November 2008 Archives by date

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Starting: Sat Nov 1 14:28:16 EDT 2008
Ending: Sun Nov 30 17:19:12 EST 2008
Messages: 254

• [Bioperl-guts-l] [14976] bioperl-live/trunk: fixed parsing of # characters so that HTML fragments are not stripped out   Lincoln Stein
• [Bioperl-guts-l] [14977] bioperl-live/trunk: restored the ability of add_feature() to set the feature's type.   Lincoln Stein
• [Bioperl-guts-l] [14978] bioperl-live/trunk: * parse ' Features in this part of subject sequence' data from some NCBI output ( string can be retrieved using new GenericHSP::hit_features method)   Christopher John Fields
• [Bioperl-guts-l] [14979] bioperl-live/trunk/Bio/SearchIO/blast.pm: * parse ' Features in this part of subject sequence:' and pass on data to GenericHSP   Christopher John Fields
• [Bioperl-guts-l] [14980] bioperl-live/trunk/Bio/Annotation/Tree.pm: wrap text   Christopher John Fields
• [Bioperl-guts-l] [Bug 2641] New: hook stomp in bioperl.lisp   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2641] hook stomp in bioperl.lisp   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2642] New: bioperl.lisp, 2 empty lines before '=cut' in templates   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2642] bioperl.lisp, 2 empty lines before '=cut' in templates   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2632] hmmpfam parsers are broken (both hmmer and hmmer_pull)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2632] hmmpfam parsers are broken (both hmmer and hmmer_pull)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2644] New: Two files using /usr/local/bin/perl instead of /usr/bin/perl   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2645] New: Infinite 'next_assembly' on a Bio::Assembly::IO (Bio::Assembly::IO::ace)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2646] New: MSG: Abstract method "Bio::Assembly::Contig::length" is not implemented by package Bio::Assembly::Contig.   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2647] New: MSG: Abstract method "Bio::Assembly::Contig::percentage_identity" is not implemented by package Bio::Assembly::Contig.   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14981] bioperl-live/trunk/Bio/Assembly/IO/ace.pm: [bug 2645]   Christopher John Fields
• [Bioperl-guts-l] [Bug 2645] Infinite 'next_assembly' on a Bio::Assembly::IO (Bio::Assembly::IO::ace)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2021] Abstract method "Bio::Assembly::Contig::slice" is not implemented by package Bio::Assembly::Contig   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2021] Unimplemented methods in Bio::Assembly classes   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2647] MSG: Abstract method "Bio::Assembly::Contig::percentage_identity" is not implemented by package Bio::Assembly::Contig.   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2021] Unimplemented methods in Bio::Assembly classes   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2646] MSG: Abstract method "Bio::Assembly::Contig::length" is not implemented by package Bio::Assembly::Contig.   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2021] Unimplemented methods in Bio::Assembly classes   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2021] Unimplemented methods in Bio::Assembly classes   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2648] New: 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 2650] New: MSG: Abstract method "Bio::SearchIO::result_count" is not implemented   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14982] bioperl-live/trunk/Bio: migrated glyphs from gbrowse distribution into bioperl main   Lincoln Stein
• [Bioperl-guts-l] [14983] bioperl-live/trunk/t/data/hmmpfam_cs.out: test data for bug 2632   Senduran Balasubramaniam
• [Bioperl-guts-l] [14984] bioperl-live/trunk: fixed significant alignment parsing bug affecting hsps, and also got rid of warnings when length not known   Senduran Balasubramaniam
• [Bioperl-guts-l] [Bug 2632] hmmpfam parsers are broken (both hmmer and hmmer_pull)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14985] bioperl-live/trunk/t/hmmer.t: [bug 2632]   Christopher John Fields
• [Bioperl-guts-l] [Bug 2632] hmmpfam parsers are broken (both hmmer and hmmer_pull)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14986] bioperl-live/trunk/Bio/SearchIO.pm: Clarify result_count ( discussions on mail list per Dan Bolser and Sendu).   Christopher John Fields
• [Bioperl-guts-l] [14987] bioperl-live/trunk: [bug 2650]   Christopher John Fields
