November 2009 Archives by author

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Starting: Sun Nov 1 23:00:56 EST 2009
Ending: Mon Nov 30 21:56:03 EST 2009
Messages: 178

• [Bioperl-guts-l] [16306] bioperl-run/trunk: Added an option to Bio::Tools::Run:: TigrAssembler to have the results be:   Florent E Angly
• [Bioperl-guts-l] [16307] bioperl-run/trunk: Bio::Tools::Cap3 improvements:   Florent E Angly
• [Bioperl-guts-l] [16323] bioperl-run/trunk: Made Bio::Tools::Run:: TigrAssembler take in a FASTA file in addition to sequence objects   Florent E Angly
• [Bioperl-guts-l] [16325] bioperl-run/trunk: Work on Bio::Tools::Run::Phrap   Florent E Angly
• [Bioperl-guts-l] [16326] bioperl-run/trunk: More love for Bio::Tools::Run::Cap3   Florent E Angly
• [Bioperl-guts-l] [16333] bioperl-run/trunk: Made the assemblers wrapper (Phrap, Cap3, TigrAssembler) share the same interfaces and code created in Bio::Tools:: Run::AssemblerBase   Florent E Angly
• [Bioperl-guts-l] [16334] bioperl-live/trunk/Bio/Assembly: Minor Bio::Assembly:: IO related updates   Florent E Angly
• [Bioperl-guts-l] [16335] bioperl-run/trunk: Created wrapper for new assembly software: Bio:: Tools::Run::Minimo   Florent E Angly
• [Bioperl-guts-l] [16336] bioperl-run/trunk: Added support for LIGR_Assembler in the Bio:: Tools::Run::TigrAssembler wrapper   Florent E Angly
• [Bioperl-guts-l] [16341] bioperl-run/trunk: Minor revision of the assembly wrappers   Florent E Angly
• [Bioperl-guts-l] [16347] bioperl-run/trunk: Added support for Newbler (454/ Roche GS de novo assembler)   Florent E Angly
• [Bioperl-guts-l] [16348] bioperl-run/trunk/lib/Bio/Tools/Run/Newbler.pm: Improved documentation for the Newbler assembler wrapper.   Florent E Angly
• [Bioperl-guts-l] [16351] bioperl-live/trunk/Bio/Assembly/Tools/ContigSpectrum.pm: Documentation update   Florent E Angly
• [Bioperl-guts-l] [16352] bioperl-live/trunk: Fixed a bug that caused directories to be returned as valid executable files by Bio ::Tools::Run::WrapperBase::executable() and Bio::Root::IO::exists_exe()   Florent E Angly
• [Bioperl-guts-l] [16353] bioperl-live/trunk: Improvement of the Bio::Assembly::Tools:: ContigSpectrum::score() code   Florent E Angly
• [Bioperl-guts-l] [16356] bioperl-live/trunk: Better sanity checks for Bio::Assembly::Tools:: ContigSpectrum::score()   Florent E Angly
• [Bioperl-guts-l] [16357] bioperl-live/trunk/Bio/Assembly/Tools/ContigSpectrum.pm:   Florent E Angly
• [Bioperl-guts-l] [16368] bioperl-live/trunk: Added a $io->next_contig method in Bio:: Assembly::IO   Florent E Angly
• [Bioperl-guts-l] [16370] bioperl-live/trunk: Fixed Singlet ID bug (#2648)   Florent E Angly
• [Bioperl-guts-l] [16371] bioperl-live/trunk: Implemented the $io->next_contig() method for the Bio::Assembly::IO::maq parser   Florent E Angly
• [Bioperl-guts-l] [16374] bioperl-run/trunk/t/data: Moved maq tests to bioperl-live   Florent E Angly
• [Bioperl-guts-l] [16375] bioperl-live/trunk: Better support for singlets in Bio::Assembly:: IO::maq parser   Florent E Angly
• [Bioperl-guts-l] [16377] bioperl-run/trunk/lib/Bio/Tools/Run: Aliased a minimum_overlap_length and minimum_overlap_similarity method for all assemblers that support it .   Florent E Angly
• [Bioperl-guts-l] [16384] bioperl-run/trunk/lib/Bio/Tools/Run/Minimo.pm: Added a file cleaning step in the Minimo wrapper   Florent E Angly
• [Bioperl-guts-l] [16385] bioperl-run/trunk: Updated assembly tests and did small fixes   Florent E Angly
• [Bioperl-guts-l] [16386] bioperl-live/trunk: Improvement of Bio::SimpleAlign:: overall_percentage_identity   Florent E Angly
