * Fix undef warnings in Bio::SeqIO::embl [fangly]
    * Fix undef warnings in Bio::DB::Fasta and Bio::DB::Qual [fangly]
    * Fix Bio::Tools::IUPAC should accept any sequence object [fangly]
    * Fix for 'Inappropriate ioctl' in Bio::DB::Store::berkeleydb3 [Olivier
      Sallou]
    * Bio::SeqFeature::Generic SeqfeatureI compliance: methods primary_tag,
      source_tag and display_name must return a string, not undef [fangly]
    * Bio::SimpleAlign and Bio::Seq compliance with Bio::FeatureHolderI
      add_SeqFeature takes a single argument [fangly]
    * Use cross-platform filenames and temporary directory in
      Bio::DB::Taxonomy::flatfile [fangly]
    * Fix bug in Bio::DB::Taxonomy::list where taxa with no ancestors were not
      properly identified as existing taxa in the database [fangly]
    * Fix issue where a Bio::DB::Taxonomy::list object could not be created
      without also passing a lineage to store [fangly]
    * Prevent passing a directory to the gi2taxid option (-g) of
      bp_classify_hits_kingdom.pl and remove an 'earlier declaration' warning
      [fangly]
    * Fixed bp_genbank2gff3.pl crash when missing source feature date [fangly]
    * Bio::PrimarySeq constructor -direct works for -seq or -ref_to_seq [fangly]
    * Bio::Cluster::SequenceFamily - checks if the sequence has a Bio::Species
      object before trying to access, and no longer returns repeated sequences.


1.6.901 May 18, 2011

    [Notes]

    * Use of AcePerl is deprecated; Ace.pm isn't actively maintained, and
      modules using Ace will also be deprecated [lds, cjfields]
    * Minor bug fix release
    * Bio::SeqIO::gbxml tests require XML::SAX [hartzell]
    * Address Build.PL issues when DBI is not present [hartzell]
    * Skip gbxml.t and Interpro tests when modules not installed [cjfields]
    * Remove deprecated code for perl 5.14.0 compat [cjfields]
    * Due to schema changes and lack of support for older versions, support
      for NeXML 0.9 is only (very) partially implemented.
      See: https://redmine.open-bio.org/issues/3207

    [Bug fixes]

    * [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
      docs [genehack, cjfields]
    * $VERSION for CPAN/cpanm-based installs was broken; force setting of
      module version from dist_version (probably not the best way to do this,
      but it seems to work) [rbuels, cjfields]


1.6.900 April 14, 201

    [Notes]

    * This will probably be the last release to add significant features to
      core modules; subsequent releases will be for bug fixes alone.
      We are planning on a restructuring of core for summer 2011, potentially
      as part of the Google Summer of Code.  This may become BioPerl 2.0.
    * Version bump represents 'just prior to v 1.7'.  We may have point
      releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc.
      This code essentially is what is on the github master branch.

    [New features]

    * Core code updated for perl 5.12.x [cjfields, Charle Tilford]
    * Bio::Tree refactor
        - major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs
        - removal of Scalar::Util::weaken code, which was causing odd headaches
          with premature GC, memory leaks with perl 5.10.0, etc [cjfields]
    * Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain,
          many others]
    * Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
          [Warren Kretzschmar]
    * Bio::SeqIO::gbxml
        - bug 2515 - new contribution [Ryan Golhar, jhannah]
    * Bio::Assembly::IO
        - support for reading Maq, Sam and Bowtie files [maj]
        - support for reading 454 GS Assembler (Newbler) ACE files [fangly]
        - bug 2483: support for writing ACE files [Joshua Udall, fangly]
        - bug 2599: support DBLINK annotation in GenBank files [cjfields]
        - bug 2726: reading/writing granularity: whole scaffold or one contig
          at a time [Joshua Udall, fangly]
    * Bio::OntologyIO
        - Added parsing of xrefs to OBO files, which are stored as secondary
            dbxrefs of the cvterm [Naama Menda]
        - General Interpro-related code refactors [dukeleto, rbuels, cjfields]
    * PAML code updated to work with PAML 4.4d [DaveMessina]

    [Bug fixes]

