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Summary of important user-visible changes for BioPerl
-----------------------------------------------------
{{$NEXT}}
* The program bp_chaos_plot has been removed.
* GD is now no longer a dependency, suggestion or requirement.
1.7.6 2019-08-28 12:37:01+01:00 Europe/London
* The program bp_classify_hits_kingdom has been removed and is
now part of the examples documentation instead.
* GD is now listed as a suggestion instead of a requirement. The
bp_chaos_plot program will now work with the GD module.
* New method Bio::Tree::Statistics::transfer_bootstrap_expectation
to compute Transfer Bootstrap Expectation (TBE) for internal
nodes based on the methods outlined in Lemoine et al, Nature,
2018.
* New method Bio::SeqIO::fasta::next_seq_fast to retrieve next
sequence in the stream faster but not perfect.
1.7.5 2019-02-11 14:57:45+00:00 Europe/London
* The following modules have been removed from the BioPerl
distribution to be part of a separate distribution with
independent development:
Bio::Symbol::*
* The Bio::Seq::SeqWithQuality module, which was deprecated since
2001, was finally removed.
* The deprecated() method has been deprecated. It is recommended
to use Carp::carp to warn.
* The following methods have been deprecated for a long while and
have now been removed:
Bio::Align::AlignI->no_residues
Bio::Align::AlignI->no_sequences
Bio::LocatableSeq->no_gap
Bio::LocatableSeq->no_sequences
Bio::SeqFeature::Generic->slurp_gff_file
Bio::SimpleAlign->no_residues
Bio::SimpleAlign->no_sequences
1.7.4 2019-02-05 16:23:53+00:00 Europe/London
* Fix Bio::Root::Test, and the testuite, to properly check for
internet connection and the NO_NETWORK_TESTING environment
variable. Previously, tests that required internet connection
were not being skipped, causing tests to fail.
1.7.3 2019-01-30 13:30:34+00:00 Europe/London
* The following modules have been removed from the BioPerl
distribution to be part of a separate distribution. They have
been integrated into other module distributions for independent
development:
Bio::Align::Graphics
Bio::AlignIO::nexml
Bio::AlignIO::stockholm
Bio::Assembly::*
Bio::Cluster::*
Bio::ClusterI::*
Bio::ClusterIO::*
Bio::DB::Ace
Bio::DB::BioFetch
Bio::DB::CUTG
Bio::DB::EMBL
Bio::DB::EntrezGene
Bio::DB::Expression::*
Bio::DB::GFF
Bio::DB::GFF::Adaptor::*
Bio::DB::GFF::Aggregator::*
Bio::DB::GFF::Featname
Bio::DB::GFF::Feature
Bio::DB::GFF::Homol
Bio::DB::GFF::RelSegment
Bio::DB::GFF::Segment
Bio::DB::GFF::Typename
Bio::DB::GenBank
Bio::DB::GenPept
Bio::DB::HIV::*
Bio::DB::MeSH
Bio::DB::NCBIHelper
Bio::DB::Query::GenBank
Bio::DB::Query::HIVQuery
Bio::DB::RefSeq
Bio::DB::SeqFeature::*
Bio::DB::SeqVersion::*
Bio::DB::SwissProt
Bio::DB::TFBS::*
Bio::DB::Taxonomy::entrez
Bio::DB::Taxonomy::sqlite
Bio::DB::Universal
Bio::Draw::Pictogram
Bio::Factory::MapFactoryI
Bio::Index::Hmmer
Bio::Index::Stockholm
Bio::LiveSeq::*
Bio::Map::*
Bio::MapIO::*
Bio::MolEvol::CodonModel
Bio::Nexml::Factory
Bio::NexmlIO
Bio::Perl
Bio::Phenotype::*
Bio::PhyloNetwork::*
Bio::PopGen::*
Bio::Restriction::*
Bio::Root::Build
Bio::Search::HSP::HMMERHSP
Bio::Search::HSP::HmmpfamHSP
Bio::Search::Hit::HMMERHit
Bio::Search::Hit::HmmpfamHit
Bio::Search::Hit::hmmer3Hit
Bio::Search::Result::HMMERResult
Bio::Search::Result::HmmpfamResult
Bio::Search::Result::hmmer3Result
Bio::SearchDist
Bio::SearchIO::hmmer
Bio::SearchIO::hmmer2
Bio::SearchIO::hmmer3
Bio::SearchIO::hmmer_pull
Bio::SeqEvolution::*
Bio::SeqFeature::SiRNA::*
Bio::SeqIO::abi
Bio::SeqIO::agave
Bio::SeqIO::alf
Bio::SeqIO::chadoxml
Bio::SeqIO::chaos
Bio::SeqIO::chaosxml
Bio::SeqIO::ctf
Bio::SeqIO::entrezgene
Bio::SeqIO::excel
Bio::SeqIO::exp
Bio::SeqIO::flybase_chadoxml
Bio::SeqIO::lasergene
Bio::SeqIO::nexml
Bio::SeqIO::pln
Bio::SeqIO::strider
Bio::SeqIO::ztr
Bio::Structure::*
Bio::Taxonomy::*
Bio::Tools::AlignFactory
Bio::Tools::Analysis::* (except SimpleAnalysisBase)
Bio::Tools::Gel
Bio::Tools::HMMER::*
Bio::Tools::Hmmpfam
Bio::Tools::Phylo::Gumby
Bio::Tools::Protparam
Bio::Tools::Run::RemoteBlast
Bio::Tools::SiRNA::*
Bio::Tools::dpAlign
Bio::Tools::pSW
Bio::Tree::AlleleNode
Bio::Tree::Draw::Cladogram
Bio::TreeIO::nexml
Bio::TreeIO::svggraph
Bio::Variation::*
* The following modules are new in the BioPerl distribution. They
have been previously released in the BioPerl-Run distribution.