• [Bioperl-guts-l] [16391] bioperl-live/trunk: Better test file for the ContigSpectrum module   Florent E Angly
• [Bioperl-guts-l] [16392] bioperl-live/trunk/Bio/Assembly/Tools/ContigSpectrum.pm: Minor change in a regular expression for cross-contig spectrum calculation   Florent E Angly
• [Bioperl-guts-l] [16397] bioperl-live/trunk: Implemented a more robust algorithm to calculate the effective assembly parameters in Bio ::Assembly::ContigSpectrum   Florent E Angly
• [Bioperl-guts-l] [16398] bioperl-run/trunk/lib/Bio/Tools/Run: Fixed typos   Florent E Angly
• [Bioperl-guts-l] [16421] bioperl-live/trunk: Bio::Assembly::Tools:: ContigSpectrum objects can now be built one contig at a time   Florent E Angly
• [Bioperl-guts-l] [16430] bioperl-live/trunk/Bio/Assembly: Small assembly-related fixes   Florent E Angly
• [Bioperl-guts-l] [16431] bioperl-run/trunk/lib/Bio/Tools/Run: Small assembly-related fixes   Florent E Angly
• [Bioperl-guts-l] [16346] bioperl-live/trunk/scripts/Bio-DB-GFF/genbank2gff3.PLS: if a random feature which doesn't get its type mapped to a SO term ( and thus is 'region') but is part of a genethe type is changed to gene_component_region.   Scott Cain
• [Bioperl-guts-l] [16355] bioperl-live/trunk/Bio/SeqFeature/Tools/IDHandler.pm: Making the error messages a little more informative when generating IDs fails   Scott Cain
• [Bioperl-guts-l] [16383] bioperl-live/trunk: added support for parsing codeml from PAML version 4.3a (August 2009).   Chris Fields
• [Bioperl-guts-l] [Bug 2937] Strand in fasta35 output does not seem to be parsed   Chris Fields
• [Bioperl-guts-l] [16309] bioperl-db/trunk: Build. PL now checks for DBD drivers and attempts to DTRT   Christopher John Fields
• [Bioperl-guts-l] [16310] bioperl-db/trunk/README: test commit to check SVN::Notify   Christopher John Fields
• [Bioperl-guts-l] [16311] bioperl-live/trunk/README: test post commit hook   Christopher John Fields
• [Bioperl-guts-l] [16312] bioperl-live/trunk/README: test again   Christopher John Fields
• [Bioperl-guts-l] [16313] bioperl-live/trunk/README: ...one more time   Christopher John Fields
• [Bioperl-guts-l] [16314] bioperl-live/trunk/README: Add USER to IRC commit hook   Christopher John Fields
• [Bioperl-guts-l] [16317] bioperl-live/trunk/README: hi to IRC (another test)   Christopher John Fields
• [Bioperl-guts-l] [16318] bioperl-live/trunk/README: ..yet another   Christopher John Fields
• [Bioperl-guts-l] [16319] bioperl-live/trunk/README: Test #51243   Christopher John Fields
• [Bioperl-guts-l] [16320] bioperl-live/trunk/README: Final one; was chopping commit msgs at first ws   Christopher John Fields
• [Bioperl-guts-l] [16324] bioperl-run/trunk/t/data/purine.all.fa: add infernal data file   Christopher John Fields
• [Bioperl-guts-l] [16329] bioperl-live/trunk/Bio/Align/Graphics.pm: POD fixes   Christopher John Fields
• [Bioperl-guts-l] [16330] bioperl-live/trunk/Bio/Tools/GFF.pm: [bug 2944]   Christopher John Fields
• [Bioperl-guts-l] [16331] bioperl-live/trunk/t/Seq/PrimarySeq.t: bump test cases   Christopher John Fields
• [Bioperl-guts-l] [16393] bioperl-network/trunk: remove named module and reference in Build. PL; experiment gone awry   Christopher John Fields
• [Bioperl-guts-l] [16401] bioperl-live/trunk/Bio/Tools/Run/StandAloneNCBIBlast.pm: add n parameter (not tested) courtesy Nevo Band (not Neko Case)   Christopher John Fields
• [Bioperl-guts-l] [16308] bioperl-live/trunk/Bio: some unification of feat/annot access   Mark Allen Jensen
• [Bioperl-guts-l] [16315] bioperl-live/trunk/INSTALL.WIN: update PPM command line instructions   Mark Allen Jensen
• [Bioperl-guts-l] [16316] bioperl-live/trunk/INSTALL.WIN: keyword subst   Mark Allen Jensen
