March 2011 Archives by subject

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Starting: Tue Mar 1 01:36:26 EST 2011
Ending: Thu Mar 31 21:09:38 EDT 2011
Messages: 128

• [Bioperl-guts-l] [BioPerl - Bug #1857] Bio::SearchDist (Bio::Ext::Align) reports incorrect E-values   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #2333] Add iterations to blastxml   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #2899] problem with t/LocalDB/SeqFeature.t when host ne localhost   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #2899] problem with t/LocalDB/SeqFeature.t when host ne localhost   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #2903] (Rejected) Large sequence fetch limits   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #2946] NodeMod issue   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #2979] (Feedback) Bio::SeqIO::multifasta   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #2985] ProtPars.t passing but with lots of warnings   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #3039] TreeIO::newick writes root node branch length incorrectly   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #3055] GFF3Loader with allow_whitespace(1) fails to load valid GFF3 with spaces in 9th column   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #3075] Bio::Tools::Run::Alignment::MAFFT: not able to specify alignment run parameters   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #3085] (Resolved) CommandExts and passing an arrays of files   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #3110] (In Progress) Found a few bugs in bp_seqfeature_load.PLS when using -namespace   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #3110] Found a few bugs in bp_seqfeature_load.PLS when using -namespace   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #3141] Add 'fast' method to bp_seqfeature_delete.PLS script, patch included   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #3143] t/Root/RootIO.t fails at least two tests   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #3149] Error with TreeIO for NHX format   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #3158] EMBL file wgs_aamc_vrt.dat fails to parse...   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #3159] (Resolved) scripts/index/bp_index.PLS does not support SwissPfam   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #3164] (Resolved) TreeFunctionsI.pm syntax bug   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #3164] TreeFunctionsI.pm syntax bug   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #3165] Bio::Index::Fastq indexing not in sync with FASTQ spec   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #3181] XMFA strandedness not parsed correctly   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #3182] (Closed) Test Issue for bioperl-guts   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #3182] (New) Test Issue for bioperl-guts   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #3182] (New) Test Issue for bioperl-guts   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #3182] (Resolved) Test Issue for bioperl-guts   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #3182] Test Issue for bioperl-guts   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #3182] Test Issue for bioperl-guts   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #3182] Test Issue for bioperl-guts   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #3182] Test Issue for bioperl-guts   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #3182] Test Issue for bioperl-guts   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #3182] Test Issue for bioperl-guts   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #3182] Test Issue for bioperl-guts   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #3182] Test Issue for bioperl-guts   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #3182] Test Issue for bioperl-guts   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #3182] Test Issue for bioperl-guts   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #3182] Test Issue for bioperl-guts   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #3185] (New) Bio::Tools::SeqStats->get_mol_wt gives incorrect weight for protein sequences ending with an asterisk   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #3190] (New) RemoteBlast GAPCOSTS regular expression input   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #3190] RemoteBlast GAPCOSTS regular expression input   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #3190] RemoteBlast GAPCOSTS regular expression input   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Bug #3190] RemoteBlast GAPCOSTS regular expression input   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Feature #1514] TCoffee parse score_ascii   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Feature #1514] TCoffee parse score_ascii   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Feature #1514] TCoffee parse score_ascii   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Feature #1874] fixedtopo random tree Bio::Tree::RandomFactory   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Feature #1877] Bio::PopGen::IO::hapmap.pm write_population method   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Feature #1881] implement Bio::PopGen::IO::haploview.pm   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Feature #1891] Implement a seqgen wrapper in bioperl-run   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Feature #2070] mumsa wrapper   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Feature #2078] informative codons method for kaks -- Bio/Align/DNAStatistics.pm   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Feature #2142] conservative/radical nonsynonymous distances method in Bio::Align::DNAStatistics   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Feature #3179] Consider interfacing with TABIX for feature file indexing and lookup for bed, gff, vcf format files.   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Support #3186] (New) Need to change Bugzilla macro in Wiki   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl - Support #3186] (New) Need to change Bugzilla macro in Wiki   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [BioPerl DB - Bug #2899] problem with t/LocalDB/SeqFeature.t when host ne localhost   redmine at redmine.open-bio.org
• [Bioperl-guts-l] [bioperl/Bio-FeatureIO] 63daef: add better error message for when there is no file...   noreply at github.com
• [Bioperl-guts-l] [bioperl/Bio-FeatureIO] 67f281: add myself to authors list for gff.pm   noreply at github.com
• [Bioperl-guts-l] [bioperl/Bio-FeatureIO] 8c0509: remove cruft from C&P   noreply at github.com
• [Bioperl-guts-l] [bioperl/Bio-FeatureIO] 96e75c: oops, that failing test was wrong. correct   noreply at github.com
