September 2008 Archives by thread

• Messages sorted by: [ subject ] [ author ] [ date ]
• More info on this list...

Starting: Mon Sep 1 02:18:57 EDT 2008
Ending: Sat Sep 27 01:13:22 EDT 2008
Messages: 97

• [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 2577] Bio::Assembly and Bio::Assembly::IO can exceed the set open file ulimit   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14841] bioperl-ext/trunk/Bio/Ext/Align/libs: include errno definition   Jason Stajich
• [Bioperl-guts-l] [14842] bioperl-ext/trunk/Bio/Ext/Align/libs/makefile: -fPIC needed for lib construction   Jason Stajich
• [Bioperl-guts-l] [14843] bioperl-ext/trunk/Bio/Ext/Align/libs/sw.h: get rid of some unended comment warnings from C compiler   Jason Stajich
• [Bioperl-guts-l] [14844] bioperl-db/trunk/Bio/DB/BioSQL/OBDA.pm: Fixed to use placeholders and a named query, rather than doing the quoting   Hilmar Lapp
• [Bioperl-guts-l] [14845] bioperl-db/trunk/t/16obda.t: Mostly cosmetic change in how the config file is written to silence a warning .   Hilmar Lapp
• [Bioperl-guts-l] [14846] bioperl-db/trunk/Bio/DB/DBI: Migrated code to capabilities of more modern DBI and DBD versions.   Hilmar Lapp
• [Bioperl-guts-l] [14847] bioperl-db/trunk/Bio/DB/BioSQL/BasePersistenceAdaptor.pm: Made sure that the persistence driver's prepare() and bind_param() front-ends   Hilmar Lapp
• [Bioperl-guts-l] [14848] bioperl-db/trunk/t/03simpleseq.t: Added test for inserting, updating, and constraining char columns using numeric   Hilmar Lapp
• [Bioperl-guts-l] [14849] bioperl-live/trunk: testing translation between nhx and phyloxml   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [14850] bioperl-live/trunk/Bio/Coordinate/Result.pm: small documentation fix   George Hartzell
• [Bioperl-guts-l] [14851] bioperl-live/trunk/Bio/Coordinate/ExtrapolatingPair.pm: small documentation typo fix   George Hartzell
• [Bioperl-guts-l] [14852] bioperl-live/trunk/Bio/Coordinate/Graph.pm: small documentation typo fix   George Hartzell
• [Bioperl-guts-l] [14853] bioperl-live/trunk/Bio/Coordinate/Graph.pm: small documentation typo and grammar fix   George Hartzell
• [Bioperl-guts-l] [14854] bioperl-live/trunk/Bio/Coordinate/Graph.pm: small documentation typo fix   George Hartzell
• [Bioperl-guts-l] [14855] bioperl-live/trunk/Bio/Coordinate/Pair.pm: remove a spurious line creating an unneeded object   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14856] bioperl-live/trunk/Bio/Graphics/Glyph/heat_map.pm: essential ideogram glyph base class missing   Lincoln Stein
• [Bioperl-guts-l] [14857] bioperl-live/trunk/Bio: fixed bugs that interfered with the display of stranded features defined using the FeatureFile format   Lincoln Stein
• [Bioperl-guts-l] [Bug 2579] New: Genbank parse gives wrong gene DNA sequence for split genes   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2579] Genbank parse gives wrong gene DNA sequence for split genes   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14858] bioperl-live/trunk/Bio/Tree/Node.pm: Document that get_tag_values() return variable is context sensitive (array of scalar)   Heikki Lehvaslaiho
• [Bioperl-guts-l] [Bug 2580] New: enhancement for Bio::SeqIO::interpro to include GO items when present   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2580] enhancement for Bio::SeqIO::interpro to include GO items when present   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2580] enhancement for Bio::SeqIO::interpro to include GO items when present   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2580] enhancement for Bio::SeqIO::interpro to include GO items when present   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2580] enhancement for Bio::SeqIO::interpro to include GO items when present   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14859] bioperl-live/trunk/Bio/Assembly/IO.pm: Documentation improvement   Florent E Angly
• [Bioperl-guts-l] [14860] bioperl-live/trunk/Bio/Assembly/Contig.pm: Update number of sequences and their order when removing a sequence from a contig   Florent E Angly
• [Bioperl-guts-l] [14861] bioperl-live/trunk/Bio/Assembly/IO/tigr.pm: Bug correction regarding read location in a contig   Florent E Angly
