April 2008 Archives by date

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Starting: Tue Apr 1 10:14:18 EDT 2008
Ending: Fri Apr 25 15:51:05 EDT 2008
Messages: 82

• [Bioperl-guts-l] [Bug 2466] NCBIHelper redirecting RefSeq sequence download to EBI server   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2466] NCBIHelper redirecting RefSeq sequence download to EBI server   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14638] bioperl-live/trunk/Bio/DB/NCBIHelper.pm: bug 2466 :   Christopher John Fields
• [Bioperl-guts-l] [14639] bioperl-live/trunk/Bio/DB: Remove extraneous code; update docs   Christopher John Fields
• [Bioperl-guts-l] [Bug 2466] NCBIHelper redirecting RefSeq sequence download to EBI server   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14640] bioperl-live/trunk/Bio/SearchIO/hmmer.pm: Squash uninit.   Christopher John Fields
• [Bioperl-guts-l] [14641] bioperl-live/trunk/t/RefSeq.t: RefSeq redirection now requires explicit setting ( note that sequence length returned by Bio::DB::RefSeq is off by one, needs investigating).   Christopher John Fields
• [Bioperl-guts-l] [14642] bioperl-live/trunk/t/RestrictionAnalysis.t: test not matching error message (oops!)   Christopher John Fields
• [Bioperl-guts-l] [14643] bioperl-live/trunk/t/Genpred.t: get rid of variable redefined warnings   Christopher John Fields
• [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] [14644] bioperl-run/trunk/Bio/Tools/Run/Phylo/Hyphy/FEL.pm: recently seems to need comma-separated values for the header in the results -- not sure if this was a problem at the very beginning   Albert Vilella
• [Bioperl-guts-l] [14645] bioperl-live/trunk: merge back previous commits from Sendu and I   Christopher John Fields
• [Bioperl-guts-l] [14646] bioperl-live/trunk/Bio/Tools/Fgenesh.pm: Fix bad silent bug which doesn't set exon tags correctly ( showed up when using -W flag with tests)   Christopher John Fields
• [Bioperl-guts-l] [14647] bioperl-live/trunk/t/Genpred.t: Add some tests to catch tag naming   Christopher John Fields
• [Bioperl-guts-l] [14648] bioperl-live/trunk/Bio/Assembly: Misc cleaning, and bug fixing   Florent E Angly
• [Bioperl-guts-l] [14649] bioperl-live/trunk/Bio/Graphics/FeatureFile.pm: restored the ability to have a "tag=value #comment" style comment   Lincoln Stein
• [Bioperl-guts-l] [14650] bioperl-live/trunk/Bio: added an API to prevent FeatureFile->render () from rendering indiscriminately without paying attention to the seq_id of the underlying reference sequence   Lincoln Stein
• [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] [14651] bioperl-live/trunk/Bio: updates; may switch some data objects over to (lightweight) Data:: Stag implementation at some point   Christopher John Fields
• [Bioperl-guts-l] [Bug 2482] New: paml4 mlc file fails to parse   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2482] paml4 mlc file fails to parse   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 2474] postgres 8.3 - load_seqdatabase.pl / swissprot   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14652] bioperl-live/trunk/Bio/Seq/Meta/Array.pm: bug 2478   Christopher John Fields
• [Bioperl-guts-l] [Bug 2478] Bio::SeqIO::fastq subqual reassignment of qualities results in replacement of end characters with '!'   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14653] bioperl-live/trunk/scripts/Bio-DB-GFF/bulk_load_gff.PLS: bug 2479   Christopher John Fields
• [Bioperl-guts-l] [Bug 2479] bp_pg_bulk_load_gff.pl postgres GFF bulk loader broken   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2483] New: request for implementation of write_assembly   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2483] request for implementation of write_assembly   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2350] Bio::Assembly::Scaffold->add_singlet has a bug   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2370] Bio::Assembly::Scaffold Source   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2482] paml4 mlc file fails to parse   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2482] paml4 mlc file fails to parse   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2482] paml4 mlc file fails to parse   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2482] paml4 mlc file fails to parse   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2482] paml4 mlc file fails to parse   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2482] paml4 mlc file fails to parse   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2482] paml4 mlc file fails to parse   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2482] paml4 mlc file fails to parse   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14654] bioperl-live/trunk/Bio: corrected case in which seq_id of Bio:: Location::Split could unintentionally be set to undef   Lincoln Stein