• [Bioperl-guts-l] [14988] bioperl-live/trunk/t/hmmer.t: corrected test to test the hmmer parser, not the hmmer_pull parser; test passes but generates big warning   Senduran Balasubramaniam
• [Bioperl-guts-l] [Bug 2650] MSG: Abstract method "Bio::SearchIO::result_count" is not implemented   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14988] bioperl-live/trunk/t/hmmer.t: corrected test to test the hmmer parser, not the hmmer_pull parser; test passes but generates big warning   Chris Fields
• [Bioperl-guts-l] [Bug 2632] hmmpfam parsers are broken (both hmmer and hmmer_pull)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14989] bioperl-live/trunk/t/hmmer.t: remove fixed verbose flag   Christopher John Fields
• [Bioperl-guts-l] [14990] bioperl-live/trunk/Bio/SearchIO/hmmer.pm: remove debugging lines   Christopher John Fields
• [Bioperl-guts-l] [Bug 2632] hmmpfam parsers are broken (both hmmer and hmmer_pull)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2656] New: typo in required module in Build.PL   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2656] typo in required module in Build.PL   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14991] bioperl-live/trunk/Build.PL: [bug 2656]   Christopher John Fields
• [Bioperl-guts-l] [Bug 2656] typo in required module in Build.PL   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2644] Two files using /usr/local/bin/perl instead of /usr/bin/perl   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14992] bioperl-run/trunk/Bio/Installer: [bug 2644]   Christopher John Fields
• [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 2636] New version of PAML changes output   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 2636] New version of PAML changes output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2663] New: seq_inds overhaul   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2630] Bio::LocatableSeq range validation does not work with translated sequence coordinates   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2630] Bio::LocatableSeq range validation does not work with translated sequence coordinates   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2633] Incorrect identity calculation in Bio::SearchIO::fasta   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14993] bioperl-live/trunk: [bug 2635]   Christopher John Fields
• [Bioperl-guts-l] [Bug 2635] New Bio::SimpleAlign method for concatenating alignments   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14994] bioperl-live/trunk/Bio/SearchIO/fasta.pm: perltidy   Christopher John Fields
• [Bioperl-guts-l] [14995] bioperl-live/trunk: [bug 2663]   Christopher John Fields
• [Bioperl-guts-l] [Bug 2665] New: Please add a --no-internet to the test suite.   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] bioperl-ext   Elöd Körtvély
• [Bioperl-guts-l] [Bug 2665] Please add a --no-internet to the test suite.   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2667] New: CODE ref problem with Build.PL and Module::Build 0.3   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2667] CODE ref problem with Build.PL and Module::Build 0.3   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2667] CODE ref problem with Build.PL and Module::Build 0.3   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14996] bioperl-live/trunk/ModuleBuildBioperl.pm: fixed bug 2667: no more complaints about code refs   Senduran Balasubramaniam
• [Bioperl-guts-l] [14997] bioperl-live/trunk: resolve long-standing issue with auto-install of circular dependency: no more! Now you must choose to install circular deps in interactive mode; they do not get installed when installing "all" modules   Senduran Balasubramaniam
• [Bioperl-guts-l] [14998] bioperl-live/trunk/Bio/Search/SearchUtils.pm: move results2hash test utility sub to SearchUtils   Christopher John Fields
• [Bioperl-guts-l] [14999] bioperl-live/trunk/t: [tests]   Christopher John Fields
• [Bioperl-guts-l] [15000] bioperl-live/trunk/t: Remove redundant test files   Christopher John Fields
• [Bioperl-guts-l] [15001] bioperl-live/trunk/INSTALL: * 'highly' (and I get r15000!)   Christopher John Fields
• [Bioperl-guts-l] [Bug 2668] New: bioperl-ext fails to compile on x86_64   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2668] bioperl-ext fails to compile on x86_64   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15002] bioperl-live/trunk: * fix POD   Christopher John Fields
• [Bioperl-guts-l] [15003] bioperl-live/trunk: * seq_inds is not defined for Model-based HSPs   Christopher John Fields