    * [3198] - sort tabular BLAST hits by score [DaveMessina]
    * [3196] - fix invalid metadata produced by latest Module::Build [cjfields]
    * [3190] - RemoteBlast GAPCOSTS regex fix [Ali Walsh, cjfields]
    * [3185] - Bio::Tools::SeqStats->get_mol_wt now gives correct MW
               [cjfields]
    * [3178] - fix tr/// issue in Bio::Range [Andrew Conley, cjfields]
    * [3172] - Bio::DB::Fasta - catch possibly bad FASTA files [cjfields]
    * [3164] - TreeFunctionsI syntax  bug [gjuggler]
    * [3163] - AssemblyIO speedup [fangly]
    * [3160] - Bio::SearchIO::Writer::TextResultWriter output [Paul Cantalupo,
               hyphaltip]
    * [3159] - add SwissPfam support to bp_index.PLS [hyphaltip]
    * [3158] - fix EMBL file mis-parsing [cjfields]
    * [3157] - Bio::Restriction::Analysis 'sizes' method fixed [Marc Perry,
               cjfields]
    * [3153] - fix SeqIO::swiss TagTree issues [Charles Tilford, cjfields]
    * [3148] - URL change for UniProt [cjfields]
    * [3145] - AXT off-by-1 error [Aaron Goodman, cjfields]
    * [3136] - HMMer3 parser fixes [kblin]
    * [3126] - catch description [Toshihiko Akiba]
    * [3122] - Catch instances where non-seekable filehandles were being
               seek'd w/o checking for status [Stefan Kirov, Roy Chaudhuri]
    * [3121] - Bio::OntologyIO cannot parse the full InterPro XML file
               [dukeleto, rbuels, cjfields]
    * [3120] - bp_seqfeature_gff3.pl round-trip fixes [genehack, David Breimann,
               jhannah]
    * [3116,3117] - perl 5.12.x warnings fixed [cjfields, Charles Tilford]
    * [3110] - Better 'namespace' support for bp_seqfeature_load.PLS [dbolser,
               cjfields]
    * [3107] - BLAST alignment column_from_residue_number() [cjfields]
    * [3104] - Bio::Species single node hierarchies [Charles Tilford, cjfields]
    * [3092, 3090] - parsing of BLAST HSP stats [Razi Khaja, cjfields]
    * [3089] - HSPTableWriter missing methods [Robson de Souza, cjfields]
    * [3086] - EMBL misparsing long tags [kblin, cjfields]
    * [3085] - CommandExts and array of files [maj, hyphaltip]
    * [3077] - Bio::SimpleAlign slice() now correctly computes seq coordinates
               for alignment slices [Ha X. Dang, cjfields]
    * [3076] - XMFA alignment strand wrong [Ha X., cjfields]
    * [3073] - fix parsing of GenBank files from RDP [cjfields]
    * [3068] - FASTQ parse failure with trailing 0 [cjfields]
    * [3064] - All-gap midline BLAST report issues [cjfields]
    * [3063] - BLASt report RID [Razi Khaja, cjfields]
    * [3058] - SearchIO::fasta parsing [DaveMessina, cjfields]
    * [3053] - LOCUS line formatting [M. Wayne, cjfields]
    * [3039] - correct Newick output root node branch length [gjuggler,
               DaveMessina]
    * [3038] - SELEX alignment error [Bernd, cjfields]
    * [3033] - PrimarySeq ID setting [Bernd, maj]
    * [3032] - Fgenesh errors [Wes Barris, hyphaltip]
    * [3034] - AlignIO::clustal output [Bernd, DaveMessina]
    * [3031] - Parse algorithm ref for BLAST [Razi Khaja, cjfields]
    * [3028] - Bio::TreeIO::nexus and FigTree compat [Kevin Balbi, cjfields]
    * [3025] - Bio::SeqIO::embl infinite loop [Adam Sjøgren, cjfields]
    * [3040, 3023, 2974, 2921, 2753, 2636, 2482] - PAML parser fixed, works with
               PAML 4.4d [DaveMessina]
    * [3015, 3022] - Bio::Restriction withrefm regexp [Emmanuel Quevillon,
               DaveMessina]
    * [3020] - GFF3Loader alias attribute [Nathan Weeks, cjfields]
    * [3018, 3019, 3021] - gmap_f9 parsing [Kiran Mukhyala, cjfields]
    * [3017] - using threads with Bio::DB::GenBank [cjfields]
    * [3012] - Bio::Root::HTTPget fixes [maj, cjfields]
    * [3011] - namespace support for SF::Store::DBI::Pg [Adam Witney, cjfields]
    * [3002] - Bio::DB::EUtilities NCBI policy updates [cjfields]
    * [3001] - seq identifier '0' dropped with FASTA [Michael Kuhn, maj]
    * [2984] - let LocatableSeq decide on length of phylip aln [Adam Witney,
               cjfields]
    * [2983] - fix score/percent ID mixup [Alexie Papanicolaou]
    * [2977] - TreeIO issues [DaveMessina]
    * [2959] - Bio::SeqUtils->revcom_with_features [Roy Chaudhuri, maj]
    * [2944] - Bio::Tools::GFF score [cjfields]
    * [2942] - correct MapTiling output [maj]
    * [2939] - PDB residue insertion codes [John May, maj]
    * [2930] - PrimarySeqI term symbol [Adam Sjøgren, maj]
    * [2928] - GuessSeqFormat raw [maj]
    * [2926] - Bio:Tools::TandemRepeatsFinder seq_id [takadonet, cjfields]
    * [2922] - open() directive issue [cjfields]
    * [2915] - GenBank parser infinite loop [Francisco Ossandon, cjfields]
    * [2901] - DNAStatistics div by zero error [Janet Young, cjfields]
    * [2899] - SeqFeature::Store host issues [lstein, dbolser]
    * [2897] - Add a "mask_below_threshold" method to Seq::Quality [dbolser,
               cjfields]
    * [2881] - .scf files don't' roundtrip [Adam Sjøgren, cjfields]
    * [2876] - CDD search with RemoteBlast [Malcolm Cook]
    * [2863] - Root::IO::_initialize_io causes crash [rbuels, maj, DaveMessina]
    * [2845] - Bio::Seq::Quality gives seq with no ID [Tristan Lefebure, cjfields]
    * [2843] - FeatureIO BED to GFF fails w/ no phase [cassjm cjfields]
    * [2773] - Bio::Tree::Node premature GC [Morgan Price, cjfields]
    * [2764] - add ID Tracker helper for SwissProt [heikki, cjfields]
    * [2758] - Bio::AssemblyIO ace problems [fangly]
    * [2744] - Bio::LocatableSeq::end [Bernd, cjfields]
    * [2726] - ace file IO [Josh, fangly]
    * [2700] - Refactor Build.PL [cjfields]
    * [2673] - addition of simple Root-based clone() method [cjfields]
    * [2648] - Bio::Assembly::Scaffold->get_all_seq_ids [dbolser, fangly]
    * [2599] - support for DBLINK annotation in GenBank files [cjfields]
    * [2594] - Bio::Species memory leak [cjfields]
    * [2515] - GenBank XML parser [jhannah]
    * [2499] - Method "pi" in package Bio::PopGen::Statistics [hyphaltip]
    * [2483] - Bio::Assembly::IO::ace write_assembly implemented [fangly]
    * [2350] - ID consistency btwn Bio::SeqI, Bio::Align::AlignI [fangly,
               cjfields]
    * [1572] - no docs Bio::Location::Simple/Atomic::trunc [hyphaltip]

    [Deprecated]

    * Bio::Expression modules - these were originally designed to go with the
      bioperl-microarray suite of tools, however they have never been completed
      and so have been removed from the distribution.  The original code has
      been moved into the inactive bioperl-microarray suite. [cjfields]

    [Other]

    * Repository moved from Subversion (SVN) to
      http://github.com/bioperl/bioperl-live [cjfields]
    * Bug database has moved to Redmine (https://redmine.open-bio.org)
    * Bio::Micrarray - the tools developed for ReSeq chip analysis by Marian
      Thieme have been moved to their own distribution (Bio-Microarray).
      [cjfields]

1.6.1   Sept. 29, 2009 (point release)
    * No change from last alpha except VERSION and doc updates [cjfields]

1.6.0_6 Sept. 27, 2009 (sixth 1.6.1 alpha)
    * Fix for silent OBDA bug related to FASTA validation [cjfields]

1.6.0_5 Sept. 27, 2009 (fifth 1.6.1 alpha)
    * Possible fix for RT 49950 (Strawberry Perl installation) [cjfields]
    * [RT 50048] - removed redundant VERSION, which was borking CPANPLUS
      [cjfields]
    * BioPerl.pod -> BioPerl.pm (Perl Best Practices) [cjfields]

1.6.0_4 Sept. 25, 2009 (fourth 1.6.1 alpha)
    * WinXP test fixes [cjfields, maj]
    * BioPerl.pod added for descriptive information, fixes CPAN indexing
      [cjfields]
    * Minor doc fixes [cjfields]

1.6.0_3 Sept. 22, 2009 (third 1.6.1 alpha)
    * Fix tests failing due to merging issues [cjfields]
    * More documentation updates for POD parsing [cjfields]

1.6.0_2 Sept. 22, 2009 (second 1.6.1 alpha)
    * Bio::Root::Build
        - fix YAML meta data generation [cjfields]