• [Bioperl-guts-l] [16321] bioperl-live/trunk/Bio/Seq.pm: full delegation of Bio:: AnnotationCollectionI   Mark Allen Jensen
• [Bioperl-guts-l] [16322] bioperl-live/trunk/Bio/Seq.pm: pod: alias   Mark Allen Jensen
• [Bioperl-guts-l] [16332] bioperl-live/trunk/t: tests+data for bug#2942   Mark Allen Jensen
• [Bioperl-guts-l] [16338] bioperl-live/trunk/t: add simple fastq test   Mark Allen Jensen
• [Bioperl-guts-l] [16339] bioperl-live/trunk/Bio/Tools/GuessSeqFormat.pm: simple fastq guesser   Mark Allen Jensen
• [Bioperl-guts-l] [16340] bioperl-live/trunk/t/SeqTools/GuessSeqFormat.t: oops; removed cruft , bumped tests   Mark Allen Jensen
• [Bioperl-guts-l] [16342] bioperl-live/trunk/Bio/Assembly/IO/maq.pm: first try at a maq Assembly::IO driver   Mark Allen Jensen
• [Bioperl-guts-l] [16343] bioperl-live/trunk/Bio/Assembly/IO.pm: beta version with tests/ test data   Mark Allen Jensen
• [Bioperl-guts-l] [16344] bioperl-live/trunk/Bio/Assembly/IO/maq.pm: beta version with tests/ test data   Mark Allen Jensen
• [Bioperl-guts-l] [16345] bioperl-live/trunk/t: added a few tests for maq format; test assembly data   Mark Allen Jensen
• [Bioperl-guts-l] [16349] bioperl-run/trunk/t: Prelim tests and data for Run::Maq   Mark Allen Jensen
• [Bioperl-guts-l] [16350] bioperl-run/trunk/lib/Bio/Tools/Run: A Maq wrapper for running maq commands separately,   Mark Allen Jensen
• [Bioperl-guts-l] [16354] bioperl-run/trunk/lib/Bio/Tools/Run/AssemblerBase.pm: inherit from ParameterBaseI and add its functionality   Mark Allen Jensen
• [Bioperl-guts-l] [16358] bioperl-run/trunk/t/data: new test data for Maq   Mark Allen Jensen
• [Bioperl-guts-l] [16359] bioperl-run/trunk/t/Maq.t: add tests for full assy (run() method) and ParameterBaseI compliance   Mark Allen Jensen
• [Bioperl-guts-l] [16360] bioperl-live/trunk/Bio/Assembly/IO/maq.pm: bug squishes   Mark Allen Jensen
• [Bioperl-guts-l] [16361] bioperl-run/trunk/lib/Bio/Tools/Run/Maq.pm: allow args specs directed to different component of the full assy (run())   Mark Allen Jensen
• [Bioperl-guts-l] [16362] bioperl-run/trunk/lib/Bio/Tools/Run/Maq/Config.pm: setup for easy( er) configuration of composite commands   Mark Allen Jensen
• [Bioperl-guts-l] [16363] bioperl-run/trunk/lib/Bio/Tools/Run: pod and a few doodads   Mark Allen Jensen
• [Bioperl-guts-l] [16364] bioperl-live/trunk/t/data/testaln.fastq: a testaln for GuessSeqFormat.t fastq   Mark Allen Jensen
• [Bioperl-guts-l] [16365] bioperl-run/trunk/t/Maq.t: rm cruft   Mark Allen Jensen
• [Bioperl-guts-l] [16366] bioperl-run/trunk/lib/Bio/Tools/Run/Maq.pm: bug squish   Mark Allen Jensen
• [Bioperl-guts-l] [16367] bioperl-run/trunk/t/Maq.t: arrgh.   Mark Allen Jensen
• [Bioperl-guts-l] [16369] bioperl-live/trunk/Bio/Tree/TreeFunctionsI.pm: let distance() take two nodes as args   Mark Allen Jensen
• [Bioperl-guts-l] [16372] bioperl-run/trunk/t/data: maq-flavored singlets ( note that both files are required for B:A:IO:maq, but only the . maq file is specified in the -file argument)   Mark Allen Jensen
• [Bioperl-guts-l] [16376] bioperl-live/trunk/ide/bioperl-mode/site-lisp: some new convenience features   Mark Allen Jensen
• [Bioperl-guts-l] [16378] bioperl-dev/trunk/ide/emacs/bioperl-mode/test/bioperl-mode-test.el: addl unit tests for bioperl-mode   Mark Allen Jensen
• [Bioperl-guts-l] [16379] bioperl-live/trunk/ide/bioperl-mode/dist: tars with new feature tweaks   Mark Allen Jensen
• [Bioperl-guts-l] [16380] bioperl-live/trunk/ide/bioperl-mode/site-lisp: tweaks + retar   Mark Allen Jensen
• [Bioperl-guts-l] [16381] bioperl-live/trunk/Bio/Assembly/IO/maq.pm: credit where it's due\!   Mark Allen Jensen
