| 2010-06-27 |
Chris Fields | catch refs that sneak through, such as during thread...
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commit | commitdiff | tree |
| 2010-06-26 |
Chris Fields | fix lower-case issue with moltype
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commit | commitdiff | tree |
| 2010-06-26 |
Chris Fields | update bad test check
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commit | commitdiff | tree |
| 2010-06-26 |
Chris Fields | fix error where, with protein seqs the division and...
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commit | commitdiff | tree |
| 2010-06-26 |
Chris Fields | protein molecule type not switched, correct bad test...
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commit | commitdiff | tree |
| 2010-06-25 |
Chris Fields | update MANIFEST
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commit | commitdiff | tree |
| 2010-06-25 |
Chris Fields | uncomment remove_dir() to cleanup files
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commit | commitdiff | tree |
| 2010-06-25 |
Chris Fields | move sub creation to BEGIN, and document the _dclone...
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commit | commitdiff | tree |
| 2010-06-25 |
Chris Fields | update MANIFEST
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commit | commitdiff | tree |
| 2010-06-25 |
Chris Fields | overhaul Root::clone to use either Clone, Storable...
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commit | commitdiff | tree |
| 2010-06-24 |
Chris Fields | move clone() method from TreeFunctionsI to Tree, as...
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commit | commitdiff | tree |
| 2010-06-24 |
Chris Fields | silence warnings with a default of 0
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commit | commitdiff | tree |
| 2010-06-24 |
Chris Fields | make this a real-world example
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commit | commitdiff | tree |
| 2010-06-22 |
Chris Fields | fix conflict
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commit | commitdiff | tree |
| 2010-06-11 |
Chris Fields | [bug 3099] initial msout Seq parser, courtesy Warren...
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commit | commitdiff | tree |
| 2010-06-10 |
Chris Fields | Ben's changes to fix bug with file, along with comment...
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commit | commitdiff | tree |
| 2010-06-07 |
Chris Fields | [bug 3028] some rearrangement for FigTree output
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commit | commitdiff | tree |
| 2010-06-07 |
Chris Fields | Merge branch 'topic/bug3089'
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commit | commitdiff | tree |
| 2010-06-07 |
Chris Fields | [bug 3089] iteration and found_again added to GenericHit...
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commit | commitdiff | tree |
| 2010-06-07 |
Chris Fields | small tweak to add for Args in docs
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commit | commitdiff | tree |
| 2010-06-07 |
Chris Fields | add is_remote docs from Bio::LocationI to Atomic and...
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commit | commitdiff | tree |
| 2010-06-06 |
Chris Fields | expected answer off by two (frameshift
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commit | commitdiff | tree |
| 2010-06-06 |
Chris Fields | more cleanup of methods
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commit | commitdiff | tree |
| 2010-06-06 |
Chris Fields | move seq offset calc into a separate method
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commit | commitdiff | tree |
| 2010-06-06 |
Chris Fields | [bug 3092] parse additional stats from text BLAST reports...
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commit | commitdiff | tree |
| 2010-06-06 |
Chris Fields | Merge Brian's branch
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commit | commitdiff | tree |
| 2010-06-06 |
Chris Fields | allow condition where no tests are passed in (for done_testi...
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commit | commitdiff | tree |
| 2010-06-06 |
Chris Fields | small doc fixes
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commit | commitdiff | tree |
| 2010-06-05 |
Chris Fields | add MYMETA.yml, any *.bak files
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commit | commitdiff | tree |
| 2010-06-05 |
Chris Fields | get_replaced_terms<- (courtesy Peng Yu)
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commit | commitdiff | tree |
| 2010-06-04 |
Chris Fields | Merge branch 'master' of github.com:bioperl/bioperl...