• [Bioperl-guts-l] [15004] bioperl-live/trunk/t/SearchIO_hmmer.t: * Double-checked data, tested results were wrong   Christopher John Fields
• [Bioperl-guts-l] [Bug 2669] New: Typo in Bio::Assembly::Contig add_seq()   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2669] Typo in Bio::Assembly::Contig add_seq()   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2632] hmmpfam parsers are broken (both hmmer and hmmer_pull)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2632] hmmpfam parsers are broken (both hmmer and hmmer_pull)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2632] hmmpfam parsers are broken (both hmmer and hmmer_pull)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2632] hmmpfam parsers are broken (both hmmer and hmmer_pull)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2632] hmmpfam parsers are broken (both hmmer and hmmer_pull)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2673] New: original fields not inherited by seq objects in alignment slices   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2632] hmmpfam parsers are broken (both hmmer and hmmer_pull)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2632] hmmpfam parsers are broken (both hmmer and hmmer_pull)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2632] hmmpfam parsers are broken (both hmmer and hmmer_pull)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2632] hmmpfam parsers are broken (both hmmer and hmmer_pull)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2632] hmmpfam parsers are broken (both hmmer and hmmer_pull)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2632] hmmpfam parsers are broken (both hmmer and hmmer_pull)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2632] hmmpfam parsers are broken (both hmmer and hmmer_pull)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2632] hmmpfam parsers are broken (both hmmer and hmmer_pull)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2632] hmmpfam parsers are broken (both hmmer and hmmer_pull)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15005] bioperl-live/trunk/Bio/SearchIO/hmmer.pm: more sensitive fix for bug 2632, courtesy of Francisco J.   Dave Messina
• [Bioperl-guts-l] [15006] bioperl-live/trunk/Bio: moved more glyphs from gbrowse into bioperl   Lincoln Stein
• [Bioperl-guts-l] [Bug 2559] Out of memory with large seqs (malloc error)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2567] AlignIO::stockholm concatenates sequences   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2594] Bio::Species memory leak   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2599] DBLINK to replace PROJECT for GenBank format annotation   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2615] Argument inconsistency in Bio::SearchIO   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2620] Bio::Assembly::IO::phrap is incomplete   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2621] Bio::SeqFeature::Collection->add_feature fails to check input correctly?   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2630] Bio::LocatableSeq range validation does not work with translated sequence coordinates   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2633] Incorrect identity calculation in Bio::SearchIO::fasta   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 2637] new modules for HIV sequence queries   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2663] seq_inds overhaul   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2673] original fields not inherited by seq objects in alignment slices   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 1707] Out of memory crash from Bio::DB::GFF::Adaptor::dbi::pg.pm (Postgres)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2218] Change in PAML module   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2247] Have Bio::SearchIO::blast methods available for other BLAST parsers   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2278] FASTA m10 output support   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2326] bp_fast_load_gff creates mostly empty tables.   