• [Bioperl-guts-l] [14862] bioperl-live/trunk: bug 2580   Christopher John Fields
• [Bioperl-guts-l] [14863] bioperl-live/trunk/Bio/SeqFeatureI.pm: bug 2579   Christopher John Fields
• [Bioperl-guts-l] [Bug 2581] New: HMMER parse error   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2581] HMMER parse error   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2581] HMMER parse error   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14864] bioperl-live/trunk/Bio/DB: fixed primary_id method to return a more rational result   Lincoln Stein
• [Bioperl-guts-l] [14865] bioperl-network/trunk/Bio/Network/ProteinNet.pm: Minor edits   Brian Osborne
• [Bioperl-guts-l] [14866] bioperl-network/trunk/Bio/Network/ProteinNet.pm: Add methods to get random node or edge   Brian Osborne
• [Bioperl-guts-l] [14867] bioperl-network/trunk: Add get_random* and tests   Brian Osborne
• [Bioperl-guts-l] [14868] bioperl-network/trunk:   Brian Osborne
• [Bioperl-guts-l] [14869] bioperl-live/trunk/Bio/Tree/Node.pm: Start counting internal IDs from 1.   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14870] bioperl-live/trunk/Bio/SeqIO/entrezgene.pm: use direct object syntax   Christopher John Fields
• [Bioperl-guts-l] [14871] bioperl-live/trunk/Bio/Tools/Run/RemoteBlast.pm: add a few new ( untested) URLAPI parameters   Christopher John Fields
• [Bioperl-guts-l] [14872] bioperl-live/trunk/Bio/Annotation/TagTree.pm: Create Data:: Stag node lazily; always use node() to grab node instance   Christopher John Fields
• [Bioperl-guts-l] [14873] bioperl-live/trunk/Build.PL: removed spurious dependency on Text:: Shellwords   Lincoln Stein
• [Bioperl-guts-l] [14874] bioperl-live/trunk/Bio/LocatableSeq.pm: * always warn about passing wrong end() coordinate   Christopher John Fields
• [Bioperl-guts-l] [14875] bioperl-live/trunk/Bio/AlignIO/psi.pm: -end parameter does not take gaps into account   Christopher John Fields
• [Bioperl-guts-l] [14876] bioperl-live/trunk/Bio/AlignIO/arp.pm: partial fix for arp ( -end now works and counts ? as ambigious sequence instead of gap)   Christopher John Fields
• [Bioperl-guts-l] [14877] bioperl-live/trunk/Bio/AlignIO/arp.pm: remove debugging statement   Christopher John Fields
• [Bioperl-guts-l] [14878] bioperl-live/trunk/Bio/DB/Query/GenBank.pm: Minor edits   Brian Osborne
• [Bioperl-guts-l] [14879] bioperl-live/trunk/scripts/utilities/download_query_genbank.PLS: Add Jason's script   Brian Osborne
• [Bioperl-guts-l] [14880] bioperl-live/trunk/Bio/TreeIO/phyloxml.pm: phyloxml more documentation   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [14881] bioperl-live/trunk/Bio/TreeIO/phyloxml.pm: phyloxml correct pod format   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [14882] bioperl-live/trunk/Bio: Relation/AnnotatableNode correct pod   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [14883] bioperl-live/trunk/Bio/AlignIO/msf.pm: match '*' and '?' as well   Jason Stajich
• [Bioperl-guts-l] [14884] bioperl-live/trunk/Bio/PrimarySeq.pm: typo   Christopher John Fields
• [Bioperl-guts-l] [14885] bioperl-live/trunk/Bio/AlignIO/stockholm.pm: * fix start/end/strand   Christopher John Fields
• [Bioperl-guts-l] [14886] bioperl-live/trunk/Bio/AlignIO/xmfa.pm: make LocatableSeq::end() consistent   Christopher John Fields
• [Bioperl-guts-l] [14887] bioperl-live/trunk/Bio/AlignIO/xmfa.pm: fix xmfa.pm parsing oops   Christopher John Fields
• [Bioperl-guts-l] [14888] bioperl-live/trunk: * XMFA alignment doesn' t correspond to XMFA spec (http://asap.ahabs.wisc.edu/mauve-aligner/ mauve-user-guide/mauve-output-file-formats.html); changed to correct start/ end coordinates (code checks this)   Christopher John Fields
• [Bioperl-guts-l] [14889] bioperl-live/trunk/t/AlignIO.t: Test data matches new XMFA example   Christopher John Fields
• [Bioperl-guts-l] [14890] bioperl-live/trunk/Bio/AlignIO/mega.pm: MEGA now resets $GAP_SYMBOLS and $OTHER_SYMBOLS to get around sequence ambiguity issues   Christopher John Fields
• [Bioperl-guts-l] [14891] bioperl-live/trunk/Bio/AlignIO/nexus.pm: Fix nexus issues with seq.   Christopher John Fields