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commit | commitdiff | tree |
| 2010-06-04 |
Chris Fields | speling mstake
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commit | commitdiff | tree |
| 2010-05-27 |
Chris Fields | move test file to proper namespace
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commit | commitdiff | tree |
| 2010-05-27 |
Chris Fields | move test file to proper namespace
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commit | commitdiff | tree |
| 2010-05-27 |
Chris Fields | non-matching VERSION removed
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commit | commitdiff | tree |
| 2010-05-27 |
Chris Fields | fix uninit value warning when no version is given
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commit | commitdiff | tree |
| 2010-05-26 |
Chris Fields | return unless taxid is given
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commit | commitdiff | tree |
| 2010-05-25 |
Chris Fields | add no_index meta for PrimarySeqI example (should probably...
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commit | commitdiff | tree |
| 2010-05-25 |
Chris Fields | Merge branch 'master' of github.com:bioperl/bioperl...
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commit | commitdiff | tree |
| 2010-05-25 |
Chris Fields | not sure why these aren't in trunk, but add default...
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commit | commitdiff | tree |
| 2010-05-21 |
Chris Fields | small doc fix, more to come
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commit | commitdiff | tree |
| 2010-05-20 |
Chris Fields | can't lookup an undefined value as an executable
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commit | commitdiff | tree |
| 2010-05-20 |
Chris Fields | updated nexml file
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commit | commitdiff | tree |
| 2010-05-20 |
Chris Fields | add updated tree nexml files, old files for comparison
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commit | commitdiff | tree |
| 2010-05-20 |
Chris Fields | updated expected test data for updated nexml file
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commit | commitdiff | tree |
| 2010-05-20 |
Chris Fields | update files, expected test data for nexml (AlignIO)
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commit | commitdiff | tree |
| 2010-05-20 |
Chris Fields | Merge branch 'master' of github.com:bioperl/bioperl...
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commit | commitdiff | tree |
| 2010-05-20 |
Chris Fields | fix odd use of isa, popping up with latest Bio::Phylo
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commit | commitdiff | tree |
| 2010-05-20 |
Chris Fields | fix brittle test based (possibly changing) file size...
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commit | commitdiff | tree |
| 2010-05-20 |
Chris Fields | uc/lc must have defined var (perl 5.12)
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commit | commitdiff | tree |
| 2010-05-20 |
Chris Fields | (re)fix assembly to cleanup up files, make skipping...
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commit | commitdiff | tree |
| 2010-05-20 |
Chris Fields | Latest Bio::DB::Sam needs -autoindex on to work
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commit | commitdiff | tree |
| 2010-05-20 |
Chris Fields | remove redeclared vars (perl 5.12)
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commit | commitdiff | tree |
| 2010-05-20 |
Chris Fields | var must be defined when using in a string or with...
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commit | commitdiff | tree |
| 2010-05-20 |
Chris Fields | Can't use uc/lc with undefined vars (perl 5.12)
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commit | commitdiff | tree |
| 2010-05-20 |
Chris Fields | can't use uc/lc with possibly undefined variables ...
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commit | commitdiff | tree |
| 2010-05-20 |
Chris Fields | uc/lc must have defined input (perl 5.12)
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commit | commitdiff | tree |
| 2010-05-20 |
Chris Fields | UNIVERSAL->import is deprecated (perl 5.12)
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commit | commitdiff | tree |
| 2010-05-20 |
Chris Fields | UNIVERSAL->import is deprecated (perl 5.12)
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commit | commitdiff | tree |
| 2010-05-20 |
Chris Fields | don't use lc/uc unless you have defined input (perl...
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commit | commitdiff | tree |
| 2010-05-20 |
Chris Fields | remove debugging
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commit | commitdiff | tree |
| 2010-05-20 |
Chris Fields | fix warning (Replacement list is longer than search...
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commit | commitdiff | tree |
| 2010-05-20 |
Chris Fields | fix warning (perl 5.12)
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commit | commitdiff | tree |
| 2010-05-20 |
Chris Fields | strand() is a set of fixed types, throw if invalid...
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commit | commitdiff | tree |
| 2010-05-20 |
Chris Fields | Merge branch 'master' of github.com:bioperl/bioperl...