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2332] Software for analysis of redundant fragments of affys human mitochip v2   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2336] bp_bioflat_index.pl and Bio::DB::Flat::BDB::fasta creates incorrect index   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2342] blastall crash & StandAloneBlast (originally described by Matthew Laird)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2345] Get mappable sequence coords after removing alignment columns   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2346] exonerate parser in bioperl-live fails when protein2dna comparison is performed   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 2439] multiple results HTMLResultWriter.pm and non-redundant entries in SearchIO   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2463] bp_seqconvert.pl & Bio::SeqIO code cleanup and user friendly interface   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2515] GenBank XML parser   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2637] new modules for HIV sequence queries   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15007] bioperl-live/trunk/Bio/Graphics/Glyph.pm: "blunting" of the generic glyph when the glyph goes off the edge of the panel is now consistent between directional (fillled arrow) and non-directional (simple box) renderings   Lincoln Stein
• [Bioperl-guts-l] [15008] bioperl-live/trunk: Fixes for the change to Bio::Annotation:: Comment that removed double quote overloading   Scott Cain
• [Bioperl-guts-l] [Bug 2567] AlignIO::stockholm concatenates sequences   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2673] original fields not inherited by seq objects in alignment slices   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2673] original fields not inherited by seq objects in alignment slices   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2673] original fields not inherited by seq objects in alignment slices   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 843] _readline() in SeqIO.pm   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2092] Can't store proteins with species using bioperl-db   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2673] original fields not inherited by seq objects in alignment slices   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2673] original fields not inherited by seq objects in alignment slices   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2637] new modules for HIV sequence queries   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2637] new modules for HIV sequence queries   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2637] new modules for HIV sequence queries   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2637] new modules for HIV sequence queries   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2338] The first 4 bytes of flatfile index is wrong (--indextype flat)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2337] BDB flatfile index should store global configuration data in BDB   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2337] BDB flatfile index should store global configuration data in BDB   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15009] bioperl-live/trunk/t/data/tmp.fst: Add for bug 2339   Brian Osborne
• [Bioperl-guts-l] [15010] bioperl-live/trunk: Add test for bug 2339, and fix   Brian Osborne
• [Bioperl-guts-l] [Bug 2339] In a flat file index, the size of the final entry of a fasta file is wrong   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2262] Bio::Seq object loses sequence data when blessed as Bio::Seq::Meta::Array   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15011] bioperl-live/trunk: [bug 2630]   Christopher John Fields
• [Bioperl-guts-l] [Bug 2630] Bio::LocatableSeq range validation does not work with translated sequence coordinates   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15012] bioperl-live/trunk/Bio/Seq: [bug 2262]   Christopher John Fields
• [Bioperl-guts-l] [15013] bioperl-live/trunk/Bio/SimpleAlign.pm: [bug 2630]   Christopher John Fields
• [Bioperl-guts-l] [15014] bioperl-live/trunk/Bio/Search/HSP: [bug 2663]   Christopher John Fields
• [Bioperl-guts-l] [15015] bioperl-live/trunk/t/SearchIO_blast.t: [bug 2663]   Christopher John Fields
• [Bioperl-guts-l] [15016] bioperl-live/trunk: [bug 2633]   Christopher John Fields
• [Bioperl-guts-l] [Bug 2682] New: ignoring gaps in Bio::PrimarySeq::subseq()   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2682] ignoring gaps in Bio::PrimarySeq::subseq()   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2682] ignoring gaps in Bio::PrimarySeq::subseq()   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15017] bioperl-live/trunk: [bug 2630]   Christopher John Fields
• [Bioperl-guts-l] [Bug 2594] Bio::Species memory leak   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15018] bioperl-live/trunk/Bio/PrimarySeq.pm: [bug 2682]   Christopher John Fields
