June 2009 Archives by thread

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Starting: Mon Jun 1 11:56:17 EDT 2009
Ending: Tue Jun 30 23:17:05 EDT 2009
Messages: 157

• [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] [15725] bioperl-dev/trunk/Bio/Search/Tiling: handling for strand-only contexts;   Mark Allen Jensen
• [Bioperl-guts-l] [15726] bioperl-dev/trunk/Bio/Search/Tiling: doh.   Mark Allen Jensen
• [Bioperl-guts-l] [15727] bioperl-dev/trunk/t/SearchIO/Tiling.t: tests ready for prime time   Mark Allen Jensen
• [Bioperl-guts-l] [15728] bioperl-dev/trunk/Bio/Search/Tiling/MapTileUtils.pm: has_strand info for tblastn   Mark Allen Jensen
• [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] [15729] bioperl-dev/tags/: create tags dir   Mark Allen Jensen
• [Bioperl-guts-l] [15730] bioperl-dev/tags/tiling-port-to-core-060109/: tag the state of Bio: :Search::Tiling upon porting   Mark Allen Jensen
• [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] [15731] bioperl-live/trunk/t/SearchIO/Tiling.t: Bio::Search::Tiling tests   Mark Allen Jensen
• [Bioperl-guts-l] [15732] bioperl-live/trunk/t/data/1ZZ19XR301R-Alignment.tblastn: big tblastn (dystrophin) for Bio::Search::Tiling   Mark Allen Jensen
• [Bioperl-guts-l] [15733] bioperl-live/trunk/Bio/Search: port Bio::Search::Tiling ( from bioperl-dev)   Mark Allen Jensen
• [Bioperl-guts-l] [15734] bioperl-live/trunk/Bio/Search: whoops.   Mark Allen Jensen
• [Bioperl-guts-l] [15735] bioperl-dev/trunk/Bio: Adding preliminary version of of Bio::SeqIO: :nexml->next_seq() and Bio::AlignIO::next_aln() methods.   Chase Miller
• [Bioperl-guts-l] [Bug 2845] New: [Bio::Seq::Quality] get_clear_range return a seq with no id   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2845] [Bio::Seq::Quality] get_clear_range return a seq with no id   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2845] [Bio::Seq::Quality] get_clear_range return a seq with no id   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2845] [Bio::Seq::Quality] get_clear_range return a seq with no id   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2845] [Bio::Seq::Quality] get_clear_range return a seq with no id   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2846] New: [TODO] Update INSTALL, README, other docs within core   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15736] bioperl-live/trunk/t/SearchIO/Tiling.t: decruft   Mark Allen Jensen
• [Bioperl-guts-l] [15737] bioperl-live/trunk/t/SearchIO/Tiling.t: quiet the diags unless BIOPERL_TILING_VERBOSE_TESTS   Mark Allen Jensen
• [Bioperl-guts-l] [15738] bioperl-live/trunk/t/data/frac_problems2.blast: added spaces to end of homology strings:   Mark Allen Jensen
• [Bioperl-guts-l] [15739] bioperl-live/trunk/t/data/frac_problems2.blast: add space   Mark Allen Jensen
• [Bioperl-guts-l] [Bug 2847] New: [Bio::Seq::Quality] get_clear_range on empty clear ranges   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2847] [Bio::Seq::Quality] get_clear_range on empty clear ranges   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2847] [Bio::Seq::Quality] get_clear_range on empty clear ranges   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15740] bioperl-live/trunk/Bio/DB/HIV/lanl-schema.xml: keyword subst   Mark Allen Jensen
• [Bioperl-guts-l] [15741] bioperl-live/trunk/t/RemoteDB/HIV/HIVQueryHelper.t: update reflects lanl-schema.xml changes   Mark Allen Jensen
• [Bioperl-guts-l] Bug in genbank.pm?   Marcos S. Barbeitos
  • [Bioperl-guts-l] Bug in genbank.pm?   Chris Fields
• [Bioperl-guts-l] [Bug 2850] New: psl.pm next_result() hangs on "empty" psl file   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2850] psl.pm next_result() hangs on "empty" psl file   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2850] psl.pm next_result() hangs on "empty" psl file   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2850] psl.pm next_result() hangs on "empty" psl file   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15742] bioperl-live/trunk/Bio/Seq/Quality.pm: fix "can' t use undefined value as HASH ref" failure   Mark Allen Jensen