This will enable smaller distributions that provide a
Bio::Tool::Run interface, to be only dependent on the BioPerl
distribution instead of the whole (very large) BioPerl-Run:
Bio::Tools::Run::Analysis
Bio::Tools::Run::AnalysisFactory
Bio::Tools::Run::Phylo::PhyloBase
Bio::Tools::Run::WrapperBase
Bio::Tools::Run::WrapperBase::CommandExts
* The following programs have been removed:
bp_biofetch_genbank_proxy
bp_blast2tree
bp_bulk_load_gff
bp_composite_LD
bp_das_server
bp_download_query_genbank
bp_fast_load_gff
bp_flanks
bp_genbank2gff
bp_generate_histogram
bp_heterogeneity_test
bp_hivq
bp_hmmer_to_table
bp_load_gff
bp_meta_gff
bp_netinstall
bp_parse_hmmsearch
bp_process_wormbase
bp_query_entrez_taxa
bp_remote_blast
bp_seqfeature_delete
bp_seqfeature_gff3
bp_seqfeature_load
* Because of the move of so many modules and programs into
separate distributions, the following modules are no longer
prerequisites:
Ace
Ace::Sequence::Homol
Algorithm::Munkres
Apache::DBI
Archive::Tar
Array::Compare
Bio::ASN1::EntrezGene
Bio::Expression::Contact
Bio::Expression::DataSet
Bio::Expression::Platform
Bio::Expression::Sample
Bio::Ext::Align
Bio::GMOD::CMap::Utils
Bio::Phylo::Factory
Bio::Phylo::Forest::Tree
Bio::Phylo::IO
Bio::Phylo::Matrices
Bio::Phylo::Matrices::Datum
Bio::Phylo::Matrices::Matrix
Bio::SeqFeature::Annotated
Bio::SeqIO::staden::read
Bio::Tools::Run::Alignment::Clustalw
Bio::Tools::Run::Ensembl
Bio::Tools::Run::Phylo::Molphy::ProtML
Bio::Tools::Run::Phylo::Phylip::Neighbor
Bio::Tools::Run::Phylo::Phylip::ProtDist
Bio::Tools::Run::Phylo::Phylip::ProtPars
Bio::Tools::Run::Samtools
CGI
CPAN
Cache::FileCache
Config
Convert::Binary::C
DBD::Pg
DBD::SQLite
Data::Stag::XMLWriter
Encode
English
ExtUtils::Install
ExtUtils::Manifest
File::Glob
GD::Simple
Getopt::Std
Graph::Undirected
GraphViz
HTML::HeadParser
HTML::TableExtract
LWP
LWP::Simple
MIME::Base64
Memoize
PostScript::TextBlock
SVG
SVG::Graph
SVG::Graph::Data
SVG::Graph::Data::Node
SVG::Graph::Data::Tree
Sort::Naturally
Spreadsheet::ParseExcel
Term::ReadLine
Text::NSP::Measures::2D::Fisher2::twotailed
Text::ParseWords
Time::Local
Tree::DAG_Node
URI::Escape
WWW::Mechanize
XML::Simple
* The following is a new prerequisite:
Test::RequiresInternet
* The deobfuscator has been removed.
* The emacs bioperl minor mode is no longer distributed as part of the
perl module distributions. See
https://github.com/bioperl/emacs-bioperl-mode
1.7.2 - "Entebbe"
[Bugs]
* #247 - Omit unnecessary parent_id attribute added by GFF3Loader [nathanweeks]
* #245 - Code coverage fixes [zmughal,cjfields]
* #237 - Fix warning in Bio::DB::IndexedBase [willmclaren,bosborne]
* #238 - Use a Travis cron job for network tests [zmughal,cjfields]
* #218 - Bio::DB::Flat::BinarySearch should use _fh() instead of fh() as fh() does not take arguments in [thibauthourlier,bosborne]
* #227 - Bio::SeqIO Ignores first line of sequence [VAR121,bosborne]
* #223 - Use Travis Perl helper script and enable coverage [zmughal,cjfields]
* #222 - Fix test RemoteDB/Taxonomy.t: requires networking [zmughal,cjfields]
* #216 - Apply carsonhh's patch (Inline::C fixes) [carsonh,bosborne]
* #213 - Support FTS5 in Bio::DB::SeqFeature::Store::DBI::SQLite [nathanweeks,bosborne]
* #210 - Sorting qualifiers while write embl files [hdevillers,cjfields]
* #209 - Fixed bug in _toDsspKey() [jvolkening,hlapp]
[Code changes]
* PAML-related code from bioperl and bioperl-run are now in a separate distribution on CPAN [carandraug]
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!
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]
1.6.923
* Major Windows support updates! [fjossandon]
* MAKER update to allow for stricter standard codon table [cjfields]
* Better support for circular sequences [fjossandon]
* Fixes for some complex location types [fjossandon]
* Address CONTIG bug in GenBank format, bug #3448 [cjfields]
* Fix bug #2978 related to BLAST report type [fjossandon]
* Deobfuscator fixes [DaveMessina]
1.6.922
* Address CPAN test failures [cjfields]
* Add BIOPROJECT support for Genbank files [hyphaltip]
* Better regex support for HMMER3 output [bosborne]
1.6.921
* Minor update to address CPAN test failures
1.6.920
* Remove Bio::Biblio and related files [carandraug]
- this cause version clashes with an independently-released
version of Bio::Biblio
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::Root::Root
- Support of Clone::Fast as a faster cloning alternative [fangly]
* Bio::Root::IO
- Moved the format() and variant() methods from Bio::*IO modules to
Bio::Root::IO [fangly]
- Can now use format() to get the type of IO format in use [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