• [Bioperl-guts-l] [Bug 2682] ignoring gaps in Bio::PrimarySeq::subseq()   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2663] seq_inds overhaul   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2281] unable to copy a sequence from one namespace to another one   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2642] bioperl.lisp, 2 empty lines before '=cut' in templates   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2641] hook stomp in bioperl.lisp   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2642] bioperl.lisp, 2 empty lines before '=cut' in templates   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15019] bioperl-live/trunk/t: Updated Bio::Assembly tests   Florent E Angly
• [Bioperl-guts-l] [Bug 2686] New: WU-BLAST XML support   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2686] WU-BLAST XML support   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15020] bioperl-live/trunk/t: split up AlignIO tests   Christopher John Fields
• [Bioperl-guts-l] [15021] bioperl-live/trunk/bioperl.lisp: [bug 2641, 2642]   Christopher John Fields
• [Bioperl-guts-l] [15022] bioperl-live/trunk/Bio/SearchIO/blastxml.pm: [bug 2686]   Christopher John Fields
• [Bioperl-guts-l] [Bug 2686] WU-BLAST XML support   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2641] hook stomp in bioperl.lisp   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2642] bioperl.lisp, 2 empty lines before '=cut' in templates   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2633] Incorrect identity calculation in Bio::SearchIO::fasta   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2633] Incorrect identity calculation in Bio::SearchIO::fasta   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2594] Bio::Species memory leak   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15023] bioperl-live/trunk/Bio/AlignIO/xmfa.pm: fix undefined value warnings   Christopher John Fields
• [Bioperl-guts-l] [15024] bioperl-live/trunk/t: po, not poa   Christopher John Fields
• [Bioperl-guts-l] [15025] bioperl-live/trunk/t: fix subversion tags   Christopher John Fields
• [Bioperl-guts-l] [15026] bioperl-live/trunk/Bio/Seq/LargeLocatableSeq.pm: silence the warnings about removing the temporary files.   Heikki Lehvaslaiho
• [Bioperl-guts-l] [15027] bioperl-live/trunk/Bio/Seq/Meta.pm: fix POD syntax   Heikki Lehvaslaiho
• [Bioperl-guts-l] [15028] bioperl-live/trunk/Bio/TreeIO/phyloxml.pm: get rid off "my" variable redeclaration warning   Heikki Lehvaslaiho
• [Bioperl-guts-l] [15029] bioperl-live/trunk/Bio/Search/SearchUtils.pm: POD fix   Heikki Lehvaslaiho
• [Bioperl-guts-l] [Bug 2337] BDB flatfile index should store global configuration data in BDB   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15030] bioperl-ext/trunk/Bio/Ext/Align: ext patches (courtesy Thomas Jahns )   Christopher John Fields
• [Bioperl-guts-l] [Bug 2637] new modules for HIV sequence queries   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2637] new modules for HIV sequence queries   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2686] WU-BLAST XML support   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2686] WU-BLAST XML support   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15031] bioperl-live/trunk/Bio/SearchIO/blastxml.pm: [bug 2686]   Christopher John Fields
• [Bioperl-guts-l] [Bug 2686] WU-BLAST XML support   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15032] bioperl-live/trunk/t/blast_pull.t: Redundant; file was renamed SearchIO_blast_pull.t.   Christopher John Fields
• [Bioperl-guts-l] [Bug 2637] new modules for HIV sequence queries   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15033] bioperl-live/trunk/Bio/AlignIO/stockholm.pm: [bug 2567]   Christopher John Fields
• [Bioperl-guts-l] [15034] bioperl-live/trunk/Bio/Graphics/FeatureFile.pm: squashed occasional unit variable warning   Lincoln Stein
• [Bioperl-guts-l] [Bug 2689] New: LocatableSeq::subseq with mapping and frameshift functionality   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2689] LocatableSeq::subseq with mapping and frameshift functionality   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2689] LocatableSeq::subseq with mapping and frameshift functionality   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2689] LocatableSeq::subseq with mapping and frameshift functionality   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2689] LocatableSeq::subseq with mapping and frameshift functionality   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15035] bioperl-live/trunk/t: Big reorganization of SeqIO tests.   Dave Messina