1.6.0_1 Sept. 15, 2009 (first 1.6.1 alpha)
    * Bio::Align::DNAStatistics
        - fix divide by zero problem [jason]
    * Bio::AlignIO::*
        - bug 2813 - fix faulty logic to detect end-of-stream [cjfields]
    * Bio::AlignIO::stockholm
        - bug 2796 - fix faulty logic to detect end-of-stream [cjfields]
    * Bio::Assembly::Tools::ContigSpectrum
        - function to score contig spectrum [fangly]
    * Bio::DB::EUtilities
        - small updates [cjfields]
    * Bio::DB::Fasta
        - berkeleydb database now autoindexes wig files and locks correctly
          [lstein]
    * Bio::DB::HIV
        - various small updates for stability; tracking changes to LANL
          database interface [maj]
    * Bio::DB::SeqFeature (lots of updates and changes)
        - add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain]
        - bug 2835 - patch [Dan Bolser]
        - bug RT 44535 - patch FeatureFileLoader [Cathy Gresham]
    * Bio::DB::SwissProt
        - bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders]
    * Bio::Factory::FTLocationFactory
        - mailing list bug fix [cjfields]
    * Bio::LocatableSeq
        - performance work on column_from_residue_number [hartzell]
    * Bio::Matrix::IO::phylip
        - bug 2800 - patch to fix phylip parsing [Wei Zou]
    * Bio::Nexml
        - Google Summer of Code project from Chase Miller - parsers for Nexml
          file format [maj, chmille4]
    * Bio::PopGen
        - Make Individual, Population, Marker objects AnnotatableI [maj]
        - simplify LD code [jason]
    * Bio::RangeI
        - deal with empty intersection [jason]
    * Bio::Restriction
        - significant overhaul of Bio::Restriction system: complete support for
          external and non-palindromic cutters. [maj]
    * Bio::Root::Build
        - CPANPLUS support, no automatic installation [sendu]
    * Bio::Root::IO
        - allow IO::String (regression fix) [cjfields]
        - catch unintentional undef values [cjfields]
        - throw if non-fh is passed to -fh [maj]
    * Bio::Root::Root/RootI
        - small debugging and core fixes [cjfields]
    * Bio::Root::Test
        - bug RT 48813 - fix for Strawberry Perl bug [kmx]
    * Bio::Root::Utilities
        - bug 2737 - better warnings [cjfields]
    * Bio::Search
        - tiling completely refactored, HOWTO added [maj]
          NOTE : Bio::Search::Hit::* classes do not use this code directly; we
          will deprecate usage of the older tiling code in the next BioPerl
          release
        - small fixes [cjfields]
    * Bio::SearchIO
        - Infernal 1.0 output now parsed [cjfields]
        - new parser for gmap -f9 output [hartzell]
        - bug 2852 - fix infinite loop in some output [cjfields]
        - blastxml output now passes all TODO tests [cjfields]
        - bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
        - RT 44782 - GbrowseGFF writer now catches evalues [Allen Day]
        - bug 2575 - add two columns of additional output to HSPTableWriter [cjfields]
    * Bio::Seq::LargePrimarySeq
        - delete tempdirs [cjfields]
        - bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
    * Bio::Seq::Quality
        - extract regions based on quality threshold value [Dan Bolser, heikki]
        - bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi)
    * Bio::SeqFeature::Lite
        - various Bio::DB::SeqFeature-related fixes [lstein]
    * Bio::SeqFeature::Tools::TypeMapper
        - additional terms for GenBank to SO map [scain]
    * Bio::SeqIO::chadoxml
        - bug 2785 - patch to get this working for bp_seqconvert [cjfields]
    * Bio::SeqIO::embl
        - support for CDS records [dave_messina, Sylvia]
    * Bio::SeqIO::fastq
        - complete refactoring to handle all FASTQ variants, perform validation,
          write output. API now conforms with other Bio* parsers and the rest of
          Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
          [cjfields]
    * Bio::SeqIO::genbank
        - bug 2784 - fix DBSOURCE issue [Phillip Garland]
        - bug RT 44536 - support for UniProt/UniProtKB tests [cjfields]
    * Bio::SeqIO::largefasta
        - parser returns a Bio::Seq::LargePrimarySeq [jhannah]
    * Bio::SeqIO::raw
        - add option for 'single' and 'multiple'
    * Bio::SeqIO::scf
        - bug 2881 - fix scf round-tripping [Adam Søgren]
    * Bio::SeqUtils
        - bug 2766, 2810 - copy over tags from features, doc fixes [David
          Jackson]
    * Bio::SimpleAlign
        - bug 2793 - patch for add_seq index issue [jhannah, maj]
        - bug 2801 - throw if args are required [cjfields]
        - bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types
          [Tristan Lefebure, maj]
        - bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi]
        - fix POD and add get_SeqFeatures filter [maj]
    * Bio::Tools::dpAlign
        - add support for LocatableSeq [ymc]
        - to be moved to a separate distribution [cjfields, rbuels]
    * Bio::Tools::EUtilities
        - fix for two bugs from mail list [Adam Whitney, cjfields]
        - add generic ItemContainerI interface for containing same methods
          [cjfields]
    * Bio::Tools::HMM
        - fix up code, add more warnings [cjfields]
        - to be moved to a separate distribution [cjfields, rbuels]
    * Bio::Tools::Primer3
        - bug 2862 - fenceposting issue fixed [maj]
    * Bio::Tools::Run::RemoteBlast
        - tests for remote RPS-BLAST [mcook]
    * Bio::Tools::SeqPattern
        - bug 2844 - backtranslate method [rbuels, jhannah, bvecchi]
    * Bio::Tools::tRNAscanSE
        - use 'gene' and 'exon' for proper SO, ensure ID is unique [jason]
    * Bio::Tree::*
        - bug 2456 - fix reroot_tree(), added create_node_on_branch() [maj]
    * Bio::Tree::Statistics
        - several methods for calculating Fitch-based score, internal trait
          values, statratio(), sum of leaf distances [heikki]
    * Bio::Tree::Tree
        - bug 2869 - add docs indicating edge case where nodes can be
          prematurely garbage-collected [cjfields]
        - add as_text() function to create Tree as a string in specified format
          [maj]
    * Bio::Tree::TreeFunctionsI
        - bug 2877 - fix bug where bootstrap assigned to the wrong node [Tristan
          Lefebure, maj]
    * Bio::TreeIO::newick
        - fix small semicolon issue [cjfields]
    * scripts
        - update to bp_seqfeature_load for SQLite [lstein]
        - hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
        - fastam9_to_table - fix for MPI output [jason]
        - gccalc - total stats [jason]
    * General Stuff
        - POD cleanup re: FEEDBACK section [maj, cjfields]
        - cleanup or fix dead links [cjfields]
        - Use of no_* methods (indicating 'number of something') is deprecated
          in favor of num_* [cjfields]
        - lots of new tests for the above bugs and refactors [everyone!]
        - new template for Komodo text editor [cjfields]

1.6.0 Winter 2009
    * Feature/Annotation rollback
        - Problematic changes introduced prior to the 1.5 release have been
          rolled back. These changes led to subtle bugs involving operator
          overloading and interface methods.
        - Behavior is very similar to that for BioPerl 1.4, with tag values
          being stored generically as simple scalars. Results in a modest
          speedup.
    * Bio::Graphics
        - Split into a separate distribution on CPAN, primarily so development
          isn't reliant on a complete BioPerl release.
        - Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but
          is only available via Subversion (via bioperl-live main trunk)
    * Bio::Root::Test
        - Common test bed for all BioPerl modules
    * Bio::Root::Build
        - Common Module::Build-based subclass for all BioPerl modules
    * Bio::DB::EUtilities
        - Complete refactoring to split up parsing (Bio::Tools::EUtilities),
          parameter handling (Bio::Tools::EUtilities::EUtilParameters),
          and user agent request posting and retrieval
    * Test implementation and reorganization
        - Tests have been reorganized into groups based on classes or use
          cases.
        - Automated test coverage is now online:
          http://www.bioperl.org/wiki/Test_Coverage
        - After this release, untested modules will be moved into a
          separate developer distribution until tests can be derived.
          Also, new modules to be added are expected to have a test suite
          and adequate test coverage.

1.5.2 Developer release

    Full details of changes since 1.5.1 are available online at:
    http://www.bioperl.org/wiki/Change_log
    The following represents a brief overview of the most important changes.

    o Bio::Map
      - Overhaul. Brand new system fully allows markers to have multiple
        positions on multiple maps, and to have relative positions. Should be
        backward compatible.

    o Bio::Taxonomy
      - This module and all the modules in the Taxonomy directory now
        deprecated in favour of Bio::Taxon and Bio::Tree::Tree

    o Bio::DB::Taxonomy

      - Taxonomy.pm
        * get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().

        * New methods ancestor(), each_Descendent() and _handle_internal_id().

        * Allows for different database modules to create Bio::Taxon objects
          with the same internal id when the same taxon is requested from each.

      - flatfile.pm
        * get_Children_Taxids() is deprecated, superceded by each_Descendent().

        * No longer includes the fake root node 'root'; there are multiple roots
          now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm

      - entrez.pm
        * get_node() has new option -full

        * Caches data retrieved from website

    o Bio::Species
      - Now a Bio::Taxon. Carries out the species name -> specific name munging
        that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
        backward compatability in species() method.

    o Bio::Search and Bio::SearchIO
      - Overhaul. The existing system has been sped up via some minor changes
        (mostly gain-of-function to the API). Bio::PullParserI is introduced
        as a potential eventual replacment for the existing system, though as
        yet only a Hmmpfam parser exists written using it.