• [Bioperl-guts-l] [16399] bioperl-live/trunk/Bio/Assembly/IO/sam.pm: pre-alpha Bio::Assembly: :IO class for bam/sam format   Mark Allen Jensen
• [Bioperl-guts-l] [16400] bioperl-live/trunk/Bio/Assembly/IO/sam.pm: keyword subst   Mark Allen Jensen
• [Bioperl-guts-l] [16402] bioperl-live/trunk/Bio/Assembly/IO/sam.pm: bug squishes, anti-cruft , and tightening   Mark Allen Jensen
• [Bioperl-guts-l] [16403] bioperl-live/trunk/Bio/Assembly/IO/sam.pm: pod buildout   Mark Allen Jensen
• [Bioperl-guts-l] [16404] bioperl-live/trunk/Bio/Assembly/IO/sam.pm: now with decompression!   Mark Allen Jensen
• [Bioperl-guts-l] [16405] bioperl-live/trunk/Bio/Assembly/IO/sam.pm: reads now have pair info attached as features   Mark Allen Jensen
• [Bioperl-guts-l] [16406] bioperl-live/trunk/Bio/Assembly/IO/sam.pm: pod tweaks   Mark Allen Jensen
• [Bioperl-guts-l] [16407] bioperl-run/trunk/lib/Bio/Tools/Run: sam/bwa run wrappers   Mark Allen Jensen
• [Bioperl-guts-l] [16408] bioperl-run/trunk/lib/Bio/Tools/Run/Maq.pm: gzip decompression   Mark Allen Jensen
• [Bioperl-guts-l] [16409] bioperl-run/trunk/t: tests progress   Mark Allen Jensen
• [Bioperl-guts-l] [16410] bioperl-run/trunk/lib/Bio/Tools/Run: config tweaks after testing   Mark Allen Jensen
• [Bioperl-guts-l] [16411] bioperl-run/trunk/t/data: test data for BWA and Samtools   Mark Allen Jensen
• [Bioperl-guts-l] [16412] bioperl-run/trunk/t/Samtools.t: Samtools wrapper tests   Mark Allen Jensen
• [Bioperl-guts-l] [16413] bioperl-run/trunk/lib/Bio/Tools/Run/Samtools/Config.pm: config tweaks for Samtools wrapper   Mark Allen Jensen
• [Bioperl-guts-l] [16414] bioperl-live/trunk/Bio/Assembly/IO.pm: admit sam to the club   Mark Allen Jensen
• [Bioperl-guts-l] [16415] bioperl-run/trunk/lib/Bio/Tools/Run/AssemblerBase.pm: tiny kludge to _export_results   Mark Allen Jensen
• [Bioperl-guts-l] [16416] bioperl-run/trunk/lib/Bio/Tools/Run: convert sam to bam at end of run(), using B:T:R:Samtools   Mark Allen Jensen
• [Bioperl-guts-l] [16417] bioperl-run/trunk/t/BWA.t: towards full assembly testing   Mark Allen Jensen
• [Bioperl-guts-l] [16418] bioperl-run/trunk/lib/Bio/Tools/Run/AssemblerBase.pm: slight tweak to preserve asm file if nec   Mark Allen Jensen
• [Bioperl-guts-l] [16419] bioperl-run/trunk/lib/Bio/Tools/Run/BWA.pm: add sort and index steps to assy pipeline (via Samtools)   Mark Allen Jensen
• [Bioperl-guts-l] [16420] bioperl-run/trunk/t/BWA.t: complete tests (incl.   Mark Allen Jensen
• [Bioperl-guts-l] [16422] bioperl-live/trunk/t/data: test data for B:A:IO::sam   Mark Allen Jensen
• [Bioperl-guts-l] [16423] bioperl-live/trunk/t/Assembly/Assembly.t: Assembly:: IO tests for sam IO   Mark Allen Jensen
• [Bioperl-guts-l] [16424] bioperl-live/trunk/Bio/Assembly/IO/sam.pm: friends don' t let friends use globals   Mark Allen Jensen
• [Bioperl-guts-l] [16425] bioperl-run/trunk/lib/Bio/Tools/Run: now beta   Mark Allen Jensen
• [Bioperl-guts-l] [16426] bioperl-live/trunk/Bio/Assembly/IO/sam.pm: now beta   Mark Allen Jensen
• [Bioperl-guts-l] [16427] bioperl-run/trunk/lib/Bio/Tools/Run/Samtools/Config.pm: config tweak   Mark Allen Jensen
• [Bioperl-guts-l] [16428] bioperl-live/trunk/Bio/Restriction/IO/base.pm: retries to 1; if neb site doesn't work the first   Mark Allen Jensen
• [Bioperl-guts-l] [16429] bioperl-live/trunk/t/SeqTools/GuessSeqFormat.t: no fastq AlignIO   Mark Allen Jensen
• [Bioperl-guts-l] [16432] bioperl-live/trunk/Bio/SearchIO: ..Search::Writer..   Mark Allen Jensen
• [Bioperl-guts-l] [16382] bioperl-live/trunk/Bio/Tools/Phylo/PAML.pm: Perltidied.   Dave Messina
• [Bioperl-guts-l] [16383] bioperl-live/trunk: added support for parsing codeml from PAML version 4.3a (August 2009).   Dave Messina