• [Bioperl-guts-l] [14892] bioperl-live/trunk/t/AlignIO.t: test result changed (start always < end)   Christopher John Fields
• [Bioperl-guts-l] [14893] bioperl-live/trunk/Bio/Align/Utilities.pm: set -end to coorespond to sequence end   Christopher John Fields
• [Bioperl-guts-l] [14894] bioperl-live/trunk/t: update tests ( seq length change in record verified)   Christopher John Fields
• [Bioperl-guts-l] [14895] bioperl-live/trunk/t: passing TODO's (?!?)   Christopher John Fields
• [Bioperl-guts-l] [14896] bioperl-live/trunk/t/InstanceSite.t: 1965 + 6 -1 = 1970, not 1999   Christopher John Fields
• [Bioperl-guts-l] [14897] bioperl-live/trunk/Bio/Annotation/TagTree.pm: * No longer a stub   Christopher John Fields
• [Bioperl-guts-l] [14898] bioperl-live/trunk/Bio/Tree/TreeFunctionsI.pm: added is_binary()   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14899] bioperl-live/trunk: Tests for is_binary().Added set_tag_value().   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14900] bioperl-live/trunk/t/seq_quality.t: Use 'warning_like' for instances where a regex match is needed   Christopher John Fields
• [Bioperl-guts-l] [14901] bioperl-live/trunk/t/BioGraphics.t: removed another text:: shellwords dependency   Lincoln Stein
• [Bioperl-guts-l] [14902] bioperl-live/trunk/Bio/DB/GFF/Aggregator/orf.pm: added missing aggregator needed by default gbrowse installation   Lincoln Stein
• [Bioperl-guts-l] [14903] bioperl-live/trunk/Bio/DB/SeqFeature/Store: killed a few uninit variable warnings   Lincoln Stein
• [Bioperl-guts-l] [14904] bioperl-live/trunk: method to add trait values in into leaf nodes ( add_trait), indicator values for trait distribution (ps, ai, mc) and tree shape (cherries)   Heikki Lehvaslaiho
• [Bioperl-guts-l] [14905] bioperl-live/trunk/Bio/Root/Version.pm: increased the version number to be higher than the current release version   Senduran Balasubramaniam
• [Bioperl-guts-l] [14906] bioperl-live/trunk/Bio/Graphics: added documentation for bicolor options   Lincoln Stein
• [Bioperl-guts-l] [14907] bioperl-live/trunk: add_phyloXML_annotation   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [Bug 2593] New: Storable fails for SeqFeatures   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2593] Storable fails for SeqFeatures   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2594] New: Bio::Species memory leak   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] [14908] bioperl-live/trunk/Bio/Species.pm: keep memory leak fix from previous commit and solve the Speciest. t test failures introduced.   Senduran Balasubramaniam
• [Bioperl-guts-l] [Bug 2595] New: COMPOSITION_BASED_STATISTICS values should be 0/1   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2595] COMPOSITION_BASED_STATISTICS values should be 0/1   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14909] bioperl-live/trunk/Bio/Tools/Run/RemoteBlast.pm: [BUG] fix bug 2595   Christopher John Fields
• [Bioperl-guts-l] [14910] bioperl-live/trunk/Bio/SeqFeature/Generic.pm: [BUG] bug 2593   Christopher John Fields
• [Bioperl-guts-l] [Bug 2559] Out of memory (malloc error)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14911] bioperl-live/trunk/Bio/TreeIO/phyloxml.pm: add default first line to phyloXML output   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [Bug 2598] New: Missing Ambiguous Protein Letter J   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2598] Missing Ambiguous Protein Letter J   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2598] Missing Ambiguous Protein Letter J   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2598] Missing Ambiguous Protein Letter J   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14912] bioperl-live/trunk/Bio/Tools/SeqStats.pm: [BUG] bugfix for # 2598 ( add 'J')   Christopher John Fields
• [Bioperl-guts-l] [Bug 2599] New: DBLINK to replace PROJECT for GenBank format annotation   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14913] bioperl-live/trunk/Bio/Tools/SeqStats.pm: [BUG] bug 2598   Christopher John Fields

Last message date: Sat Sep 27 01:13:22 EDT 2008
Archived on: Sat Sep 27 01:13:24 EDT 2008

• Messages sorted by: [ subject ] [ author ] [ date ]
• More info on this list...