• [Bioperl-guts-l] [15743] bioperl-live/trunk/Build.PL: t/SeqTools/SeqUtils.t barfs if List:: MoreUtils   Mark Allen Jensen
  • [Bioperl-guts-l] [15743] bioperl-live/trunk/Build.PL: t/SeqTools/SeqUtils.t barfs if List:: MoreUtils   Chris Fields
• [Bioperl-guts-l] [15744] bioperl-live/trunk/t/SeqTools/SeqUtils.t: rewrite to remove dependency on List::Utils   Mark Allen Jensen
• [Bioperl-guts-l] [15745] bioperl-live/trunk/Build.PL: never mind.   Mark Allen Jensen
• [Bioperl-guts-l] [15746] bioperl-dev/trunk/Bio: Changed the way Bio::Phylo objects' data were being accessed   Chase Miller
• [Bioperl-guts-l] [15747] bioperl-dev/trunk/Bio/TreeIO/nexml.pm: Preliminary version of TreeIO::nexml->next_tree() method.   Chase Miller
• [Bioperl-guts-l] [15748] bioperl-dev/trunk/Bio/SeqIO/nexml.pm: some helpful(?) comments to Chase   Mark Allen Jensen
• [Bioperl-guts-l] [15749] bioperl-dev/trunk/Bio/AlignIO/nexml.pm: some helpful(?) comments to Chase   Mark Allen Jensen
• [Bioperl-guts-l] [15750] bioperl-dev/trunk/Bio/TreeIO/nexml.pm: some helpful(?) comments to Chase   Mark Allen Jensen
• [Bioperl-guts-l] [Bug 2852] New: -L option of Fasta 3.5 breaks SearchIO parsing   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2852] -L option of Fasta 3.5 breaks SearchIO parsing   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2852] -L option of Fasta 3.5 breaks SearchIO parsing   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15751] bioperl-live/trunk/Bio/AlignIO: [bug 2813]   Christopher John Fields
• [Bioperl-guts-l] [Bug 2813] AlignIO returns undef when last sequence has zero end   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15752] bioperl-live/trunk: * fix up deprecated() so we can go ahead and add this to some methods   Christopher John Fields
• [Bioperl-guts-l] [15753] bioperl-live/trunk: deprecate no_sequences/ no_residues in main trunk (we can switch the version to 1. 7 if deemed necessary)   Christopher John Fields
• [Bioperl-guts-l] [15754] bioperl-live/trunk: deprecation of no_sequences/ residues for num_sequences/residues (cont'd)   Christopher John Fields
• [Bioperl-guts-l] [15755] bioperl-live/trunk/Bio/Root/RootI.pm: tweak code to get proper error message   Christopher John Fields
• [Bioperl-guts-l] [15756] bioperl-live/trunk/Bio/Tools/EUtilities/Link/LinkSet.pm: fix two bugs found on mail list (thx to Adam Witney)   Christopher John Fields
• [Bioperl-guts-l] [15757] bioperl-live/trunk/Bio/Tools/EUtilities/Summary: * genericize the appropriate Item-related methods into a common ItemContainer interface (so Items and DocSums can use the same methods if needed, see the cookbook for an example)   Christopher John Fields
• [Bioperl-guts-l] [15758] bioperl-live/trunk/Bio/SearchIO/fasta.pm: [bug 2852]   Christopher John Fields
• [Bioperl-guts-l] [15759] bioperl-live/trunk/Bio/SearchIO/fasta.pm: * tweak last bugfix to get any residual description info   Christopher John Fields
• [Bioperl-guts-l] [Bug 2855] New: Bio::Restriction::Analysis borks when cutting on certain enzymes   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2855] Bio::Restriction::Analysis borks when cutting on certain enzymes   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2855] Bio::Restriction::Analysis borks when cutting on certain enzymes   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2855] Bio::Restriction::Analysis borks when cutting on certain enzymes   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2855] Bio::Restriction::Analysis borks when cutting on certain enzymes   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2855] Bio::Restriction::Analysis borks when cutting on certain enzymes   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2855] Bio::Restriction::Analysis borks when cutting on certain enzymes   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2855] Bio::Restriction::Analysis borks when cutting on certain enzymes   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2855] Bio::Restriction::Analysis borks when cutting on certain enzymes   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2855] Bio::Restriction::Analysis borks when cutting on certain enzymes   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2855] Bio::Restriction::Analysis borks when cutting on certain enzymes   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15760] bioperl-live/branches/restriction-refactor/: Developing a fairly serious refactor in the Bio::Restriction namespace   Mark Allen Jensen