1.5.1 Developer release

    o Major problem with how Annotations were written out with
      Bio::Seq is fixed by reverting to old behavior for
      Bio::Annotation objects.

    o Bio::SeqIO

     - genbank.pm
       * bug #1871; REFLOOP' parsing loop, I changed the pattern to
         expect at l east 9 spaces at the beginning of a line to
         indicate line wrapping.

       * Treat multi-line SOURCE sections correctly, this defect broke
         both common_name() and classification()

       * parse swissprot fields in genpept file

       * parse WGS genbank records

     - embl.pm
        * Changed regexp for ID line. The capturing parentheses are
          the same, the difference is an optional repeated-not-semi-
          colon expression following the captured \S+. This means the
          regexp works when the division looks like /PRO;/ or when the
          division looks like /ANG ;/ - the latter is from EMBL
          repbase

        * fix ID line parsing: the molecule string can have spaces in
          it. Like: "genomic DNA"

     - swiss.pm: bugs  #1727, #1734

     - entrezgene.pm
        * Added parser for entrezgene ASN1 (text format) files.
          Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)

    o Bio::AlignIO

     -  maf.pm coordinate problem fixed

    o Bio::Taxonomy and Bio::DB::Taxonomy

     - Parse NCBI XML now so that nearly all the taxonomy up-and-down
       can be done via Web without downloading all the sequence.

    o Bio::Tools::Run::RemoteBlast supports more options and complies
      to changes to the NCBI interface. It is reccomended that you
      retrieve the data in XML instead of plain-text BLAST report to
      insure proper parsing and retrieval of all information as NCBI
      fully expects to change things in the future.

    o Bio::Tree and Bio::TreeIO

      - Fixes so that re-rooting a tree works properly

      - Writing out nhx format from a newick/nexus file will properly output
        bootstrap information.  The use must move the internal node labels over
        to bootstraps.
         for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
            $node->bootstrap($node->id);
            $node->id('');
         }
      - Nexus parsing is much more flexible now, does not care about
        LF.

      - Cladogram drawing module in Bio::Tree::Draw

      - Node height and depth now properly calculated

      - fix tree pruning algorithm so that node with 1 child gets merged

    o Graphics tweaks.  Glyph::xyplot improved.  Many other small-medium sized
      bugs and improvements were added, see Gbrowse mailing list for most of
      these.

    o Bio::DB::GFF partially supports GFF3.  See information about
      gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.

    o Better location parsing in Bio::Factory::FTLocationFactory -
      this is part of the engine for parsing EMBL/GenBank feature table
      locations.  Nested join/order-by/complement are allowed now

    o Bio::PrimarySeqI->translate now takes named parameters

    o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
      reconstruction) is now supported.  Parsing different models and
      branch specific parametes are now supported.

    o Bio::Factory::FTLocationFactory - parse hierarchical locations
      (joins of joins)

    o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
      for getter/setter functions

    o Bio::SearchIO

      - blast bug #1739; match scientific notation in score
        and possible e+ values

      - blast.pm reads more WU-BLAST parameters and parameters, match
        a full database pathname,

      - Handle NCBI WEB and newer BLAST formats specifically
        (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).

      - psl off-by-one error fixed

      - exonerate parsing much improved, CIGAR and VULGAR can be parsed
        and HSPs can be constructed from them.

      - HSPs query/hit now have a seqdesc field filled out (this was
        always available via $hit->description and
        $result->query_description

      - hmmer.pm can parse -A0 hmmpfam files

      - Writer::GbrowseGFF more customizeable.

    o Bio::Tools::Hmmpfam
      make e-value default score displayed in gff, rather than raw score
      allow parse of multiple records


1.5 Developer release

    o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
      provide Jukes-Cantor and Kimura pairwise distance methods,
      respectively.

    o Bio::AlignIO support for "po" format of POA, and "maf";
      Bio::AlignIO::largemultifasta is a new alternative to
      Bio::AlignIO::fasta for temporary file-based manipulation of
      particularly large multiple sequence alignments.

    o Bio::Assembly::Singlet allows orphan, unassembled sequences to
      be treated similarly as an assembled contig.

    o Bio::CodonUsage provides new rare_codon() and probable_codons()
      methods for identifying particular codons that encode a given
      amino acid.

    o Bio::Coordinate::Utils provides new from_align() method to build
      a Bio::Coordinate pair directly from a
      Bio::Align::AlignI-conforming object.

    o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
      Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
      web service using standard Pubmed query syntax, and retrieve
      results as XML.

    o Bio::DB::GFF has various sundry bug fixes.

    o Bio::FeatureIO is a new SeqIO-style subsystem for
      writing/reading genomic features to/from files.  I/O classes
      exist for BED, GTF (aka GFF v2.5), and GFF v3.  Bio::FeatureIO
      classes only read/write Bio::SeqFeature::Annotated objects.
      Notably, the GFF v3 class requires features to be typed into the
      Sequence Ontology.

    o Bio::Graph namespace contains new modules for manipulation and
      analysis of protein interaction graphs.

    o Bio::Graphics has many bug fixes and shiny new glyphs.

    o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
      indexing for HMMER reports and FASTA qual files, respectively.

    o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
      new objects that can be placed within a Bio::Map::MapI-compliant
      genetic/physical map; Bio::Map::Physical provides a new physical
      map type; Bio::MapIO::fpc provides finger-printed clone mapping
      import.

    o Bio::Matrix::PSM provide new support for postion-specific
      (scoring) matrices (e.g. profiles, or "possums").

    o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
      be instantiated without explicitly using Bio::OntologyIO.  This
      is possible through changes to Bio::Ontology::OntologyStore to
      download ontology files from the web as necessary.  Locations of
      ontology files are hard-coded into
      Bio::Ontology::DocumentRegistry.

    o Bio::PopGen includes many new methods and data types for
      population genetics analyses.

    o New constructor to Bio::Range, unions().  Given a list of
      ranges, returns another list of "flattened" ranges --
      overlapping ranges are merged into a single range with the
      mininum and maximum coordinates of the entire overlapping group.

    o Bio::Root::IO now supports -url, in addition to -file and -fh.
      The new -url argument allows one to specify the network address
      of a file for input.  -url currently only works for GET
      requests, and thus is read-only.

    o Bio::SearchIO::hmmer now returns individual Hit objects for each
      domain alignment (thus containing only one HSP); previously
      separate alignments would be merged into one hit if the domain
      involved in the alignments was the same, but this only worked
      when the repeated domain occured without interruption by any
      other domain, leading to a confusing mixture of Hit and HSP
      objects.

    o Bio::Search::Result::ResultI-compliant report objects now
      implement the "get_statistics" method to access
      Bio::Search::StatisticsI objects that encapsulate any
      statistical parameters associated with the search (e.g. Karlin's
      lambda for BLAST/FASTA).

    o Bio::Seq::LargeLocatableSeq combines the functionality already
      found in Bio::Seq::LargeSeq and Bio::LocatableSeq.

    o Bio::SeqFeature::Annotated is a replacement for
      Bio::SeqFeature::Generic.  It breaks compliance with the
      Bio::SeqFeatureI interface because the author was sick of
      dealing with untyped annotation tags.  All
      Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
      compliant, and accessible through Bio::Annotation::Collection.

    o Bio::SeqFeature::Primer implements a Tm() method for primer
      melting point predictions.

    o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
      InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.

    o Bio::Taxonomy::Node now implements the methods necessary for
      Bio::Species interoperability.

    o Bio::Tools::CodonTable has new reverse_translate_all() and
      make_iupac_string() methods.

    o Bio::Tools::dpAlign now provides sequence profile alignments.

    o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).

    o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
      parsers.

    o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
      for designing small inhibitory RNA.

    o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
      methods based on a distance matrix.

    o Bio::Tree::Statistics provides an assess_bootstrap() method to
      calculate bootstrap support values on a guide tree topology,
      based on provided bootstrap tree topologies.

    o Bio::TreeIO now supports the Pagel (PAG) tree format.

