January 2010 Archives by thread

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Starting: Sat Jan 2 13:50:55 EST 2010
Ending: Sun Jan 31 23:48:41 EST 2010
Messages: 330

• [Bioperl-guts-l] [16570] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run: begin entrez soap client (on branch)   Mark Allen Jensen
• [Bioperl-guts-l] [16571] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/ESoap/WSDL. pm: build out WSDL.pm   Mark Allen Jensen
• [Bioperl-guts-l] [16572] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/ESoap/WSDL. pm: modularizatation   Mark Allen Jensen
• [Bioperl-guts-l] [16573] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/ESoap/WSDL. pm: extracting request and result params from wsdl   Mark Allen Jensen
• [Bioperl-guts-l] [16574] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/ESoap/WSDL. pm: deal with ref attribute as well   Mark Allen Jensen
• [Bioperl-guts-l] [16575] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/ESoap/WSDL. pm: check for circularities   Mark Allen Jensen
• [Bioperl-guts-l] [16576] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/ESoap/WSDL. pm: pod build-out   Mark Allen Jensen
• [Bioperl-guts-l] [16577] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run: pod tweak   Mark Allen Jensen
• [Bioperl-guts-l] [16578] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run: building out main module   Mark Allen Jensen
• [Bioperl-guts-l] [16579] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/ESoap/WSDL. pm: bug squish   Mark Allen Jensen
• [Bioperl-guts-l] [16580] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/ESoap.pm: ParameterBaseI compliance   Mark Allen Jensen
• [Bioperl-guts-l] [16581] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/ESoap/WSDL. pm: WSDL now imports 'xs:import'ed schemas   Mark Allen Jensen
• [Bioperl-guts-l] [16582] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run: added basic SOAP call   Mark Allen Jensen
• [Bioperl-guts-l] [16583] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run: provide local copy of wsdl   Mark Allen Jensen
• [Bioperl-guts-l] [16584] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run: starting on soap result message parsing; propset   Mark Allen Jensen
• [Bioperl-guts-l] [16585] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run: round out pod for ESoap; tweak some WSDL return values   Mark Allen Jensen
• [Bioperl-guts-l] [16586] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/ESoap/ FetchAdaptor.pm: bug squish   Mark Allen Jensen
• [Bioperl-guts-l] [16587] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/ESoap/WSDL. pm: Bio::WebAgent everywhere   Mark Allen Jensen
• [Bioperl-guts-l] [16588] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/ SoapEUtilities.pm: start the high-level module   Mark Allen Jensen
• [Bioperl-guts-l] [16589] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/ SoapEUtilities.pm: begin central run method; more accessors   Mark Allen Jensen
• [Bioperl-guts-l] [16590] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/ SoapEUtilities.pm: provide for raw xml retrieval; bug squishes   Mark Allen Jensen
• [Bioperl-guts-l] [16591] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run: Result object to parse/wrap soap repsonse   Mark Allen Jensen
• [Bioperl-guts-l] [16592] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/ SoapEUtilities/Result.pm: some conveniences and back-compat   Mark Allen Jensen
• [Bioperl-guts-l] [16593] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/ SoapEUtilities/Result.pm: propset   Mark Allen Jensen
• [Bioperl-guts-l] [16594] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run: facilities for usehistory/webenv/querykey; tweaks   Mark Allen Jensen
• [Bioperl-guts-l] [16595] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run: Result POD; tweaks   Mark Allen Jensen
• [Bioperl-guts-l] [16596] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/ESoap.pm: fix for multiple ids   Mark Allen Jensen
• [Bioperl-guts-l] [16597] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/ SoapEUtilities/Result.pm: add some goodies   Mark Allen Jensen
• [Bioperl-guts-l] [16598] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/ESoap/WSDL. pm: also handle included schemata   Mark Allen Jensen
• [Bioperl-guts-l] [16599] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/ SoapEUtilities.pm: working on autofetch   Mark Allen Jensen
• [Bioperl-guts-l] [16600] bioperl-live/trunk/Bio/Index/Blast.pm: Allow other SearchIO text-based parsers, even though they're borked ATM   Christopher John Fields
• [Bioperl-guts-l] [16601] bioperl-live/trunk/Bio/Index/Abstract.pm: speling eror   Christopher John Fields
• [Bioperl-guts-l] [16602] bioperl-live/trunk/Bio/Search/Result/BlastPullResult.pm: At least parse the query bits if no hit is returned.   Christopher John Fields
• [Bioperl-guts-l] [Bug 2978] New: Bio::SimpleAlign returned Bio::LocatableSeq objects subject strand undef   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [16603] bioperl-live/trunk/Bio/Search/Result/BlastPullResult.pm: fix to return w/o hits if no hits are found   Christopher John Fields
• [Bioperl-guts-l] [16604] bioperl-run/trunk/lib/Bio/Tools/Run/Bowtie.pm: Will now create a Bio::Assembly::Scaffold object.   Dan Kortschak
• [Bioperl-guts-l] [Bug 2979] New: Bio::SeqIO::multifasta   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2979] Bio::SeqIO::multifasta   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [16605] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run: work   Mark Allen Jensen