• [Bioperl-guts-l] [15761] bioperl-live/branches/restriction-refactor/Bio/Restriction: Multiple changes here; summary:   Mark Allen Jensen
• [Bioperl-guts-l] [15762] bioperl-live/branches/restriction-refactor/Bio/Restriction: keyword subst   Mark Allen Jensen
• [Bioperl-guts-l] [15763] bioperl-live/branches/restriction-refactor/Bio/Restriction/IO: cleanup   Mark Allen Jensen
• [Bioperl-guts-l] [15764] bioperl-live/branches/restriction-refactor/Bio/Restriction/IO: completely factored out _cuts_from_site,   Mark Allen Jensen
• [Bioperl-guts-l] [15765] bioperl-live/branches/restriction-refactor/Bio/Restriction: summary :   Mark Allen Jensen
• [Bioperl-guts-l] [15766] bioperl-live/branches/restriction-refactor/Bio/Restriction/Enzyme: fix pod   Mark Allen Jensen
  • [Bioperl-guts-l] [15766] bioperl-live/branches/restriction-refactor/Bio/Restriction/Enzyme: fix pod   Chris Fields
• [Bioperl-guts-l] [15767] bioperl-live/branches/restriction-refactor/Bio/Restriction/ EnzymeCollection.pm: add the pod-advertised "-enzymes" parameter   Mark Allen Jensen
• [Bioperl-guts-l] [15768] bioperl-live/branches/restriction-refactor/Bio/Restriction/Enzyme. pm: added a cut site translation parameter to constructor;   Mark Allen Jensen
• [Bioperl-guts-l] [15769] bioperl-live/branches/restriction-refactor/Bio/Restriction/Analysis .pm: enable _make_cuts to follow and cut with Enzyme   Mark Allen Jensen
• [Bioperl-guts-l] [15770] bioperl-live/branches/restriction-refactor/t/data/withrefm.906: additional REBASE file (assoc with bug 2855)   Mark Allen Jensen
• [Bioperl-guts-l] [15771] bioperl-live/branches/restriction-refactor/Bio/Restriction/Enzyme: per cjf advice   Mark Allen Jensen
• [Bioperl-guts-l] [15772] bioperl-live/branches/restriction-refactor/Bio/Restriction/Enzyme. pm: bugfix clone() method;   Mark Allen Jensen
• [Bioperl-guts-l] [15773] bioperl-dev/trunk/Bio/AlignIO/nexml.pm: Implemented write_aln function.   Chase Miller
• [Bioperl-guts-l] [15774] bioperl-dev/trunk/Bio/SeqIO/nexml.pm: Implemented write_seq function.   Chase Miller
• [Bioperl-guts-l] [15775] bioperl-dev/trunk/Bio/TreeIO/nexml.pm: Implemented write_tree function.   Chase Miller
• [Bioperl-guts-l] [15776] bioperl-live/branches/restriction-refactor/Bio/Restriction/Enzyme. pm: default cut site conversion is just the identity   Mark Allen Jensen
• [Bioperl-guts-l] [15777] bioperl-live/branches/restriction-refactor/Bio/Restriction/IO: changes to reflect the refactoring;   Mark Allen Jensen
• [Bioperl-guts-l] [15778] bioperl-live/branches/restriction-refactor/Bio/Restriction/Enzyme. pm: couple of aliases   Mark Allen Jensen
• [Bioperl-guts-l] [15779] bioperl-live/branches/restriction-refactor/Bio/Restriction/Analysis .pm: refactoring _circular()   Mark Allen Jensen
• [Bioperl-guts-l] [15780] bioperl-live/branches/restriction-refactor/Bio/Restriction/Analysis .pm: - refactored the revcom machinery (no padding)   Mark Allen Jensen
• [Bioperl-guts-l] [15781] bioperl-live/branches/restriction-refactor/Bio/Restriction/Enzyme. pm: - revcom refactoring   Mark Allen Jensen
• [Bioperl-guts-l] [15782] bioperl-live/branches/restriction-refactor/Bio/Restriction/IO: bug squish   Mark Allen Jensen
• [Bioperl-guts-l] [15783] bioperl-live/branches/restriction-refactor/Bio/Restriction: odds-n-ends   Mark Allen Jensen
• [Bioperl-guts-l] [Bug 2828] Unrecognized line error, when parsing hmmsearch output, in module Bio::SearchIO::hmmer   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15784] bioperl-dev/trunk/Bio/TreeIO/nexml.pm: bug fixes   Chase Miller