1.4 branch

1.4.1

  o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files

  o Bio::Graphics will work with gd1 or gd2

  o Bio::SearchIO
   - hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
     (RF lines alone)
   - blast.pm Parse multi-line query fields properly
   - small speed improvements to blasttable.pm and others

  o Bio::DB::Taxonomy has better support for hierarchy traversal so that
    Bio::Taxonomy::Node can be as simple as Bio::Species object while still
    supporting more complex queries


1.4. Stable major release

Since initial 1.2.0, 3000 separate changes have been made to make this release.

   o installable scripts

   o global module version from Bio::Root:Version

   o Bio::Graphics
      - major improvements; SVG support

   o Bio::Popgen
     - population genetics
     - support several population genetics types of questions.
     - Tests for statistical neutrality of mutations
       (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics.
       Tests of population structure (Wright's F-statistic: Fst) is in
       Bio::PopGen::PopStats. Calculating composite linkage
       disequilibrium (LD) is available in Bio::PopGen::Statistics as
       well.
     - Bio::PopGen::IO for reading in prettybase (SeattleSNPs)
       and csv (comma delimited formatted) data.

     - a directory for implementing population simulations has
       been added Bio::PopGen::Simulation and 2 simulations - a
       Coalescent and a simple single-locus multi-allele genetic drift
       simulation have been provided.  This replaces the code in
       Bio::Tree::RandomTree which has been deprecated until proper
       methods for generating random phylogenetic trees are
       implemented.

   o Bio::Restriction
      - new restrion analysis modules

   o Bio::Tools::Analysis
      - web based DNA and Protein analysis framework and several
        implementations

   o Bio::Seq::Meta
     - per residue annotable sequences

   o Bio::Matrix
      - Bio::Matrix::PSM - Position Scoring Matrix
      - Bio::Matrix::IO has been added for generalized parsing of
        matrix data.  Matrix::IO::scoring and Matrix::IO::phylip are
        initial implementations for parsing BLOSUM/PAM and Phylip
        Distance matricies respectively.  A generic matrix
        implementation for general use was added in
        Bio::Matrix::Generic.

   o Bio::Ontology
     - major changes

   o Bio:Tree

   o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
     - small inhibitory RNA

   o Bio::SeqFeature::Tools
     - seqFeature mapping tools
     - Bio::SeqFeature::Tools::Unflattener.pm
       -- deal with mapping GenBank feature collections into
          Chado/GFF3 processable feature sets (with SO term mappings)

   o Bio::Tools::dpAlign
     - pure perl dynamic programming sequence alignment
     - needs Bioperl-ext

   o new Bio::SearchIO formats
     - axt and psl:  UCSC formats.
     - blasttable: NCBI -m 8 or -m 9 format from blastall

   o new Bio::SeqIO formats
     - chado, tab, kegg, tigr, game
     - important fixes for old modules

   o Bio::AlignIO: maf

   o improved Bio::Tools::Genewise

   o Bio::SeqIO now can recongnize sequence formats automatically from
     stream

   o new parsers in Bio::Tools:
      Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,

   o Bio::DB::Registry bugs fixed
     - BerkeleyDB-indexed flat files can be used by the OBDA system
     - Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all
       used by the OBDA system

   o several new HOWTOs
     - SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat
       Databases

   o hundreds of new and improved files


   o
   o Bio::Tree::AlleleNode has been updated to be a container of
     an Bio::PopGen::Individual object for use in the Coalescent simulations.


1.2 Branch

1.2.3 Stable release update
    o Bug #1475 - Fix and add speedup to spliced_seq for remote location
                  handling.
    o Bug #1477 - Sel --> Sec abbreviation fixed
    o Fix bug #1487 where paring in-between locations when
      end < start caused the FTLocationFactory logic to fail.
    o Fix bug #1489 which was not dealing with keywords as an
      arrayref properly (this is fixed on the main trunk because
      keywords returns a string and the array is accessible via
      get_keywords).
    o Bio::Tree::Tree memory leak (bug #1480) fixed
      Added a new initialization option -nodelete which
      won't try and cleanup the containing nodes if this
      is true.
     o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed
       this was only present on the branch for the 1.2.1 and 1.2.2 series
       - Also merged main trunk changes to the branch which make
         newick -> nhx round tripping more effective (storing branch length
         and bootstrap values in same locate for NodeNHX and Node
         implementations.)  Fixes to TreeIO parsing for labeled internal
         also required small changes to TreeIO::nhx.  Improved
         tests for this module as well.
    o Bio::SearchIO
      - Fixed bugs in BLAST parsing which couldn't parse NCBI
        gapped blast properly (was losing hit significance values due to
        the extra unexpeted column).
      - Parsing of blastcl3 (netblast from NCBI) now can handle case of
        integer overflow (# of letters in nt seq dbs is > MAX_INT)
        although doesn't try to correct it - will get the negative
        number for you.  Added a test for this as well.
      - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report
        has no top-level family classification scores but does have scores and
        alignments for individual domains.
      - Parsing FASTA reports where ungapped percent ID is < 10 and the
        regular expression to match the line was missing the possibility of
        an extra space.  This is rare, which is why we probably did not
        catch it before.
      - BLAST parsing picks up more of the statistics/parameter fields
        at the bottom of reports.  Still not fully complete.
      - SearchIO::Writer::HTMLResultWriter and TextResultWriter
        were fixed to include many improvements and added flexiblity
        in outputting the files.  Bug #1495 was also fixed in the process.
     o Bio::DB::GFF
      - Update for GFF3 compatibility.
      - Added scripts for importing from UCSC and GenBank.
      - Added a 1.2003 version number.
     o Bio::Graphics
      - Updated tutorial.
      - Added a 1.2003 version number.
     o SeqIO::swiss Bug #1504 fixed with swiss writing which was not
       properly writing keywords out.
     o Bio::SeqIO::genbank
      - Fixed bug/enhancement #1513 where dates of
        the form D-MMM-YYYY were not parsed.  Even though this is
        invalid format we can handle it - and also cleanup the date
        string so it is properly formatted.
      - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed
        and written with Genbank format.  Similarly bug #1515 is fixed to
        parse in the ORIGIN text.
     o Bio::SeqIO::fasta, a new method called preferred_id_type allows you
       to specify the ID type, one of (accession accession.version
       display primary).  See Bio::SeqIO::preferred_id_type method
       documentation for more information.
     o Unigene parsing updated to handle file format changes by NCBI

1.2.2 Stable release update

    o A series of bug fixes of the Bio::OntologyIO dagflat-related parsers:
      - auto-discover ontology name
      - bug in parsing relationships when certain characters are in the term
      - fixed hard-coded prefix for term identifiers
      - various smaller issues

    o Fixed bug in Bio::Annotation::OntologyTerm of not implementing all
      of Bio::Ontology::TermI

    o brought the OBDA Registry code up to latest specs

    o Bio::DB::GenBank
      - eutils URL change
      - accession number retrieval fixed

    o Bio::SearchIO::blast - fix bug #1443 (missing last hits), parse megablast

    o Bio::SearchIO::Writer::(HTML|Text)ResultWriter fix bugs #1458,
      #1459 which now properly report alignment start/end info
      for translated BLAST/FASTA searches.