• [Bioperl-guts-l] [16606] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run: refactor   Mark Allen Jensen
• [Bioperl-guts-l] [16607] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/ESoap.pm: REALLY fix ids   Mark Allen Jensen
• [Bioperl-guts-l] [16608] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run: Result returns a real count on efetch; start seq adaptor   Mark Allen Jensen
• [Bioperl-guts-l] [16609] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/ SoapEUtilities: model FetchAdaptor after SeqIO system   Mark Allen Jensen
• [Bioperl-guts-l] [16610] bioperl-live/trunk/Bio/DB/SeqFeature/Segment.pm: removed hanging debug statement   Lincoln Stein
• [Bioperl-guts-l] [16611] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/ SoapEUtilities/FetchAdaptor/seq.pm: progress on seq adaptor   Mark Allen Jensen
• [Bioperl-guts-l] [16612] bioperl-live/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: bugfix - fileswitch token for filespec was not removed during validation   Dan Kortschak
• [Bioperl-guts-l] [16613] bioperl-run/trunk/lib/Bio/Tools/Run/Bowtie.pm: POD improvements, change default state to object creation and SAM output   Dan Kortschak
• [Bioperl-guts-l] [16614] bioperl-live/trunk/Bio/PullParserI.pm: add an exception if the position passed is not defined   Christopher John Fields
• [Bioperl-guts-l] [16615] bioperl-live/trunk/Bio/Search/Hit/BlastPullHit.pm: return unless a chunk position is defined   Christopher John Fields
• [Bioperl-guts-l] [16616] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/ SoapEUtilities/FetchAdaptor/seq.pm: now parsing species, references, comments successfully; on to features   Mark Allen Jensen
• [Bioperl-guts-l] [16617] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/ SoapEUtilities/FetchAdaptor/seq.pm: features and species appear workable ( thanks Bio::SeqIO::genbank peeps!)   Mark Allen Jensen
• [Bioperl-guts-l] [Bug 2981] New: Bio::Seq::Quality->trunc() doesn't trim raw_quality in Bio::SeqIO::fastq   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2981] Bio::Seq::Quality->trunc() doesn't trim raw_quality in Bio::SeqIO::fastq   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [16618] bioperl-live/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: POD fix   Dan Kortschak
• [Bioperl-guts-l] [16619] bioperl-live/trunk/Bio/Assembly/Tools/ContigSpectrum.pm: Improvements in the calculation of the contig spectrum effective assembly parameters   Florent E Angly
• [Bioperl-guts-l] [16620] bioperl-live/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: bug fix - %args out of sync with @args/@req -> filespec requirement throw   Dan Kortschak
  • [Bioperl-guts-l] [16620] bioperl-live/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: bug fix - %args out of sync with @args/@req -> filespec requirement throw   Jason Stajich
    • [Bioperl-guts-l] [16620] bioperl-live/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: bug fix - %args out of sync with @args/@req -> filespec requirement throw   Dan Kortschak
      • [Bioperl-guts-l] [16620] bioperl-live/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: bug fix - %args out of sync with @args/@req -> filespec requirement throw   Mark A. Jensen
      • [Bioperl-guts-l] [16620] bioperl-live/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: bug fix - %args out of sync with @args/@req -> filespec requirement throw   Dan Kortschak
• [Bioperl-guts-l] [16621] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/ SoapEUtilities/LinkAdaptor.pm: adaptor/iterator for link sets (via elink)   Mark Allen Jensen
• [Bioperl-guts-l] [16622] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run: various massages for elink   Mark Allen Jensen
• [Bioperl-guts-l] [16623] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/ SoapEUtilities/LinkAdaptor.pm: add id_map() - provides from_id => to_id correspondence   Mark Allen Jensen
• [Bioperl-guts-l] [16624] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/ SoapEUtilities: a docsum adaptor/iterator for esummary results   Mark Allen Jensen
• [Bioperl-guts-l] [16625] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run/ SoapEUtilities/DocSumAdaptor.pm: docsum iterator now parses all items ( one way or other)   Mark Allen Jensen
• [Bioperl-guts-l] [16626] bioperl-dev/branches/eutils-soap-run/lib/Bio/DB/: create DB in bioperl-run/lib/Bio (on branch); for SoapEU refactor   Mark Allen Jensen
• [Bioperl-guts-l] [16627] bioperl-dev/branches/eutils-soap-run/lib/Bio/DB: refactor SoapEU and friends to bioperl-run/lib/Bio/DB   Mark Allen Jensen
• [Bioperl-guts-l] [16628] bioperl-dev/branches/eutils-soap-run/lib/Bio/Tools/Run: SoapEU refactor cleanup   Mark Allen Jensen
• [Bioperl-guts-l] [16629] bioperl-dev/branches/eutils-soap-run/lib/Bio/DB/SoapEUtilities.pm: work in auto adaptor; fetches, links, docsums (oh my)   Mark Allen Jensen
• [Bioperl-guts-l] [16630] bioperl-dev/branches/eutils-soap-run/lib/Bio/DB: tweaks   Mark Allen Jensen
• [Bioperl-guts-l] [16631] bioperl-dev/branches/eutils-soap-run/t: begin SoapEU test suite   Mark Allen Jensen
• [Bioperl-guts-l] [16632] bioperl-dev/branches/eutils-soap-run: fix parameters_changed in ESoap; allow parameter accessor delegation in SoapEU; more tests   Mark Allen Jensen
• [Bioperl-guts-l] [16633] bioperl-dev/branches/eutils-soap-run/lib/Bio/DB/SoapEUtilities/ Result.pm: futz with ids() accessor: specials for different eutils   Mark Allen Jensen