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commit | commitdiff | tree |
| 2010-05-20 |
Chris Fields | require, not use
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commit | commitdiff | tree |
| 2010-05-17 |
Chris Fields | add some file cleanup from samtools testing
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commit | commitdiff | tree |
| 2010-05-17 |
Chris Fields | Merge branch 'master' of git@github.com:bioperl/bioperl...
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commit | commitdiff | tree |
| 2010-05-17 |
Chris Fields | make assembly tests a little easier re: number of tests
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commit | commitdiff | tree |
| 2010-05-17 |
Chris Fields | featureio bug extends to any gff3 or raw fasta
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commit | commitdiff | tree |
| 2010-05-17 |
Chris Fields | minor tweak to tests
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commit | commitdiff | tree |
| 2010-05-17 |
Chris Fields | bug in FeatureIO, TODO demonstrates the problem
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commit | commitdiff | tree |
| 2010-05-16 |
Chris Fields | add basic shipit file
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commit | commitdiff | tree |
| 2010-05-16 |
Chris Fields | revert spaces added for tests
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commit | commitdiff | tree |
| 2010-05-16 |
Chris Fields | a few more ignored files/directories
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commit | commitdiff | tree |
| 2010-05-15 |
Chris Fields | more Changes, ellipses indicate more needs to be added...
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commit | commitdiff | tree |
| 2010-05-14 |
Chris Fields | test forking and pull requests
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commit | commitdiff | tree |
| 2010-05-13 |
Chris Fields | fix coordinate logic error, patch courtesy Ha X. Dang
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commit | commitdiff | tree |
| 2010-05-13 |
Chris Fields | commit some simple fixes to EUtilities print output
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commit | commitdiff | tree |
| 2010-05-12 |
Chris Fields | retest hooks
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commit | commitdiff | tree |
| 2010-05-12 |
Chris Fields | revert last commit
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commit | commitdiff | tree |
| 2010-05-12 |
Chris Fields | test bioperl-live post-commit hook to bioperl-guts
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commit | commitdiff | tree |
| 2010-05-11 |
cjfields | [bug 3076]
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commit | commitdiff | tree |
| 2010-05-11 |
cjfields | [bug 3058]
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commit | commitdiff | tree |
| 2010-05-11 |
cjfields | [bug 3073]
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commit | commitdiff | tree |
| 2010-05-10 |
cjfields | rework assembly tests to be more modular, should make...
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commit | commitdiff | tree |
| 2010-05-10 |
cjfields | commenting out a section of code fixes test crashes...
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commit | commitdiff | tree |
| 2010-05-10 |
cjfields | 1170 -> 1770 (matches data)
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commit | commitdiff | tree |
| 2010-05-10 |
cjfields | remote change in ensembl, make a little less prone...
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commit | commitdiff | tree |
| 2010-05-10 |
cjfields | load Bio::DB::Fasta (this fails with SQLite tests)
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commit | commitdiff | tree |
| 2010-05-10 |
cjfields | remote database update, local dump file needed to be...
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commit | commitdiff | tree |
| 2010-05-10 |
cjfields | HSP n defaults to 1 (must have at least one HSP used...
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commit | commitdiff | tree |
| 2010-05-10 |
cjfields | use settable n, fall back to num_hsps (more consistent...
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commit | commitdiff | tree |
| 2010-05-10 |
cjfields | make test less prone to volatile changes
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commit | commitdiff | tree |
| 2010-05-10 |
cjfields | missing test file
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commit | commitdiff | tree |
| 2010-05-10 |
cjfields | Razi's patch for parsing out the algorithm reference...
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commit | commitdiff | tree |
| 2010-04-27 |
cjfields | [bug 3064]
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commit | commitdiff | tree |
| 2010-04-26 |
cjfields | [bug 3063]
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commit | commitdiff | tree |
| 2010-04-15 |
cjfields | [bug 3031]
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commit | commitdiff | tree |
| 2010-04-07 |
cjfields | Add a -string parameter, allows one to pass a string...
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commit | commitdiff | tree |