• [Bioperl-guts-l] [15785] bioperl-live/branches/restriction-refactor/Bio/Restriction/Analysis .pm: bug squish   Mark Allen Jensen
• [Bioperl-guts-l] [15786] bioperl-live/trunk/Bio/Root/Root.pm: Debugging info is producing warning conditions and incorrect caller info; this corrects that behavior ( and adds a corresponding default message if one is not provided, instead of the CORE::warn "Something's wrong at" default)   Christopher John Fields
• [Bioperl-guts-l] [15787] bioperl-live/trunk/Bio/Root/Root.pm: wrap that last bit of code inside the loop ( no need to do the work if we intend on returning when verbose==0 anyway)   Christopher John Fields
• [Bioperl-guts-l] [15788] bioperl-live/branches/restriction-refactor/Bio/Restriction: Fix multisite enzyme builders in parsers:   Mark Allen Jensen
• [Bioperl-guts-l] [15789] bioperl-live/branches/restriction-refactor/Bio/Restriction: surgically remove some wrong 'uninitialized'   Mark Allen Jensen
• [Bioperl-guts-l] [15790] bioperl-live/branches/restriction-refactor/t/Restriction/ Analysis-refac.t: tests for Bio::Restriction::* refactor   Mark Allen Jensen
• [Bioperl-guts-l] [15791] bioperl-live/branches/restriction-refactor/t/Restriction/ Analysis-refac.t: keyword subst   Mark Allen Jensen
• [Bioperl-guts-l] [15792] bioperl-dev/trunk/Bio/SeqIO/nexml.pm: updated code to make use of factory for sequence creation.   Chase Miller
• [Bioperl-guts-l] [15793] bioperl-dev/trunk/Bio/AlignIO/nexml.pm: Updated code to address several comments by Mark Jensen.   Chase Miller
• [Bioperl-guts-l] [15794] bioperl-dev/trunk/Bio/Nexml.pm: Created Bio::Nexml. pm module with very minimal functionality   Chase Miller
• [Bioperl-guts-l] [15795] bioperl-live/branches/restriction-refactor/Bio/Root/Root.pm: merged to trunk r15759:15794   Mark Allen Jensen
• [Bioperl-guts-l] [15796] bioperl-live/trunk: merge bioperl-live/branches/ restriction-refactor   Mark Allen Jensen
• [Bioperl-guts-l] [15797] bioperl-live/branches/restriction-refactor/: branch removal, post-merge w/ trunk   Mark Allen Jensen
• [Bioperl-guts-l] [15798] bioperl-dev/trunk/t: Test scripts for Bio::AlignIO::nexml, Bio:: SeqIO::nexml, and Bio::TreeIO::nexml modules   Chase Miller
• [Bioperl-guts-l] [Bug 2857] New: [TODO] NextGen sequencing updates   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2858] New: Trace data in Bio::SeqIO::scf appears scrambled   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2859] New: META.yml in BioPerl-1.6.0 breaks CPANPLUS installation   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2859] META.yml in BioPerl-1.6.0 breaks CPANPLUS installation   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2831] Build.PL appears to break automated testing with CPANPLUS   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2861] New: blastxml and bsml_sax tests try to access internet even when network tests are skipped.   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15799] bioperl-dev/trunk/t/data: these are are a bunch of NeXML test data set up by Arlin   Mark Allen Jensen
• [Bioperl-guts-l] [15800] bioperl-dev/trunk/scripts/nexvl.pl: This script uses Rutger's www. nexml.org site to   Mark Allen Jensen
• [Bioperl-guts-l] [15801] bioperl-dev/trunk/Bio: Created Bio::Nexml:: Util to handle parsing of nexml document.   Chase Miller
• [Bioperl-guts-l] [15802] bioperl-dev/trunk/Bio/AlignIO/nexml.pm: Now supports reading of an entire Nexml document while parsing it only once .   Chase Miller