    o Bio::TreeIO::newick can parse labeled internal nodes

    o Bio::Tools::BPbl2seq can properly report strand info for HSPs
      for BLASTX if if you provide -report_type => 'BLASTX' when
      initializing a BPbl2seq object.  Bioperl 1.3 will have better
      support for bl2seq in the SearchIO system.

    o Bio::Root::IO support a -noclose boolean flag which will not
      close a filehandle upon object cleanup - useful when sharing
      a filehandle among objects.  Additionally code added s.t.
      STDOUT/STDIN/STDERR will never be closed by Root::IO cleanup.

    o Bio::Tools::Genemark bug #1435 fixed which was missing last prediction

    o Bio::SeqIO::genbank
      - bug #1456 fixed which generated extra sequence lines
      - write moltype correctly for genpept

1.2.1 Stable release update

    o Inclusion of WrapperBase, a needed component for StandAloneBlast

    o Addition from main trunk of Ontology objects, principly to allow
      BioSQL releases against 1.2.1

    o Fixes and cleanup of Bio::Coordinate modules

    o A fix to Bio::Index::EMBL allowing  retrieval of entries using
      the primary accession number

    o Other bug fixes, including bpindex GenBank fix

    o Bio::SeqIO::genbank bug #1389 fixed

1.2  Stable major release

    o More functionality added to Bio::Perl, the newbie module

    o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2
      Support for New Hampshire Extended (NHX) format parsing.

    o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome,
      Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight
      Hmmpfam parser.

    o New ontology parsing Bio::Ontology

    o Bug fixes in Bio::SearchIO for HMMer parsing, support for
      multi-report (mlib) fasta reports, support for waba and exonerate.

    o Bio::ClusterIO for parsing Unigene clusters

    o Bio::Assembly added for representing phrap and ace assembly clusters.

    o Rudimentary support for writing Chado XML (see
      GMOD project: www.gmod.org for more information)

    o Bio::Coordinate for mapping between different coordinate systems such
      as protein -> cDNA -> Exon -> DNA and back.  Useful for mapping
      features into different coordinate systems.

    o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries
      with the get_Stream_by_query method and supports the latest
      NCBI eutils interface.

    o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast
      object for extracting subsets of features : currently only
      supports extraction by location.

1.1.1 Developer release

    o Deprecated modules are now listed in the DEPRECATED file

    o New HowTo documents located in doc/howto describing
      a domain of Bioperl.

    o Note that bugs are now stored at redmine.open-bio.org/projects/bioperl/
      and all old bugs are searchable through the bugzilla interface.

    o Several reported bugs in Bio::Tools::Sigcleave and Bio::SimpleAlign
      have been addressed.

    o Support for Genewise parsing in Bio::Tools::Genewise

    o Start of Ontology framework with Bio::Ontology

    o Speedup to the Bio::Root::Root object method _rearrange.
      A global _load_module method was implemented to simplify the
      dynamic loading of modules ala Bio::SeqIO::genbank.  This
      method is now used by all the XXIO (AlignIO,TreeIO,SearchIO,SeqIO,
      etc).

    o Several performance improvements to sequence parsing in Bio::SeqIO.
      Attempt to speedup by reducing object creation overhead.

    o Bio::DB::GenBank and Bio::DB::GenPept use the NCBI's approved
      method for sequence retrieval with their E-utils CGI scripts.
      More work to support Entrez queries to their fullest is planned
      before 1.2 release.

    o Numerous fixes to Bio::SearchIO and sequence parsing (swissprot)

1.1 Developer release

    o Bio::Tools::Run has been broken off into a new pkg bioperl-run,
      this separation removes some of the complexity in our test suite
      and separates the core modules in bioperl from those that need
      external programs to run.

    o With latest ExtUtils::MakeMaker module installed SGI/IRIX should
      not run into trouble running the makefile

    o Bio::Location and Bio::SeqIO::FTHelper are fixed to properly
      read,create,and write locations for grouped/split locations
      (like mRNA features on genomic sequence).

    o Bio::Tools::Phlyo added for wrappers for parsing Molphy (protml)
      and PAML (codeml,aaml, etc) parsing.

    o Bio::Tree:: objects expanded to handle testing monophyly,
      paraphyly, least common ancestor, etc.

    o Bio::Coordinate for mapping locations from different coordinate spaces

    o Bio::SearchIO::waba added for parsing WABA, Bio::SearchIO::hmmer
      added for parsing hmmpfam and hmmsearch output.

    o Bio::SearchIO::Writer::TextResultWriter for outputting
      a pseudo-blast textfile format


1.0.2 Bug fix release

    o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided
      in this release will not work after December 2002 when NCBI
      shuts off the old Entrez cgi scripts.  We have already fixed
      on our main development branch and the functionality will be
      available in the next stable bioperl release (1.2) slated for
      Fall 2002.

    o Numerous parsing bugs in Bio::SearchIO::fasta found through
      testset by Robin Emig.  These were fixed as was the get_aln
      method in Bio::Search::HSP::GenericHSP to handle the extra
      context sequence that is provided with a FastA alignment.

    o Migrating differences between Bio::Search::XX::BlastXX to
      Bio::Search::XX::GenericXX objects.  This included mechanism
      to retrieve whole list of HSPs from Hits and whole list of Hits from
      Results in addition to the current next_XX iterator methods that
      are available.  Added seq_inds() method to GenericHSP which identifies
      indexes in the query or hit sequences where conserved,identical,gaps,
      or mismatch residues are located (adapted from Steve Chervitz's
      implementation in BlastHSP).

    o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release.
      Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.

    o Bio::Graphics glyph set improved and extended for GBrowse release

    o Bio::Tree::Tree get_nodes implementation improvement thanks
      to Howard Ross notice performance problem when writing out
      unbalanced trees.

    o Bio::Location::Fuzzy::new named parameter -loc_type became
      -location_type, Bio::Location::Simple::new named parameter
      -seqid becamse -seq_id.

    o Fixed major Bio::AlignIO::emboss parsing bug on needle output,
      was mis-detecting that gaps should be placed at the beginning of
      the alignment when the best alignment starts internally in the
      sequence.

1.0.1 Bug fix release

    o Minor bug fixes to Bio::DB:GFF.  Glyph sets improved.

    o Parser fixes in SearchIO blast, fasta for more complete WU BLAST
      and mixed (3.3 - 3.4) versions of FASTA.

    o Small API change to add methods for completeness across
      implementations of Bio::Search objects.  These new methods
      in the interface are implemented by the GenericXX object as well
      as the BlastXX objects.
        * Bio::Search::Result::ResultI
         - hits() method returns list of all Hits (next_hit is an
           iterator method)

        * Bio::Search::Hit::HitI
         - hsps() method returns list of all HSPs (next_hsp is an
           iterator method)

    o The Bio::SearchIO::Writer classes have been fixed to handle results
       created from either psiblast (Search::BlastXX objects) or
       blast|fasta|blastxml objects (Search::GenericXX objects).  More work
       has to be done here to make it work properly and will nee major
       API changes.

    o Bugs in Bio::Tools::HMMER fixed, including
       * #1178 - Root::IO destructor wasn't being called
       * #1034 - filter_on_cutoff now behaves properly

    o Bio::SeqFeature::Computation initialization args fixed and
      tests added.

    o Tests are somewhat cleaner, flat.t now properly cleans up after itsself,

    o Updated FAQ with more example based answers to typical questions

    o Bug #1202 was fixed which would improperly join together qual values
      parsed by Bio::SeqIO::qual when a trailing space was not present before
      the newline.