• [Bioperl-guts-l] [16634] bioperl-dev/branches/eutils-soap-run/lib/Bio/DB: bug squishes   Mark Allen Jensen
• [Bioperl-guts-l] [16635] bioperl-dev/branches/eutils-soap-run/t: more SoapEU tests   Mark Allen Jensen
• [Bioperl-guts-l] [16636] bioperl-live/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: Bugfixes and refactor/revise executable/executables.   Dan Kortschak
• [Bioperl-guts-l] [16637] bioperl-dev/branches/eutils-soap-run/t/SoapEU.t: most non-network tests done   Mark Allen Jensen
• [Bioperl-guts-l] [16638] bioperl-dev/branches/eutils-soap-run/lib/Bio/DB/SoapEUtilities/ Result.pm: bug squishes   Mark Allen Jensen
• [Bioperl-guts-l] [16639] bioperl-dev/branches/eutils-soap-run/t: separate unit and functional tests   Mark Allen Jensen
• [Bioperl-guts-l] [16640] bioperl-run/trunk/lib/Bio/Tools/Run: Rewrite bowtie module to use MAJ's CommandExts.   Dan Kortschak
• [Bioperl-guts-l] [16641] bioperl-dev/branches/eutils-soap-run/lib/Bio/DB/SoapEUtilities/ DocSumAdaptor.pm: fix item_list()   Mark Allen Jensen
• [Bioperl-guts-l] [16642] bioperl-dev/branches/eutils-soap-run/t/SoapEU-unit.t: linkset and docsum adaptor tests   Mark Allen Jensen
• [Bioperl-guts-l] [16643] bioperl-dev/branches/eutils-soap-run/t/SoapEU-unit.t: propset   Mark Allen Jensen
• [Bioperl-guts-l] [16644] bioperl-dev/branches/eutils-soap-run/lib/Bio/DB: allow for local wsdl file in SoapEU constructor   Mark Allen Jensen
• [Bioperl-guts-l] [16645] bioperl-dev/branches/eutils-soap-run/lib/Bio/DB/ESoap/WSDL.pm: get fetch db directly from wsdl namespace nsef   Mark Allen Jensen
• [Bioperl-guts-l] [16646] bioperl-dev/branches/eutils-soap-run/lib/Bio/DB/ESoap/WSDL.pm: oops   Mark Allen Jensen
• [Bioperl-guts-l] [16647] bioperl-dev/branches/eutils-soap-run/lib/Bio/DB: oops X 2   Mark Allen Jensen
• [Bioperl-guts-l] [16648] bioperl-dev/branches/eutils-soap-run/t: (some not all) tests for seq FetchAdaptor; local wsdl   Mark Allen Jensen
• [Bioperl-guts-l] [Bug 2956] ranges in EMBL output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [16649] bioperl-dev/branches/eutils-soap-run/t/SoapEU-unit.t: unit tests finished   Mark Allen Jensen
• [Bioperl-guts-l] [16650] bioperl-dev/branches/eutils-soap-run/lib/Bio/DB/SoapEUtilities/ FetchAdaptor/seq.pm: try to speed it up a bit   Mark Allen Jensen
• [Bioperl-guts-l] [Bug 2982] New: Parsing multiple contig EMBL records (CO lines instead of SQ lines)   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2982] Parsing multiple contig EMBL records (CO lines instead of SQ lines)   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2982] Parsing multiple contig EMBL records (CO lines instead of SQ lines)   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2982] Parsing multiple contig EMBL records (CO lines instead of SQ lines)   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2982] Parsing multiple contig EMBL records (CO lines instead of SQ lines)   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2982] Parsing multiple contig EMBL records (CO lines instead of SQ lines)   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2982] Parsing multiple contig EMBL records (CO lines instead of SQ lines)   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2982] Parsing multiple contig EMBL records (CO lines instead of SQ lines)   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2982] Parsing multiple contig EMBL records (CO lines instead of SQ lines)   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2982] Parsing multiple contig EMBL records (CO lines instead of SQ lines)   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2982] Parsing multiple contig EMBL records (CO lines instead of SQ lines)   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2982] Parsing multiple contig EMBL records (CO lines instead of SQ lines)   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2982] Parsing multiple contig EMBL records (CO lines instead of SQ lines)   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2982] Parsing multiple contig EMBL records (CO lines instead of SQ lines)   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2982] Parsing multiple contig EMBL records (CO lines instead of SQ lines)   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2982] Parsing multiple contig EMBL records (CO lines instead of SQ lines)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2956] ranges in EMBL output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [16651] bioperl-dev/branches/eutils-soap-run/lib/Bio/DB/SoapEUtilities/ FetchAdaptor/species.pm: FetchAdaptor for taxonomy (species) iteration ( returns Bio::Species objs)   Mark Allen Jensen
• [Bioperl-guts-l] [16652] bioperl-dev/branches/eutils-soap-run/lib/Bio/DB: mods for autoadapting lone efetches, selecting correct fetchadaptors   Mark Allen Jensen
• [Bioperl-guts-l] [16653] bioperl-dev/branches/eutils-soap-run/lib/Bio/DB/SoapEUtilities/ FetchAdaptor/species.pm: propset   Mark Allen Jensen
• [Bioperl-guts-l] [16654] bioperl-dev/branches/eutils-soap-run/t/SoapEU-function.t: functional (network-requiring) tests for SoapEU, based on the EUtils Cookbook   Mark Allen Jensen
• [Bioperl-guts-l] [16655] bioperl-dev/branches/eutils-soap-run/lib/Bio/DB: kludges around NCBI WSDL inconsistencies; aliases for einfo results   Mark Allen Jensen
• [Bioperl-guts-l] [16656] bioperl-dev/branches/eutils-soap-run/t/SoapEU-function.t: SoapEU function tests proceeding through EUtils Cookbook...   Mark Allen Jensen