• [Bioperl-guts-l] [Bug 2384] Segmentation Fault in Bio::Tools::dpAlign::pairwise_alignment_score   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2514] Run tests with binaries installed   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2384] Segmentation Fault in Bio::Tools::dpAlign::pairwise_alignment_score   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 2492] Method "pi" in package Bio::PopGen::Statistics   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15036] bioperl-live/trunk/t: move into directory structure (DaveM++)   Christopher John Fields
• [Bioperl-guts-l] [15037] bioperl-live/trunk/t: move into directory structure   Christopher John Fields
• [Bioperl-guts-l] [15038] bioperl-live/trunk/t/cross_match.t: remove redundant copy   Christopher John Fields
• [Bioperl-guts-l] [15039] bioperl-live/trunk/Build.PL: recurse into test subdirectories ( means any non-test filed in t/ must not end in *.t!)   Christopher John Fields
• [Bioperl-guts-l] [15040] bioperl-live/trunk/t/data/codeml_lysozyme: rename ( recursive tests think this is a test file)   Christopher John Fields
• [Bioperl-guts-l] [15041] bioperl-live/trunk/t/SeqIO: '::', not ':'   Christopher John Fields
• [Bioperl-guts-l] [Bug 2689] LocatableSeq::subseq with mapping and frameshift functionality   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15042] bioperl-live/trunk/t/SeqIO/abi.t: correct test file name   Christopher John Fields
• [Bioperl-guts-l] [15043] bioperl-live/trunk/t/SeqIO/ctf.t: test file name and test # correction   Christopher John Fields
• [Bioperl-guts-l] [15044] bioperl-live/trunk/Bio/SeqIO/chadoxml.pm: hash ref, not a hash   Christopher John Fields
• [Bioperl-guts-l] [15045] bioperl-live/trunk/Bio/SeqIO/bsml.pm: Add warning for missing data (real bug)   Christopher John Fields
• [Bioperl-guts-l] [15046] bioperl-live/trunk/Bio/SeqIO/bsml.pm: rearrange to avoid unnecessary warnings   Christopher John Fields
• [Bioperl-guts-l] [15047] bioperl-live/trunk/t/EUtilities.t: switching EUtilities. t over to BioperlTest style test initialization.   Dave Messina
• [Bioperl-guts-l] [15048] bioperl-live/trunk: verbose mistakenly left on in PrimarySeq->new, which was causing RootIO to be verbose about its tempfile handling after.   Dave Messina
• [Bioperl-guts-l] [Bug 2689] LocatableSeq::subseq with mapping and frameshift functionality   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2336] bp_bioflat_index.pl and Bio::DB::Flat::BDB::fasta creates incorrect index   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15049] bioperl-live/trunk/t/SeqIO/interpro.t: adding more diagnostic messages to t/SeqIO/intepro.t   Dave Messina
• [Bioperl-guts-l] [Bug 2513] creating a Bio::SeqFeature::Annotation object downloads the entire so.obo   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2439] multiple results HTMLResultWriter.pm and non-redundant entries in SearchIO   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2456] reroot function (Bio::Tree::TreeFunctionsI) shifts bootstrap values   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2213] crashes on downloading NCBI records   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2247] Have Bio::SearchIO::blast methods available for other BLAST parsers   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2213] crashes on downloading NCBI records   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2280] crash on the attempt to store same sequence in a diff. namespace   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2275] GO Upload with bp_load_ontology.pl throws errors   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2275] GO Upload with bp_load_ontology.pl throws errors   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2092] Can't store proteins with species using bioperl-db   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2472] postgreSQL v8.3 automatic casts limited may necessitate explicit cast   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2474] postgres 8.3 - load_seqdatabase.pl / swissprot   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2337] BDB flatfile index should store global configuration data in BDB   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15050] bioperl-live/trunk/t/flat.t: Bug 2336, test length of each sequence in tmp.fst   Brian Osborne
• [Bioperl-guts-l] [15051] bioperl-live/trunk/t/data/testaln.stockholm: silence GuessSeqFormat .t warnings (not sure if old version was even legal Stockholm format)   Christopher John Fields

Last message date: Sun Nov 30 17:19:12 EST 2008
Archived on: Wed Dec 3 19:15:23 EST 2008

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