• [Bioperl-guts-l] [16383] bioperl-live/trunk: added support for parsing codeml from PAML version 4.3a (August 2009).   Dave Messina
• [Bioperl-guts-l] [16388] bioperl-live/trunk/Bio/AlignIO/phylip.pm: fixing typo in write_aln( )'s POD   Dave Messina
• [Bioperl-guts-l] [16389] bioperl-live/trunk: Validated PAML parser against codeml 4. 3a run with two NSSites models.   Dave Messina
• [Bioperl-guts-l] [16390] bioperl-live/trunk/Bio/Tools/Phylo/PAML.pm: fix for bug 2482.   Dave Messina
• [Bioperl-guts-l] [16394] bioperl-live/trunk/Bio/SearchIO/fasta.pm: fix for bug 2937: FASTN ' _reporttype' wasn't being propagated properly for FASTA version 35 reports.   Dave Messina
• [Bioperl-guts-l] [16395] bioperl-live/trunk/t: adding tests and testfiile for bug 2937.   Dave Messina
• [Bioperl-guts-l] [Bug 2937] Strand in fasta35 output does not seem to be parsed   Dave Messina
• [Bioperl-guts-l] [16396] bioperl-live/trunk/Bio/Root/IO.pm: fixing bug #2863.   Dave Messina
• [Bioperl-guts-l] [16337] bioperl-dev/branches/guess-db/Bio/DB/GuessDB.pm: Added Han' s code for determining NCBI, and UNIPROT accesions   Chase Miller
• [Bioperl-guts-l] [16327] bioperl-live/trunk: PhyloXML update: xsd1.1 and add_attribute()   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [16328] bioperl-live/trunk/Bio/TreeIO/phyloxml.pm: typo: =ehead to =head   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [16373] bioperl-live/trunk/Bio: phyloXML bug fix in _relation/confidence   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [16387] bioperl-live/trunk/Bio/TreeIO/phyloxml.pm: phyloXML bug fix sequence_relation   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [Bug 2944] New: When using Bio::Tools::GFF, score is always added as a Tag Value.   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2944] When using Bio::Tools::GFF, score is always added as a Tag Value.   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2944] When using Bio::Tools::GFF, score is always added as a Tag Value.   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2944] When using Bio::Tools::GFF, score is always added as a Tag Value.   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2944] When using Bio::Tools::GFF, score is always added as a Tag Value.   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2942] MapTiling returning incorrect lengths   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2942] MapTiling returning incorrect lengths   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2946] New: NodeMod issue   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2648] The results of "Bio::Assembly::Scaffold->get_all_seq_ids" does NOT behave as documented   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2648] The results of "Bio::Assembly::Scaffold->get_all_seq_ids" does NOT behave as documented   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2726] ace file IO   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2483] request for implementation of write_assembly   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2577] Bio::Assembly and Bio::Assembly::IO can exceed the set open file ulimit   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2921] Getting model from codeml results   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2753] Unknown format of PAML output did not see seqtype in Yn00   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2482] paml4 mlc file fails to parse   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2636] New version of PAML changes output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2347] Bio::Tools::Run::Phylo::PAML::Baseml