• [Bioperl-guts-l] [Bug 2485] New: Bio::SearchIO::Writer::HSPTableWriter - 'frame' column messes up the output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2485] Bio::SearchIO::Writer::HSPTableWriter - 'frame' column messes up the output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2485] Bio::SearchIO::Writer::HSPTableWriter - 'frame' column messes up the output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2485] Bio::SearchIO::Writer::HSPTableWriter - 'frame' column messes up the output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14655] bioperl-live/trunk/Bio/Factory/SequenceFactoryI.pm: Applied SYNOPSIS patch by Adam Sjogre (asjo at koldfront dot dk).   Hilmar Lapp
• [Bioperl-guts-l] [14656] bioperl-live/trunk: added a clone() method to support the (uncommon ) case of passing database adaptors across a fork()   Lincoln Stein
• [Bioperl-guts-l] [Bug 2484] This bug is repeated for several sequences   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2484] This bug is repeated for several sequences   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2484] This bug is repeated for several sequences   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14657] bioperl-live/trunk/Bio/SeqIO/embl.pm: bug 2484   Christopher John Fields
• [Bioperl-guts-l] [Bug 2484] This bug is repeated for several sequences   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14658] bioperl-live/trunk/Bio/Align/DNAStatistics.pm: typo   Jason Stajich
• [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] [14659] bioperl-live/trunk/Bio/Microarray/Tools/ReseqChip.pm: Minor changes in the main processing function calc_sequence(), Logmessages are buffered, hence only one file open/write/ close operation is needed per processed chip, udpated version of testscript is provided via Bug #2332 in Bioperl bugzilla , Documentation updated   Marian Thieme
• [Bioperl-guts-l] [14660] bioperl-live/trunk/Bio/Microarray/Tools/MitoChipV2Parser.pm: Function for counting number of alternative probes added   Marian Thieme
• [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] [14661] bioperl-run/trunk/Bio/Tools/Run/Infernal.pm: Update to 0.81 params.   Christopher John Fields
• [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] [14662] bioperl-live/trunk/Bio/Graphics: added ability to get at the parent feature in callbacks   Lincoln Stein
• [Bioperl-guts-l] [Bug 2485] Bio::SearchIO::Writer::HSPTableWriter - 'frame' column messes up the output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14663] bioperl-live/trunk/t/Biblio_eutils.t: bullet-proof; this needs more stringent tests   Christopher John Fields
• [Bioperl-guts-l] [14664] bioperl-live/trunk/t/BioFetch_DB.t: update test ( seq in remote db has changed)   Christopher John Fields
• [Bioperl-guts-l] [14665] bioperl-live/trunk/Bio/Assembly/Scaffold.pm: Fix failing tests   Christopher John Fields
• [Bioperl-guts-l] [Bug 2476] "Undefined sub-sequence" when processing tblastx output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2490] New: Bio::SeqIO::fasta is not careful about handling Bio::Seq::LargeSeqI sequences   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2490] Bio::SeqIO::fasta is not careful about handling Bio::Seq::LargeSeqI sequences   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14666] bioperl-live/trunk/Bio/SeqIO/fasta.pm: bug 2490   Christopher John Fields
• [Bioperl-guts-l] [Bug 2490] Bio::SeqIO::fasta is not careful about handling Bio::Seq::LargeSeqI sequences   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2491] New: Method "derived_mutations" in package Bio::PopGen::Statistics   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2492] New: Method "pi" in package Bio::PopGen::Statistics   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14667] bioperl-live/trunk/Bio/PopGen/Statistics.pm: bug #2491   Jason Stajich
• [Bioperl-guts-l] [Bug 2491] Method "derived_mutations" in package Bio::PopGen::Statistics   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2490] Bio::SeqIO::fasta is not careful about handling Bio::Seq::LargeSeqI sequences   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2490] Bio::SeqIO::fasta is not careful about handling Bio::Seq::LargeSeqI sequences   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14668] bioperl-live/trunk/Bio/Tools/Run/RemoteBlast.pm: new NCBI BLAST URL (works with RemoteBlast.t)   Christopher John Fields
• [Bioperl-guts-l] [14669] bioperl-live/trunk/Bio/SeqIO/fasta.pm: bug 2490   Christopher John Fields
• [Bioperl-guts-l] [14670] bioperl-live/trunk/t/largepseq.t: bug 2490 (small test)   Christopher John Fields
• [Bioperl-guts-l] [Bug 2490] Bio::SeqIO::fasta is not careful about handling Bio::Seq::LargeSeqI sequences   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14671] bioperl-live/trunk/t/largepseq.t: correct # of skipped tests   Christopher John Fields
• [Bioperl-guts-l] [14672] bioperl-live/trunk: bug 2485 and related fixes   Christopher John Fields
• [Bioperl-guts-l] [Bug 2485] Bio::SearchIO::Writer::HSPTableWriter - 'frame' column messes up the output   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [14673] bioperl-live/trunk/Bio/Perl.pm: uneven tr///, thanks to Lskatz for the report.   Dave Messina

Last message date: Fri Apr 25 15:51:05 EDT 2008
Archived on: Fri Apr 25 15:51:14 EDT 2008

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