• [Bioperl-guts-l] [16657] bioperl-dev/branches/eutils-soap-run/lib/Bio/DB/SoapEUtilities/ GQueryAdaptor.pm: Entrez global query adaptor for SoapEU   Mark Allen Jensen
• [Bioperl-guts-l] [16658] bioperl-dev/branches/eutils-soap-run/lib/Bio/DB/SoapEUtilities/ GQueryAdaptor.pm: propset   Mark Allen Jensen
• [Bioperl-guts-l] [16659] bioperl-dev/branches/eutils-soap-run/t/SoapEU-function.t: linksets tests   Mark Allen Jensen
• [Bioperl-guts-l] [16660] bioperl-dev/branches/eutils-soap-run/lib/Bio/DB: continuing futzing   Mark Allen Jensen
• [Bioperl-guts-l] [16661] bioperl-live/trunk/Bio/Assembly/Tools/ContigSpectrum.pm: Providing explicit Bio::LocatableSeq end() in Bio::Assembly::Tools:: ContigSpectrum::_overlap_alignment   Florent E Angly
• [Bioperl-guts-l] [16662] bioperl-live/trunk/Bio/Assembly/Tools/ContigSpectrum.pm: Removed some debugging code   Florent E Angly
• [Bioperl-guts-l] [16663] bioperl-dev/branches/eutils-soap-run/lib/Bio/DB/SoapEUtilities: adaptor futzes; added TSeq parsing (for fasta rettype) to FetchAdaptor:: seq.pm (very much faster than GBSeq parsing)   Mark Allen Jensen
• [Bioperl-guts-l] [16664] bioperl-dev/branches/eutils-soap-run/t/SoapEU-function.t: most simple Cookbook recipes tested here; am now official sick of writing tests (but more to come)   Mark Allen Jensen
• [Bioperl-guts-l] [16665] bioperl-dev/branches/eutils-soap-run/t/SoapEU-function.t: propset   Mark Allen Jensen
• [Bioperl-guts-l] [16666] bioperl-live/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: POD clean   Dan Kortschak
• [Bioperl-guts-l] [16667] bioperl-dev/branches/eutils-soap-run/lib/Bio/DB/SoapEUtilities: fill out pod for adaptor classes   Mark Allen Jensen
• [Bioperl-guts-l] [16668] bioperl-dev/branches/eutils-soap-run/lib/Bio/DB/SoapEUtilities: build out pod for fetch adaptors   Mark Allen Jensen
• [Bioperl-guts-l] [16669] bioperl-dev/branches/eutils-soap-run/lib/Bio/DB/SoapEUtilities.pm: building out the main SoapEU pod   Mark Allen Jensen
• [Bioperl-guts-l] [16670] bioperl-dev/branches/eutils-soap-run/lib/Bio/DB: main SoapEU pod   Mark Allen Jensen
• [Bioperl-guts-l] [16671] bioperl-dev/branches/eutils-soap-run/lib/Bio/DB/SoapEUtilities.pm: main SoapEU pod pretty much done   Mark Allen Jensen
• [Bioperl-guts-l] [Bug 2983] New: parsing via Bio::Tools::est2genome   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2983] parsing via Bio::Tools::est2genome   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2983] parsing via Bio::Tools::est2genome   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [16672] bioperl-dev/branches/eutils-soap-run/lib/Bio/DB/SoapEUtilities.pm: pod finish   Mark Allen Jensen
• [Bioperl-guts-l] [16673] bioperl-run/trunk/lib/Bio/DB/: DB path for bioperl-run   Mark Allen Jensen
• [Bioperl-guts-l] [16674] bioperl-dev/tags/soapeu-port-to-run-011210/: tag SoapEU port bioperl-dev -> bioperl-run/trunk   Mark Allen Jensen
• [Bioperl-guts-l] [16675] bioperl-run/trunk/lib/Bio/DB: merge SoapEU to bioperl-run trunk   Mark Allen Jensen
• [Bioperl-guts-l] [16676] bioperl-run/trunk/t: SoapEU tests to bioperl-run trunk   Mark Allen Jensen
• [Bioperl-guts-l] [16677] bioperl-run/trunk/t: remove cruft   Mark Allen Jensen
• [Bioperl-guts-l] [16678] bioperl-run/trunk/lib/Bio/DB: remove cruft   Mark Allen Jensen
• [Bioperl-guts-l] [16679] bioperl-run/trunk/t/SoapEU-function.t: require networking   Mark Allen Jensen
• [Bioperl-guts-l] [16680] bioperl-run/trunk/lib/Bio/DB/SoapEUtilities.pm: bug squish   Mark Allen Jensen
• [Bioperl-guts-l] [16681] bioperl-run/trunk/t: case   Mark Allen Jensen
• [Bioperl-guts-l] [16682] bioperl-run/trunk/lib/Bio/DB/SoapEUtilities.pm: pod fix   Mark Allen Jensen
• [Bioperl-guts-l] [16683] bioperl-run/trunk/lib/Bio/DB/SoapEUtilities/DocSumAdaptor.pm: soap issue   Mark Allen Jensen
• [Bioperl-guts-l] [16684] bioperl-run/trunk/lib/Bio/DB: eliminate warnings   Mark Allen Jensen
• [Bioperl-guts-l] [16685] bioperl-run/trunk/lib/Bio/DB/SoapEUtilities.pm: bug squish   Mark Allen Jensen
• [Bioperl-guts-l] [16686] bioperl-run/trunk/lib/Bio/DB/SoapEUtilities.pm: remove cruft   Mark Allen Jensen
• [Bioperl-guts-l] [16687] bioperl-run/trunk/lib/Bio/DB/SoapEUtilities.pm: bug squish   Mark Allen Jensen
• [Bioperl-guts-l] [Bug 2984] New: Only allows letters as characters in phylip format   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2984] Only allows letters as characters in phylip format   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2985] New: ProtPars.t passing but with lots of warnings   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2985] ProtPars.t passing but with lots of warnings   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2986] New: Documentation update for Phylip/Base.pm   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2986] Documentation update for Phylip/Base.pm   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2986] Documentation update for Phylip/Base.pm   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2987] New: Remove ClustalW warning when version checked   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2987] Remove ClustalW warning when version checked   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2988] New: New package Phylip/Pars.pm   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2988] New package Phylip/Pars.pm   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2988] New package Phylip/Pars.pm   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2988] New package Phylip/Pars.pm   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2988] New package Phylip/Pars.pm   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2988] New package Phylip/Pars.pm   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2988] New package Phylip/Pars.pm   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2989] New: SeqFeature with different sequence IDs but same range return true with overlaps()   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2989] SeqFeature with different sequence IDs but same range return true with overlaps()   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2990] New: Reconciling RangeI methods for split and fuzzy locations   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [16688] bioperl-live/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: Bug fix   Dan Kortschak
