August 2010 Archives by author

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

Starting: Mon Aug 2 09:52:53 EDT 2010
Ending: Tue Aug 31 22:57:08 EDT 2010
Messages: 108

• [Bioperl-guts-l] [bioperl/bioperl-live] 0f34da: remove debugging   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 09e010: Didn't realize there was already a subroutine to g...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 6f1285: [bug 2725] some updates to tests so they actually ...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 0abbbd: updates   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 10dcb4: [bug 2982] score<->percID mixup, patch courtesy Al...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 563e92: [bug 2984] end was calculated based on arbitrary s...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 503c73: partial revert, some small code changes snuck in   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 228117: Fixed convert_to_name() to name tag features with ...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 86d573: [bug 3101] mbs parser (pure perl) and tests, court...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 197eda: [bug 2702] silence annoying script copying   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 06a53a: typo   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-run] 91bfbd: [bug 2987] remove warning (patch courtesy Adam Wit...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] f7d14f: Bump our minimum Perl version to 5.10 ::rejoices::   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 783e36: Revert "Bump our minimum Perl version to 5.10 ::re...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 5c18e2: tr/// lists must be same length, switch to s///   noreply at github.com
• [Bioperl-guts-l] [bioperl/Bio-FeatureIO] 8df530: given/when   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 70f00d: Revert "tr/// lists must be same length, switch to...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 56ba53: return the first note (scalar context of array, wa...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 53a4b6: Merge remote branch 'upstream/master'   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] db7796: Add test and test data for InterPro parsing bug   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] aa9bde: ne, not !=   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 721872: tiny change to Bio::FeatureIO::gff to allow the gm...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 30616b: Add test and test data for InterPro parsing bug   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 83f6ec: Add a test and data for a bug in InterPro relation...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-run] e81728: StandaloneBlastPlus: don't automatically add ./ to...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 21fabd: small change to exception, demonstrate name change   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] f7d366: change exception on unknown moltype to debugging s...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] aaba18: correct erroneous assumption that terms must be fl...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 430866: Revert "correct erroneous assumption that terms mu...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] f5c7c9: interim fix for inverse IDs, uses cache of marshal...   noreply at github.com
• [Bioperl-guts-l] [bioperl/Bio-FeatureIO] f0d45c: update .gitignore for any komodo project stuff   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] d5baa7: Merge branch 'circular'   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] b76313: The use of $stop here is inconsistent, using $end.   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 1ea39f: throw, not croak   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] fa93c5: clarify range   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 21e409: add some synopsis info, remove TODO item (GET/POST...   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 56d625: more docs, for esummary   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] aa23a8: Fix File::Path calls for older File::Path versions   noreply at github.com
• [Bioperl-guts-l] [bioperl/Bio-FeatureIO] f17eba: add new bed example; old one is shite   noreply at github.com
• [Bioperl-guts-l] [bioperl/Bio-FeatureIO] b7d410: a bit further with bed format, but still borken   noreply at github.com
• [Bioperl-guts-l] [bioperl/Bio-FeatureIO] 98d233: small link fix   noreply at github.com
• [Bioperl-guts-l] [bioperl/Bio-FeatureIO] 16c06a: finish initial work on bed format, work on ptt   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] d5faf5: add primary_id as a constructor parameter   noreply at github.com
• [Bioperl-guts-l] [bioperl/Bio-FeatureIO] 1de555: make all arguments specific to the bioperl interfa...   noreply at github.com
• [Bioperl-guts-l] [bioperl/Bio-FeatureIO] bc1190: some updates and comments   noreply at github.com
• [Bioperl-guts-l] [bioperl/Bio-FeatureIO] 467501: work on genericzing handler; all pass but gff, wit...   noreply at github.com
• [Bioperl-guts-l] [bioperl/Bio-FeatureIO] 394c99: check mode and type for sequence; gff now passes   noreply at github.com
• [Bioperl-guts-l] [bioperl/Bio-FeatureIO] 9ad606: remove debugging   noreply at github.com
• [Bioperl-guts-l] [bioperl/Bio-FeatureIO] 467501: work on genericzing handler; all pass but gff, wit...   noreply at github.com
• [Bioperl-guts-l] [bioperl/Bio-FeatureIO] 20f3e4: add GTF/GFF-ish/GFF3 from UCSC and Ensembl, same r...   noreply at github.com
• [Bioperl-guts-l] [bioperl/Bio-FeatureIO] 0e55dd: add one more example, GTF from ensembl   noreply at github.com