1.0.0 Major Stable Release

  This represents a major release of bioperl with significant
  improvements over the 0.7.x series of releases.

    o Bio::Tools::Blast is officially deprecated.  Please see
      Bio::SearchIO for BLAST and FastA parsing.

    o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
      Bio::LocationI objects as well as start/end.

    o Bio::Biblio contains modules for Bibliographic data.
      Bio::DB::Biblio contains the query modules.  Additionally one can
      parse medlinexml from the ebi bibliographic query service (BQS)
      system and Pubmed xml from NCBI.  See Martin Senger's
      documentation in Bio::Biblio for more information.

    o Bio::DB::Registry is a sequence database registry part of
      Open Bioinformatics Database Access.  See
      http://obda.open-bio.org for more information.

    o File-based and In-Memory Sequence caching is provided by
      Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
      local database.

    o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has
      been added by Lincoln Stein.

    o XEMBL SOAP service access in provided in Bio::DB::XEMBL.

    o A FAQ has been started and is included in the release to provide
      a starting point for frequent questions and issues.

0.9.3 Developer's release

    o Event based parsing system improved (SearchIO).  With parsers for
      XML Blast (blastxml), Text Blast (blast), and FASTA results (fasta).
      Additionally a lazy parsing system for text and html blast reports was
      added and is called psiblast (name subject to change in future releases).

    o Bio::Search objects improved and standardized with associated Interfaces
      written.  The concept of a search "Hit" was standardized to be called
      "hit" consistently and the use of "subject" was deprecated in all active
      modules.

    o Bio::Structure added (since 0.9.1) for Protein structure objects
      and PDB parser to retrieve and write these structures from data files.

    o Several important Bio::DB::GFF bug fixes for handling features that
      are mapped to multiple reference points.  Updated mysql adaptor
      so as to be able to store large (>100 megabase) chunks of DNA into
      Bio::DB::GFF databases.

0.9.2 Developer's release

    o Bio::Search and Bio::SearchIO system introduced for event based
      parsing of Blast,Fasta reports Bio::SearchIO supports ncbi BLAST
      in text and XML and FASTA reports in standard output format.

    o Bio::Tree and Bio::TreeIO for phylogenetic trees.  A Random tree
      generator is included in Bio::TreeIO::RandomTrees and a
      statistics module for evaluating.

    o Bio::DB::GFF, Lincoln Stein's GFF database suitable as a DB
      server for DAS servers.

    o Bio::Tools::BPlite is provides more robust parsing of BLAST
      files.  The entire BPlite system migrated to using Bio::Root::IO
      for the data stream.

    o Bio::Tools::Alignment for Consed and sequence Trimming
      functionality.

    o Bio::Structure for Protein structure information and parsing

    o Bio::DB::GenBank/Bio::DB::GenPept updated to new NCBI Entrez
      cgi-bin entry point which should be more reliable.

    o Bio::Map and Bio::MapIO for biological map navigation and a
      framework afor parsing them in.  Only preliminary work here.

    o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
      Future work will integrate Pise and allow submission of analysis on
      remote servers.

    o Bio::AnnotationCollectionI and Bio::Annotation::Collection
      introduced as new objects for handling Sequence Annotation
      information (dblinks, references, etc) and is more robust that
      previous system.

    o Bio::Tools::FASTAParser introduced.

    o Scripts from the bioperl script submission project and new
      scripts from bioperl authors are included in "scripts" directory.

    o Factory objects and interfaces are being introduced and are more
      strictly enforced.

    o Bio::Root::Root introduced as the base object while
      Bio::Root::RootI is now simply an interface.

    o Bio::DB::RefSeq provides database access to copy of the NCBI
      RefSeq database using the EBI dbfetch script.

0.9.0 Developer's release

    o perl version at least 5.005 is now required instead of perl 5.004

    o Bio::Tools::Run::RemoteBlast is available for running remote
      blast jobs at NCBI.

    o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs.

    o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene.
      Also added are related modules UTR3, UTR5, Exon, Intron,
      Promotor, PolyA and Transcript.

    o Speedup of translate method in PrimarySeq

    o Bio::SimpleAlign has new methods: location_from_column(), slice(),
      select(), dot(), get_seq_by_pos(), column_from_residue_number()

    o Various fixes to Variation toolkit

    o Bio::DB::EMBL provides database access to EMBL sequence data.
      Bio::DB::Universal provides a central way to point to indexes
      and dbs in a single interface.

    o Bio::DB::GFF - a database suitable for running DAS servers locally.

    o Bio::Factory::EMBOSS is still in design phase as is
      Bio::Factory::ApplicationFactoryI

    o Dia models for bioperl design are provided in the models/ directory

0.7.2 Bug fix release

    o documentation fixes in many modules - SYNOPSIS code verified
      to be runnable in many (but not all modules)

    o corrected MANIFEST file from 0.7.1 release

    o Bug fix in Bio::SeqIO::FTHelper to properly handle
      split locations

    o Bio::SeqIO::genbank
        * Correct parsing and writing of genbank format with protein data
        * moltype and molecule separation

    o Bio::SeqIO::largefasta fix to avoid inifinite loops

    o Bio::SimpleAlign fixed to correctly handle consensus
      sequence calculation

    o Bio::Tools::HMMER supports hmmer 2.2g

    o Bio::Tools::BPlite to support report type specific parsing.  Most
      major changes are not on the 0.7 branch.

    o Bio::Tools::Run::StandAloneBlast exists_blast() fixed and works
      with File::Spec

    o Bio::Variation::AAChange/RNAChange corrected labels and mutated alleles
        in several types of mutations:
        1.) AA level: deletion, complex
        2.) AA level: complex, inframe
        3.) RNA level: silent

    o  BPbl2seq parsing of empty reports will not die, but will return
       a valid, empty, Bio::SeqFeature::SimilarityFeature for
       $report->query() and $report->subject() methods.  So an easy
       way to test if report was empty is to see if
       $report->query->seqname is undefined.

0.7.1 Bug fix release

    o Better parsing of genbank/EMBL files especially fixing bugs
      related to Feature table parsing and locations on remote
      sequences.  Additionally, species name parsing was better.

    o Bio::SeqIO::genbank can parse now NCBI produced genbank database
      which include a number of header lines.

    o More strict genbank and EMBL format writing (corrected number of
      spaces where appropriate).

    o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS
      for related BPlite BUGS that are unresolved in this release.

    o Bio::DB::GenBank, Bio::DB::GenPept have less problems
      downloading sequences from NCBI via HTTP.  Bio::DB::SwissProt can
      use expasy mirrors or EBI dbfetch cgi-script.

    o A moderate number of documentation improvements were made as
      well to provide a better code synopsis in each module.