• [Bioperl-guts-l] [16689] bioperl-run/trunk/lib/Bio/Tools/Run/Bowtie.pm: Bug fix   Dan Kortschak
• [Bioperl-guts-l] [16690] bioperl-live/trunk/Bio/Assembly: Added Bio::Assembly::IO:: bowtie module.   Dan Kortschak
• [Bioperl-guts-l] [Bug 2991] New: StandAloneBlastPlus, can't locate object method "no_throw_on_crash"   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2991] StandAloneBlastPlus, can't locate object method "no_throw_on_crash"   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2991] StandAloneBlastPlus, can't locate object method "no_throw_on_crash"   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2991] StandAloneBlastPlus, can't locate object method "no_throw_on_crash"   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [16691] bioperl-live/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: revert to WrapperBase namespace (bug #2991)   Mark Allen Jensen
• [Bioperl-guts-l] [16692] bioperl-live/trunk/Bio/SeqIO/seqxml.pm: Updated header tag writing code such that only one of source or sourceVersion need be set , not both (to comply with spec).   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 2515] GenBank XML parser   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [16693] bioperl-run/trunk/lib/Bio/Tools/Run/Bowtie.pm: Revert WrapperBase include to follow its definition change.   Dan Kortschak
• [Bioperl-guts-l] [16694] bioperl-run/trunk/lib/Bio/Tools/Run/Bowtie/Config.pm: INIT block definition removed as unnecessary.   Dan Kortschak
• [Bioperl-guts-l] [Bug 2993] New: WrapperBase derived object cannot use Bio::DB::Sam when extended with CommandExts   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2993] WrapperBase derived object cannot use Bio::DB::Sam when extended with CommandExts   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2993] WrapperBase derived object cannot use Bio::DB::Sam when extended with CommandExts   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2993] WrapperBase derived object cannot use Bio::DB::Sam when extended with CommandExts   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2993] WrapperBase derived object cannot use Bio::DB::Sam when extended with CommandExts   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2993] WrapperBase derived object cannot use Bio::DB::Sam when extended with CommandExts   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2993] WrapperBase derived object cannot use Bio::DB::Sam when extended with CommandExts   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2993] WrapperBase derived object cannot use Bio::DB::Sam when extended with CommandExts   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [16695] bioperl-live/trunk/Bio/DB/SeqFeature/Store/memory.pm: Mitch' s patch for SF::Store   Christopher John Fields
• [Bioperl-guts-l] [16696] bioperl-live/trunk/Bio/SeqIO/seqxml.pm: Fixed reading and writing just the species (e.g.   Dave Messina
• [Bioperl-guts-l] [16697] bioperl-run/trunk/lib/Bio/Tools/Run: support for remote (NCBI) dbs   Mark Allen Jensen
• [Bioperl-guts-l] [Bug 2994] New: add new return codes for Bio::Tools::Run::RemoteBlast's retrieve_blast   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2994] add new return codes for Bio::Tools::Run::RemoteBlast's retrieve_blast   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2994] add new return codes for Bio::Tools::Run::RemoteBlast's retrieve_blast   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2994] add new return codes for Bio::Tools::Run::RemoteBlast's retrieve_blast   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [16698] bioperl-live/trunk/Bio/Tools/Run/RemoteBlast.pm: added informative return error constants; updated pod   Mark Allen Jensen
• [Bioperl-guts-l] [16699] bioperl-live/trunk/Bio/Tools/Run/RemoteBlast.pm: export return constants   Mark Allen Jensen
• [Bioperl-guts-l] [Bug 2970] Doesn't like: LVLNNNNNNNNNNLVNNNNNNNNNNNNNNNNNNNNNNNNVTTKPNK   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [16700] bioperl-live/trunk/Bio/Species.pm: updating species() POD to reflect its role as a getter/ setter for *just* species and not genus and species.   Dave Messina
• [Bioperl-guts-l] [16701] bioperl-live/trunk/Bio/Assembly/IO/bowtie.pm: Add capacity to use fasta refdb directly.   Dan Kortschak
• [Bioperl-guts-l] [Bug 2995] New: [TODO] Add tests for Mitch's patch to Bio::DB::SeqFeature::Store   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [16702] bioperl-live/trunk/Bio/SeqIO/embl.pm: fix for bug#2982   Mark Allen Jensen
• [Bioperl-guts-l] [16703] bioperl-live/trunk/t/SeqIO/embl.t: tests for bug#2982 fix   Mark Allen Jensen
• [Bioperl-guts-l] [16704] bioperl-live/trunk/t/data/bug2982.embl: test data for bug#2982   Mark Allen Jensen