• [Bioperl-guts-l] [bioperl/Bio-FeatureIO] 35eed9: initial URI decoding   noreply at github.com
• [Bioperl-guts-l] [bioperl/Bio-FeatureIO] cc4887: rename gff3.t   noreply at github.com
• [Bioperl-guts-l] [bioperl/bioperl-live] 2ac26b: move Bio::AlignIO::mummer to proper location   noreply at github.com
• [Bioperl-guts-l] [bioperl/Bio-FeatureIO] dee3aa: add a GTF test file, comment out config stuff NYI ...   noreply at github.com
• [Bioperl-guts-l] [Bug 3039] TreeIO::newick writes root node branch length incorrectly   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3039] TreeIO::newick writes root node branch length incorrectly   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 2834] Bio::Root::Build breaks Module::Build API   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2946] NodeMod issue   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] [Bug 2773] Bio::Tree::Node gets destroyed even though it is still live   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2869] Bio::Tree, fail to get children of root node through some way   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2701] New MUMmer AlignIO support   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2702] [TODO] scripts recopied upon each call to './Build test'   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2701] New MUMmer AlignIO support   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3128] New: phyloxml and wrong element order   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2773] Bio::Tree::Node gets destroyed even though it is still live   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2773] Bio::Tree::Node gets destroyed even though it is still live   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2773] Bio::Tree::Node gets destroyed even though it is still live   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2725] New modules for alignment graphics   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2901] non-overlapping sequences: DNAStatistics.pm division by zero issue   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3101] New SeqIO parser to read output created by Teshima and Innan's mbs   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3116] tr/// warning with Bio::Range in Perl 5.12   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3117] Bio::Tree::TreeFunctionsI use()ing UNIVERSAL   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy?   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3055] GFF3Loader with allow_whitespace(1) fails to load valid GFF3 with spaces in 9th column   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3055] GFF3Loader with allow_whitespace(1) fails to load valid GFF3 with spaces in 9th column   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3101] New SeqIO parser to read output created by Teshima and Innan's mbs   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] [Bug 2982] Parsing multiple contig EMBL records (CO lines instead of SQ lines)   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 2984] Only allows letters as characters in phylip format   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3129] New: Problems with Bio::LocatableSeq::length() and strand()   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3120] Bio::DB::SeqFeature::Store::DBI::SQLite + bp_seqfeature_gff3.PLS = unhappy?   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3101] New SeqIO parser to read output created by Teshima and Innan's mbs   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] [Bug 2700] [TODO] Refactor Build.PL   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2703] Bio::Tools::GuessSeqFormat guesses SELEX as PHYLIP   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 2987] Remove ClustalW warning when version checked   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2703] Bio::Tools::GuessSeqFormat guesses SELEX as PHYLIP   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3131] New: Manual builld on Perl 5.12 and Windows using CPAN   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3131] Manual builld on Perl 5.12 and Windows using CPAN   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3131] Manual builld on Perl 5.12 and Windows using CPAN   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3131] Manual builld on Perl 5.12 and Windows using CPAN   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3131] Manual builld on Perl 5.12 and Windows using CPAN   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3131] Manual builld on Perl 5.12 and Windows using CPAN   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3131] Manual builld on Perl 5.12 and Windows using CPAN   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3131] Manual builld on Perl 5.12 and Windows using CPAN   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3131] Manual builld on Perl 5.12 and Windows using CPAN   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3131] Manual builld on Perl 5.12 and Windows using CPAN   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2946] NodeMod issue   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 3133] New: Failure to write quality header in fastq   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3133] Failure to write quality header in fastq   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3133] Failure to write quality header in fastq   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 3133] Failure to write quality header in fastq   bugzilla-daemon at portal.open-bio.org

Last message date: Tue Aug 31 22:57:08 EDT 2010
Archived on: Tue Aug 31 22:57:11 EDT 2010

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