0.7  Large number of changes, including refactoring of the
     Object system, new parsers, new functionality and
     all round better system. Highlights are:


     o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
       Bio::Root::IO for I/O and file/handle capabilities.

     o Imported BPlite modules from Ian Korf for BLAST
       parsing. This is considered the supported BLAST parser;
       Bio::Tools::Blast.pm will eventually phase out due to lack of support.

     o Improved Sequence Feature model. Added complete location
       modelling (with fuzzy and compound locations).  See
       Bio::LocationI and the modules under Bio/Location.  Added
       support in Genbank/EMBL format parsing to completely parse
       feature tables for complex locations.

     o Moved special support for databanks etc to specialized modules under
       Bio/Seq/. One of these supports very large sequences through
       a temporary file as a backend.

     o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
       CDS retrieval and exon shuffling.

     o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF

     o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
       DB/GDB (the latter has platform-specific limitations).

     o New analysis parser framework for HT sequence annotation (see
       Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)

     o New Alignment IO framework

     o New Index modules (Swissprot)

     o New modules for running Blast within perl
       (Bio::Tools::Run::StandAloneBlast). Added modules for running
       Multiple Sequence Alignment tools ClustalW and TCoffee
       (Bio::Tools::Run::Alignment).

     o New Cookbook-style tutorial (see bptutorial.pl). Improved
       documentation across the package.

     o Much improved cross platform support. Many known incompatibilities
       have been fixed; however, NT and Mac do not work across the entire
       setup (see PLATFORMS).

     o Many bug fixes, code restructuring, etc. Overall stability and
       maintainability benefit a lot.

     o A total of 957 automatic tests


0.6.2

   There are very few functionality changes but a large
   number of software improvements/bug fixes across the package.

   o The EMBL/GenBank parsing are improved.

   o The Swissprot reading is improved. Swissprot writing
     is disabled as it doesn't work at all. This needs to
     wait for 0.7 release

   o BLAST reports with no hits are correctly parsed.

   o Several other bugs of the BLAST parser (regular expressions, ...)
     fixed.

   o Old syntax calls have been replaced with more modern syntax

   o Modules that did not work at all, in particular the Sim4
     set have been removed

   o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
     have improved compliance with interface specs and documentation

   o Mailing list documentation updated throughout the distribution

   o Most minor bug fixes have happened.

   o The scripts in /examples now work and have the modern syntax
     rather than the deprecated syntax


0.6.1  Sun April 2 2000

   o Sequences can have Sequence Features attached to them
        - The sequence features can be read from or written to
          EMBL and GenBank style flat files

   o Objects for Annotation, including References (but not
     full medline abstracts), Database links and Comments are
     provided

   o A Species object to represent nodes on a taxonomy tree
     is provided

   o The ability to parse HMMER and Sim4 output has been added

   o The Blast parsing has been improved, with better PSI-BLAST
     support and better overall behaviour.

   o Flat file indexed databases provide both random access
     and sequential access to their component sequences.

   o A CodonTable object has been written with all known
     CodonTables accessible.

   o A number of new lightweight analysis tools have been
     added, such as molecular weight determination.

    The 0.6 release also has improved software engineering

   o The sequence objects have been rewritten, providing more
     maintainable and easier to implement objects. These
     objects are backwardly compatible with the 0.05.1 objects

   o Many objects are defined in terms of interfaces and then
     a Perl implementation has been provided. The interfaces
     are found in the 'I' files (module names ending in 'I').

     This means that it is possible to wrap C/CORBA/SQL access
     as true "bioperl" objects, compatible with the rest of
     bioperl.

   o The SeqIO system has been overhauled to provide better
     processing and perl-like automatic interpretation of <>
     over arguments.

   o Many more tests have been added (a total of 172 automatic
     tests are now run before release).



0.05.1 Tue Jun 29 05:30:44 1999
        - Central distribution now requires Perl 5.004. This was
          done to get around 5.003-based problems in Bio/Index/*
          and SimpleAlign.
        - Various bug fixes in the Bio::Tools::Blast modules
          including better exception handling and PSI-Blast
          support. See Bio/Tools/Blast/CHANGES for more.
        - Fixed the Parse mechanism in Seq.pm to use readseq.
          Follow the instructions in README for how to install
          it (basically, you have to edit Parse.pm).
        - Improved documentation of Seq.pm, indicating where
          objects are returned and where strings are returned.
        - Fixed uninitialized warnings in Bio::Root::Object.pm
          and Bio::Tools::SeqPattern.pm.
        - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.

0.05  Sun Apr 25 01:14:11 1999
        - Bio::Tools::Blast modules have less memory problems
          and faster parsing. Webblast uses LWP and supports
          more functionality. See Bio/Tools/Blast/CHANGES for more.
        - The Bio::SeqIO system has been started, moving the
          sequence reformatting code out of the sequence object
        - The Bio::Index:: system has been started, providing
          generic index capabilities and specifically works for
          Fasta formatted databases and EMBL .dat formatted
          databases
        - The Bio::DB:: system started, providing access to
          databases, both via flat file + index (see above) and
          via http to NCBI
        - The scripts/ directory, where industrial strength scripts
          are put has been started.
        - Many changes - a better distribution all round.

0.04.4  Wed Feb 17 02:20:13 1999
        - Bug fixes in the Bio::Tools::Blast modules and postclient.pl
          (see Bio::Tools::Blast::CHANGES).
        - Fixed a bug in Bio::Tools::Fasta::num_seqs().
        - Beefed up the t/Fasta.t test script.
        - Small fix in Bio::Seq::type() (now always returns a string).
        - Changed Bio::Root::Utilities::get_newline_char() to
          get_newline() since it could return more than one char.
        - Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global.
        - Changed default timeout to 20 seconds (was 3).
        - Moved lengthy modification notes to the bottom of some files.
        - Fixed SimpleAlign write_fasta bug.
        - Beefed up SimpleAlign.t test

0.04.3  Thu Feb  4 07:48:53 1999
        - Bio::Root::Object.pm and Global.pm now detect when
          script is run as a CGI and suppress output that is only
          appropriate when running interactively.
        - Bio::Root::Err::_set_context() adds name of script ($0).
        - Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm
          regarding the use of the static objects via the qw(:obj) tag.
        - Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to
          CORE::reverse, avoiding Perl warnings.
        - Bug fixes in Bio::Tools::Blast modules (version 0.074) and
          example scripts (see Bio::Tools::Blast::CHANGES).
        - examples/seq/seqtools.pl no longer always warns about using
          -prot or -nucl command-line arguments; only when using the
          -debug argument.
        - Methods added to Bio::Root::Utilities: create_filehandle(),
          get_newline_char(), and taste_file() to generalize filehandle
          creation and autodetect newline characters in files/streams
          (see bug report #19).
        - Bio::Root::IOManager::read() now handles timeouts and uses
          Utilities::create_filehandle().
        - Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead
          of hardwiring in "\n".
        - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW

0.04.2  Wed Dec 30 02:27:36 1998
        - Bug fixes in Bio::Tools::Blast modules, version 0.073
          (see Bio::Tools::Blast::CHANGES).
        - Changed reverse calls in Bio/Seq.pm and Bio/UnivAln.pm
          to CORE::reverse (prevents ambiguous warnings with 5.005).
        - Appending '.tmp.bioperl' to temporary files created by
          Bio::Root::Utilities::compress() or uncompress() to
          make it easy to identify & cleanup these files as needed.
        - Developers: Created CVS branch release-0-04-bug from
          release-0-04-1. Before making bug fixes to the 0.04.1 release,
          be sure to cvs checkout this branch into a clean area.

0.04.1  Wed Dec 16 05:39:15 1998
        - Bug fixes in Bio::Tools::Blast modules, version 0.072
          (see Bio::Tools::Blast::CHANGES).
        - Compile/SW/Makefile.PL now removes *.o and *.a files
          with make clean.

0.04  Tue Dec  8 07:49:19 1998
        - Lots of new modules added including:
           * Ewan Birney's Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm,
             and Bio/Compile directory containing XS-linked C code for
             creating Smith-Waterman sequence alignments from within Perl.
           * Steve Chervitz's Blast distribution has been incorporated.
           * Georg Fuellen's Bio::UnivAln.pm for multiple alignment objects.
        - Bio/examples directory for demo scripts for all included modules.
        - Bio/t directory containing test suit for all included modules.
        - For changes specific to the Blast-related modules prior to
          incorporation in this central distribution, see the CHANGES
          file in the Bio/Tools/Blast directory.

0.01  Tue Sep  8 14:23:22 1998
        - original version from central CVS tree; created by h2xs 1.18