needs polishing and completion   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2482] paml4 mlc file fails to parse   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2636] New version of PAML changes output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2937] Strand in fasta35 output does not seem to be parsed   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2937] Strand in fasta35 output does not seem to be parsed   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2937] Strand in fasta35 output does not seem to be parsed   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2937] Strand in fasta35 output does not seem to be parsed   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2863] crash from Bio::Root::IO::_initialize_io causes crash when validating -fh argument   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2863] crash from Bio::Root::IO::_initialize_io causes crash when validating -fh argument   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2863] crash from Bio::Root::IO::_initialize_io causes crash when validating -fh argument   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2863] crash from Bio::Root::IO::_initialize_io causes crash when validating -fh argument   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2863] crash from Bio::Root::IO::_initialize_io causes crash when validating -fh argument   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2863] crash from Bio::Root::IO::_initialize_io causes crash when validating -fh argument   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2863] crash from Bio::Root::IO::_initialize_io causes crash when validating -fh argument   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2863] crash from Bio::Root::IO::_initialize_io causes crash when validating -fh argument   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2863] crash from Bio::Root::IO::_initialize_io causes crash when validating -fh argument   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2952] New: Bio::Tools::GFF, Target Tag disappears when editing a gff3 file   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2953] New: Bio::Tools::GFF, Target Tag disappears when editing a gff3 file   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2953] Bio::Tools::GFF, Target Tag disappears when editing a gff3 file   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2953] Bio::Tools::GFF, Target Tag disappears when editing a gff3 file   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2952] Bio::Tools::GFF, Target Tag disappears when editing a gff3 file   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2953] Bio::Tools::GFF, Target Tag disappears when editing a gff3 file   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2955] New: Bio::DB::Refseq   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2956] New: ranges in EMBL output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2955] Bio::DB::Refseq   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2958] New: association table alias is not honored   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2958] association table alias is not honored   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2958] association table alias is not honored   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2958] association table alias is not honored   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2958] association table alias is not honored   bugzilla-daemon at portal.open-bio.org

Last message date: Mon Nov 30 21:56:03 EST 2009
Archived on: Mon Nov 30 21:56:05 EST 2009

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