• [Bioperl-guts-l] [Bug 2862] New: Bio::Tools::Primer3 don't give the last pair   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2862] Bio::Tools::Primer3 don't give the last pair   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2862] Bio::Tools::Primer3 don't give the last pair   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2862] Bio::Tools::Primer3 don't give the last pair   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2862] Bio::Tools::Primer3 don't give the last pair   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2862] Bio::Tools::Primer3 don't give the last pair   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2862] Bio::Tools::Primer3 don't give the last pair   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2862] Bio::Tools::Primer3 don't give the last pair   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2862] Bio::Tools::Primer3 don't give the last pair   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2862] Bio::Tools::Primer3 don't give the last pair   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15803] bioperl-live/trunk/Bio/Tools/Primer3.pm: patch to solve Bug#2862   Mark Allen Jensen
• [Bioperl-guts-l] [Bug 2156] Bio::DB::REBASE module and t/DBREBASE.t test script   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2537] num_conserved reports incorrect value during FASTA34 parsing   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2844] Patch to add "revtrans" method to Bio::Tools::SeqPattern   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2863] New: crash from Bio::Root::IO::_initialize_io causes crash when validating -fh argument   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2346] exonerate parser in bioperl-live fails when protein2dna comparison is performed   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2864] New: Bio::Seq will lost display_id, if use 0 as id   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2864] Bio::Seq will lost display_id, if use 0 as id   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2864] Bio::Seq will lost display_id, if use 0 as id   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2864] Bio::Seq will lost display_id, if use 0 as id   bugzilla-daemon at portal.open-bio.org
  • [Bioperl-guts-l] [Bug 2864] Bio::Seq will lost display_id, if use 0 as id   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15804] bioperl-live/trunk/scripts/DB-HIV/hivq.PLS: Term:: ReadLine support added   Mark Allen Jensen
• [Bioperl-guts-l] [Bug 2842] add mask_columns to SimpleAlign.pm   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15805] bioperl-live/trunk/t: new tests for Bug 2862-   Mark Allen Jensen
• [Bioperl-guts-l] [15806] bioperl-live/trunk: Bruno's patch+tests - thanks!   Mark Allen Jensen
• [Bioperl-guts-l] [Bug 2842] add mask_columns to SimpleAlign.pm   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [Bug 2842] add mask_columns to SimpleAlign.pm   bugzilla-daemon at portal.open-bio.org
• [Bioperl-guts-l] [15807] bioperl-dev/trunk/Bio: Refactored unparsing code from Bio::*IO:: nexml modules into Bio::Nexml::Util module   Chase Miller
• [Bioperl-guts-l] [15808] bioperl-dev/trunk/t: Added More test for nexml, focusing on tests for writing to a nexml document   Chase Miller
• [Bioperl-guts-l] [15809] bioperl-live/trunk/Bio/SeqFeature/Lite.pm: added missing -seq argument in documentation for new() constructor   Lincoln Stein
• [Bioperl-guts-l] [15810] bioperl-live/trunk/t/data: test data   Christopher John Fields
• [Bioperl-guts-l] [15811] bioperl-live/trunk/t/data/bug2335.fastq: remove old file   Christopher John Fields
• [Bioperl-guts-l] [15812] bioperl-live/trunk: * initial run at fastq parsing of illumina, solexa, sanger   Christopher John Fields
• [Bioperl-guts-l] [15813] bioperl-live/trunk/t/Tools/EUtilities/esummary.t: small test additions   Christopher John Fields
• [Bioperl-guts-l] [15814] bioperl-live/trunk/Bio/SeqIO/fastq.pm: small revert to get write_qual working with sanger output   Christopher John Fields
• [Bioperl-guts-l] [15815] bioperl-live/trunk/Bio/SeqIO/fastq.pm: enable write_fastq for illumina   Christopher John Fields
• [Bioperl-guts-l] [15816] bioperl-live/trunk/Bio/SeqIO/fastq.pm: * cache mapping for variants   Christopher John Fields

Last message date: Tue Jun 30 23:17:05 EDT 2009
Archived on: Tue Jun 30 23:17:09 EDT 2009

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