• [Bioperl-guts-l] [16705] bioperl-live/trunk: Bug fix and add tests.   Dan Kortschak
• [Bioperl-guts-l] [16706] bioperl-run/trunk/lib/Bio/Tools/Run/Phylo/Phylip/Base.pm: patch pod (bug#2986); thanks Adam   Mark Allen Jensen
• [Bioperl-guts-l] [Bug 2996] New: StandAloneBlastPlus is looking for a program called "blast+"   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2996] StandAloneBlastPlus is looking for a program called "blast+"   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2996] StandAloneBlastPlus is looking for a program called "blast+"   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2996] StandAloneBlastPlus is looking for a program called "blast+"   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2996] StandAloneBlastPlus is looking for a program called "blast+"   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [16707] bioperl-live/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: fix _find_executable for pseudo-programs (like BlastPlus) (bug#2996)   Mark Allen Jensen
• [Bioperl-guts-l] [16708] bioperl-run/trunk/lib/Bio/Tools/Run/StandAloneBlastPlus.pm: bug squish   Mark Allen Jensen
• [Bioperl-guts-l] [16709] bioperl-live/trunk/Bio/Assembly/IO/bowtie.pm: Bug fix - dum.   Dan Kortschak
• [Bioperl-guts-l] [16710] bioperl-live/trunk/Bio/Assembly/IO/bowtie.pm: Bug fix - dum.   Dan Kortschak
• [Bioperl-guts-l] [16711] bioperl-live/trunk/Bio/Assembly/IO/bowtie.pm: Bug fix - dum.   Dan Kortschak
• [Bioperl-guts-l] [16712] bioperl-live/trunk/Bio/Assembly/IO/bowtie.pm: Bug fix - dum.   Dan Kortschak
• [Bioperl-guts-l] [16713] bioperl-live/trunk/Bio/Assembly/IO/bowtie.pm: Bug fix - dum.   Dan Kortschak
• [Bioperl-guts-l] [16714] bioperl-live/trunk/Bio/Assembly/IO/bowtie.pm: Bug fix   Dan Kortschak
• [Bioperl-guts-l] [16715] bioperl-live/trunk/Bio/Tools/GuessSeqFormat.pm: Crossbow is a subset of tab, so can't have both   Dan Kortschak
• [Bioperl-guts-l] [16716] bioperl-live/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: Bug fix   Dan Kortschak
• [Bioperl-guts-l] [16717] bioperl-live/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: Bug fix   Dan Kortschak
• [Bioperl-guts-l] [16718] bioperl-run/trunk/lib/Bio/Tools/Run/Bowtie.pm: Refactored preparation for object creation and make use of B:A:IO: bowtie for bowtie format object output.   Dan Kortschak
• [Bioperl-guts-l] [16719] bioperl-run/trunk: Bowtie tests - now largely working ( inline processing not compatible with CommandExts).   Dan Kortschak
• [Bioperl-guts-l] [16720] bioperl-live/trunk/Bio/SeqFeature/Lite.pm: fixed a bug in gff3 dumping   Lincoln Stein
• [Bioperl-guts-l] [16721] bioperl-live/trunk/Bio/DB/SeqFeature/Store/FeatureFileLoader.pm: under some circumstances, child features would have different ( and incorrect) types than their parent feature   Lincoln Stein
• [Bioperl-guts-l] [16722] bioperl-run/trunk/t/Bowtie.t: Clean up void warnings   Dan Kortschak
• [Bioperl-guts-l] [16723] bioperl-run/trunk: Make Bowtie array filespec args compatible with CommandExts   Dan Kortschak
• [Bioperl-guts-l] [16724] bioperl-run/trunk/lib/Bio/Tools/Run/Bowtie.pm: Fix coreq param bug   Dan Kortschak
• [Bioperl-guts-l] [16725] bioperl-run/trunk: Bug fix - last test failure.   Dan Kortschak
• [Bioperl-guts-l] [16726] bioperl-run/trunk/lib/Bio/Tools/Run/Bowtie.pm: Minor POD addition.   Dan Kortschak
• [Bioperl-guts-l] [16727] bioperl-live/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: Bug fix   Dan Kortschak
• [Bioperl-guts-l] [16728] bioperl-run/trunk: Config now in technicolor - should work with colourspace if colourseq is alpha encoded , may work if colourseq is num encoded (no CS seq to test with).   Dan Kortschak
• [Bioperl-guts-l] [16729] bioperl-run/trunk/lib/Bio/Tools/Run: Added named args to run().   Dan Kortschak
• [Bioperl-guts-l] [16730] bioperl-live/trunk/Bio/Assembly/IO/bowtie.pm: Add color space conversion - tested with csfasta, but not csfastq   Dan Kortschak
• [Bioperl-guts-l] [16731] bioperl-live/trunk/Bio/Assembly/IO/bowtie.pm: Revert to non-handling of CM comment - discussion with Ben Langmead indicates it is not reliably determinable from bowtie format .   Dan Kortschak
• [Bioperl-guts-l] [16732] bioperl-live/trunk/Bio/SeqIO: bug#2982 embl/genbank contig handling   Mark Allen Jensen
• [Bioperl-guts-l] [16733] bioperl-live/trunk/t: bug#2982 embl/genbank contig handling tests   Mark Allen Jensen
• [Bioperl-guts-l] [16734] bioperl-run/trunk/lib/Bio/Tools/Run: POD fixes   Dan Kortschak
• [Bioperl-guts-l] [16735] bioperl-run/trunk: Make bowtie result return extensible - NB API change: want_raw removed -> want 'type'.   Dan Kortschak
• [Bioperl-guts-l] [16736] bioperl-run/trunk/lib/Bio/Tools/Run/Bowtie.pm: POD changes to reflect API change   Dan Kortschak
• [Bioperl-guts-l] [16737] bioperl-live/trunk/Bio/AlignIO.pm: add an alphabet init arg and get /setter   Jason Stajich
• [Bioperl-guts-l] [16738] bioperl-live/trunk/Bio/AlignIO/stockholm.pm: migrate alphabet method up to Bio::AlignIO parent.   Jason Stajich
• [Bioperl-guts-l] [16739] bioperl-live/trunk/Bio/AlignIO: Can pass in -alphabet as init argument to Bio:: AlignIO to prevent alphabet guessing code in Bio:: PrimarySeq from being invoked.   Jason Stajich
• [Bioperl-guts-l] [16740] bioperl-run/trunk/lib/Bio/Tools/Run/Bowtie.pm: More reliable format determination for stored results.   Dan Kortschak
• [Bioperl-guts-l] [16741] bioperl-live/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: Switched filespecs can now be optional   Dan Kortschak