• [Bioperl-guts-l] [bioperl/Bio-FeatureIO] bd88ea: <headsmack>unescape, not escape</headsmack>   noreply at github.com
• [Bioperl-guts-l] [bioperl/Bio-FeatureIO] cfc8b4: add failing test for proper gff3 unescaping in par...   noreply at github.com
• [Bioperl-guts-l] [bioperl/Bio-FeatureIO] d6f64a: fix gff3 tests to cover more of the data. a coupl...   noreply at github.com
• [Bioperl-guts-l] [bioperl/Bio-FeatureIO] ec940a: fix another little parsing bug, repeated attrs not...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-db] 022402: buzgilla -> redmine   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 033029: Add enclosed_leaves_string method to NodeFunctions...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 108312: improved Bio::SeqFeature::Generic::has_tag perform...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 117af4: bug reported by sebastien.theil at clermont.inra.fr -...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 1c8616: Bio::PrimarySeq:_guess_alphabet is now IUPAC-compl...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 1ef660: rectify a conflict in behavior between PrimarySeq:...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 216092: fixing IssueID #2899   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 3394bb: SSL is default for redmine connection   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 44d8f0: revert some changes from the global redmine conver...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 474df1: retest using https post-rec hook: refs #3181, @2.5   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 4b69c5: volatile data broke test   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 52e52e: within_element works better   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 52e52e: within_element works better   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 532dcf: Worked around changes in memory adapter without ab...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 549e26: minor formatting   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 54fb1e: Revert "volatile data broke test". Remote databas...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 597808: squash XML::Writer issue, still get a warning thou...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 5f4554: only add tags if the value is defined   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 6a79bd: add tests and a few other fixes to account for cut...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 6c8186: changed varchar definition from 256 to 255 to "fix...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 7602f9: please use a source tag   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 7fabbf: fix CUTG skipped test count   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 8267ea: not using subversion   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 82f72d: test redmine   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 843ac8: add tests for bug 3181   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 848dca: A few things going on here:   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 86dbca: localize $_ if you are going to modify it in a lib...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 890552: Add VCF guesser. Example vcf format for testing - ...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 8907c0: add tests: refs #3181   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 8c5851: test redmine post-receive hook   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 903a24: bugzilla -> redmine URL modify   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 97074c: update manifest   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 992529: test post-receive again   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] a81e18: squash warning   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] a8c109: commented out accidentally uncommented code   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] b10ef8: WIP on Bio::Index::Ace   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] b24365: Minor clarifications   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] b3c634: test hook again   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] b67875: within_element works better   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] be5ec1: test post-receive hook, post-SSL   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] c148ee: retest hook to make sure it works, refs #3189   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] cdf38e: Merge branch 'master' of github.com:bioperl/bioper...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] d0c366: Add pretty_print method for Bio::SimpleAlign   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] d4e270: add a bit of caching magic; with large sequence pa...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] d5de02: test hook again   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] e0376d: fix for bad condition check, via Elia Stupka   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] e40cfe: add test for leading whitespace before exonerate q...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] e4e70a: make exception messages match whether one has Erro...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] e614d2: Replaced 'phylip' with 'stockholm' in documentatio...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] e7c430: reduce warning message, was overly verbose and gav...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] ef979d: improved _rearrange performance by 30%   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-run] 2c0438: don't need this lib include   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-run] 572df4: test for bug #3085   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-run] 584dd2: Update BEDTools module for v2.10.1   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-run] bdfba8: use the 1a file -- still problem in parsing the tr...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-run] d1b549: bugzilla -> redmine   noreply at github.com
• [Bioperl-guts-l] [Bug 3163] AssemblyIO takes too long (especially 454)   Chris Fields
• [Bioperl-guts-l] [Bug 3163] AssemblyIO takes too long (especially 454)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3163] AssemblyIO takes too long (especially 454)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3163] AssemblyIO takes too long (especially 454)   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3179] Consider interfacing with TABIX for feature file indexing and lookup for bed, gff, vcf format files.   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3181] New: XMFA strandedness not parsed correctly   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] test   Christopher Fields

Last message date: Thu Mar 31 21:09:38 EDT 2011
Archived on: Thu Mar 31 21:09:41 EDT 2011

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