• [Bioperl-guts-l] [16742] bioperl-live/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: Bug fix - optional fileswitched filespecs not safe for perl-false filenames .   Dan Kortschak
• [Bioperl-guts-l] [16743] bioperl-run/trunk: BEDTools *ALPHA* Tests need work - some tests not executed.   Dan Kortschak
• [Bioperl-guts-l] [16744] bioperl-run/trunk: BEDTools test revision and test-driven fixes.   Dan Kortschak
• [Bioperl-guts-l] [16745] bioperl-run/trunk/lib/Bio/Tools/Run/BEDTools.pm: Quick results file option   Dan Kortschak
• [Bioperl-guts-l] [16746] bioperl-run/trunk: Quick results option can now create objects   Dan Kortschak
• [Bioperl-guts-l] [16747] bioperl-live/trunk/Bio/PrimarySeqI.pm: silence error if $id is undef   Christopher John Fields
• [Bioperl-guts-l] [16748] bioperl-live/trunk/scripts/Bio-SeqFeature-Store/bp_seqfeature_load. PLS: [bug 2836] add namespace to command line args, other bits ( courtesy Dan Bolser)   Christopher John Fields
• [Bioperl-guts-l] [Bug 2836] The bp_seqfeature_load.pl script dosn't support the '-namespace' option to new Bio::DB::SeqFeature::Store   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [16749] bioperl-live/trunk/Bio/Search/HSP/BlastHSP.pm: remove leftover debugging fluff   Christopher John Fields
• [Bioperl-guts-l] [16750] bioperl-live/trunk/Bio/DB/TFBS/transfac_pro.pm: deal with som eodd strand issues popping up   Christopher John Fields
• [Bioperl-guts-l] [Bug 2846] [TODO] Update INSTALL, README, other docs within core   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2868] Can't parse Arabidopsis TAIR9 release in TIGR XML format   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2888] When reading blast results: spaces at end of line in multi-line query description are lost   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2899] problem with t/LocalDB/SeqFeature.t when host ne localhost   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [16751] bioperl-live/trunk/Bio/Align/DNAStatistics.pm: [bug 2901] Deal with div by zero in cases where gaps exist (per Janet Young).   Christopher John Fields
• [Bioperl-guts-l] [16752] bioperl-live/trunk/Bio/Align/DNAStatistics.pm: some docs for that last commit (tests to come)   Christopher John Fields
• [Bioperl-guts-l] [16753] bioperl-live/trunk/t: tests for bug 2901   Christopher John Fields
• [Bioperl-guts-l] [16754] bioperl-run/trunk: Paired end tests - Now *BETA*   Dan Kortschak
• [Bioperl-guts-l] [16755] bioperl-live/trunk/Bio/Align/DNAStatistics.pm: prettier output   Christopher John Fields
• [Bioperl-guts-l] [Bug 2901] non-overlapping sequences: DNAStatistics.pm division by zero issue   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [16756] bioperl-live/trunk/Bio/PrimarySeqI.pm: transcribe and rev_transcribe   Mark Allen Jensen
• [Bioperl-guts-l] [16757] bioperl-live/trunk/t/Seq/Seq.t: tests for transcribe and rev_transcribe   Mark Allen Jensen
• [Bioperl-guts-l] [16758] bioperl-live/trunk: change NA to -1   Christopher John Fields
• [Bioperl-guts-l] [16759] bioperl-live/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: check for is_pseudo on executable/executables call   Mark Allen Jensen
• [Bioperl-guts-l] [16760] bioperl-live/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: last change was redundant, this better   Mark Allen Jensen
• [Bioperl-guts-l] [16761] bioperl-live/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: remove a cygwin kludge   Mark Allen Jensen
• [Bioperl-guts-l] [16762] bioperl-run/trunk/lib/Bio/Tools/Run: base Samtools completely on WrapperBase::CommandExts   Mark Allen Jensen
• [Bioperl-guts-l] [Bug 3001] New: sequence identifier "0" dropped when writing to a fasta file   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 3001] sequence identifier "0" dropped when writing to a fasta file   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 3001] sequence identifier "0" dropped when writing to a fasta file   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 3001] sequence identifier "0" dropped when writing to a fasta file   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 3001] sequence identifier "0" dropped when writing to a fasta file   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [16763] bioperl-live/trunk/Bio/TreeIO/phyloxml.pm: change to remove newline at the end of phyloxml   miraceti at dev.open-bio.org
• [Bioperl-guts-l] [16764] bioperl-live/trunk/Bio/Seq/SeqFastaSpeedFactory.pm: bug#3001 : the Naked Zero (fixed)   Mark Allen Jensen
• [Bioperl-guts-l] [16765] bioperl-run/trunk/lib/Bio/Tools/Run/Bowtie.pm: Add Bio::SeqFeature: :Collection creation   Dan Kortschak
• [Bioperl-guts-l] [16766] bioperl-live/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: quieten _find_executable when exec not found (make like WrapperBase:: executable) (thanks Dan)   Mark Allen Jensen
• [Bioperl-guts-l] [16767] bioperl-run/trunk/lib/Bio/Tools/Run/BWA.pm: remove cygwin kludge   Mark Allen Jensen
• [Bioperl-guts-l] [16768] bioperl-live/trunk: 'added mysql_local_infile=1' to mysql data sources when fast loading is requested; prevents issues with mysql servers that have this facility turned off   Lincoln Stein
• [Bioperl-guts-l] [16769] bioperl-live/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: use the contents of stderr and not $! (which always seems to contain " Illegal seek" after an IPC::Run::run() call   Mark Allen Jensen
• [Bioperl-guts-l] [16770] bioperl-live/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: arrgh.   Mark Allen Jensen
• [Bioperl-guts-l] [16771] bioperl-live/trunk/Bio/Tools/EUtilities/EUtilParameters.pm: -email now required, see http://bioperl.org/pipermail/bioperl-l/ 2009-December/031698.html   Christopher John Fields
• [Bioperl-guts-l] [16772] bioperl-live/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: cruft byebye   Mark Allen Jensen
• [Bioperl-guts-l] [16773] bioperl-run/trunk/lib/Bio/Tools/Run/BlastPlus.pm: note to self: delete notes to self   Mark Allen Jensen
• [Bioperl-guts-l] [16774] bioperl-run/trunk/lib/Bio/Tools/Run/StandAloneBlastPlus/ BlastMethods.pm: real bug fix for Mike   Mark Allen Jensen
• [Bioperl-guts-l] [16775] bioperl-run/trunk/lib/Bio/Tools/Run/StandAloneBlastPlus/ BlastMethods.pm: for completeness   Mark Allen Jensen
• [Bioperl-guts-l] [16776] bioperl-live/trunk/Bio/Tools/EUtilities/EUtilParameters.pm: make that a warn instead of a throw, caveat emptor   Christopher John Fields
• [Bioperl-guts-l] [16777] bioperl-live/trunk/Bio: warn lazily, tool=BioPerl   Christopher John Fields
• [Bioperl-guts-l] [16778] bioperl-run/trunk/lib/Bio/DB/SoapEUtilities.pm: warn on no email specification, per NCBI edict   Mark Allen Jensen
• [Bioperl-guts-l] [Bug 3002] New: [TODO] Modify *EUtilities tests to reflect NCBI email policies   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 3002] [TODO] Modify *EUtilities tests to reflect NCBI email policies   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 3002] [TODO] Modify *EUtilities tests to reflect NCBI email policies   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3003] New: Bio::Tools::Run::StandAloneBlastPlus can't find an exising blast db   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 3003] Bio::Tools::Run::StandAloneBlastPlus can't find an exising blast db   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 3003] Bio::Tools::Run::StandAloneBlastPlus can't find an exising blast db   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 3003] Bio::Tools::Run::StandAloneBlastPlus can't find an exising blast db   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 3003] Bio::Tools::Run::StandAloneBlastPlus can't find an exising blast db   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 3003] Bio::Tools::Run::StandAloneBlastPlus can't find an exising blast db   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] [16779] bioperl-run/trunk/t/SABlastPlus.t: clean up tests   Mark Allen Jensen
• [Bioperl-guts-l] [16780] bioperl-live/trunk/Bio/Tools/Run/WrapperBase/CommandExts.pm: more informative messages   Mark Allen Jensen
• [Bioperl-guts-l] [16781] bioperl-run/trunk/lib/Bio/Tools/Run: refactor based on bug#3003; strip gaps from B:PS objs before fastizing   Mark Allen Jensen
• [Bioperl-guts-l] [16782] bioperl-run/trunk/lib/Bio/Tools/Run/StandAloneBlastPlus.pm: one more (ha!) tweak   Mark Allen Jensen
• [Bioperl-guts-l] [16783] bioperl-run/trunk/lib/Bio/Tools/Run/StandAloneBlastPlus.pm: more informative msg   Mark Allen Jensen
• [Bioperl-guts-l] [16784] bioperl-run/trunk/t/SABlastPlus.t: tests for bug#3003   Mark Allen Jensen
• [Bioperl-guts-l] [16785] bioperl-live/trunk/Bio/Root/Test.pm: email check   Christopher John Fields
• [Bioperl-guts-l] [16786] bioperl-live/trunk/README: bot test   Christopher John Fields
• [Bioperl-guts-l] [16787] bioperl-live/trunk/README: bot test   Christopher John Fields
• [Bioperl-guts-l] [16788] bioperl-live/trunk/README: bot test   Christopher John Fields
• [Bioperl-guts-l] [16789] bioperl-live/trunk/README: bot test   Christopher John Fields
• [Bioperl-guts-l] [16790] bioperl-live/trunk/README: bot test   Christopher John Fields
• [Bioperl-guts-l] [16791] bioperl-live/trunk/README: bot test   Christopher John Fields
• [Bioperl-guts-l] [16792] bioperl-dev/trunk/Bio: starting WrapperMaker; will automagically create run wrappers via WrapperBase and CommandExts using an XML program definitions file (specced in XSD)   Mark Allen Jensen
• [Bioperl-guts-l] [16793] bioperl-dev/trunk/Bio/Tools: building out; fixes to schema   Mark Allen Jensen
• [Bioperl-guts-l] [16794] bioperl-live/branches/TRY_featureio_refactor/: init GFF/ FeatureIO branch   Christopher John Fields
• [Bioperl-guts-l] [16795] bioperl-live/branches/TRY_featureio_refactor: remove FeatureIO from core into a separate distribution ( will need to add it optionally post-install)   Christopher John Fields
• [Bioperl-guts-l] [16796] Bio-FeatureIO: initial import of Bio::FeatureIO   Christopher John Fields
• [Bioperl-guts-l] [16797] Bio-FeatureIO/: rm FeatureIO (need to create dir structure)   Christopher John Fields
• [Bioperl-guts-l] [16798] Bio-FeatureIO/: create FeatureIO dir   Christopher John Fields
• [Bioperl-guts-l] [16799] Bio-FeatureIO: now add this to trunk   Christopher John Fields
• [Bioperl-guts-l] [16800] Bio-FeatureIO/branches/: add branches   Christopher John Fields
• [Bioperl-guts-l] [16801] Bio-FeatureIO/tags/: add tags   Christopher John Fields
• [Bioperl-guts-l] [16802] bioperl-dev/trunk/Bio/Tools/WrapperMaker/maker.xsd: tweak schema   Mark Allen Jensen
• [Bioperl-guts-l] [16803] bioperl-dev/trunk/Bio/Tools/WrapperMaker/maker.xsd: restructure   Mark Allen Jensen
• [Bioperl-guts-l] [16804] bioperl-dev/trunk/Bio/Tools: WrapperMaker now (apparently) reads, loads globals, and exports to namespace, yay   Mark Allen Jensen

Last message date: Sun Jan 31 23:48:41 EST 2010
Archived on: Sun Jan 31 23:48:52 EST 2010

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