Activity for JCVI VIGOR
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James Christensen committed [r54]
fix db attribute
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jinman committed [r53]
MODIFIED: VIGOR3.pm - modified blast+ calls to have new minimum wordsize of 2, based on blast+ constraints; numerous changes to regexes for parsing blast+ output
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MODIFIED: README.txt - removed references to removed modules, added reference to Config::IniFiles
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database updates
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MODIFIED: numerous changes to allow transition from blast to blast+
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swetha nettem committed [r49]
Deleting junk
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Converted fastacmd calls to blast+ blastdbcmd
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Migration of formatdb calls to blast+ makeblast...
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Creating branch for jinman to change blast call...
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Added flavors/ to prod3/config
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Added flavors/ to prod3/config
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Added flavors/ to prod3/config
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Tagging VIGOR3.2
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jinman merge of config .ini changes
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Merged jmiller's changes back into this branch
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Changed default path in runRegressionTests.pl
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removing db.pm as it's no longer needed with sw...
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Changes to VIGOR3.pl and VIGOR3.pm to use .ini ...
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Adding config dir to store .ini files
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Creating branch for jinman's switch from sqlite...
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Jason Miller committed [r33]
The -K command line option. 1 means narrow the ...
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Put back the branch called select_more_candidates.
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I removed the branch with this command.
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I merged the branch into the trunk with this co...
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I merged the trunk into the branch with this co...
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runRegressionTests.pl - now correctly counts th...
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The -K option, when set, skips the logic of sel...
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Create a branch for testing ways to select more...
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Add two sequences to flu A: AKN08864, YP_308665...
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Add 10 sequences from DQ011855, the complete ge...
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Add jcvi_testing directory
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Create branch devel1
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Tag release with Zika db
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According to this documentation from NCBI written for BLAST 2.2.18, the 'fastacmd'...
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Update BioLinux with VIGOR
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Install BLAST's fastacmd with VIGOR
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Installation script to configure paths to blast and scratch
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Install BLAST's fastacmd with VIGOR
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Support NCBI BLAST 2.3
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Installation script to configure paths to blast and scratch
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Installation script to configure paths to blast and scratch
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Migrate from svn to git
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JCVI VIGOR released /VIGOR3.r20/VIGOR3.r20.tgz
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Paolo Amedeo committed [r20]
Updated flu databases; added Zika Virus databas...
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Updated Respiratory syntactical virus (RSV) dat...
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Corrected headers in Chikungunya virus databases.
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Added Chikungunya virus annotation capability, ...
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Corrected bug that made Vigor crashing when usi...
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Updated the README file
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Updated Obunya virus database and corrected the...
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Small changes in the code to tolerate Blast cra...
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Cleaned up some more unused code and improved t...
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Added West Nile Virus Lineage I (wnvI_db), Line...
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1 committed [r10]
Added the Canine Distemper Virus database (cdv_...
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Cleaned up the code by commenting out unused fu...
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Corrected path to command in VIGOR3.pm and upda...
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VIGOR3.pm - Fixed bug of 3'-partial genes not b...
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VIGOR3.pm - gene_name_to_locus() Corrected the ...
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Updated cov_g1b and flua databases, Corrected t...
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Bug fixed with the latest code update. Paolo
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bug in subsequence subroutine (VIGOR3.pm)
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VIGOR3.pm
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Jeffrey Hoover created ticket #10
many changes to allow exons to span origin in circular genomes
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see JCVI development directory for code fix
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improved handling of wraparound coordinates on circular genomes
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Revised handling of non-canonical splicing to be consistent with database documentation.
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-G option doesn't work and should be deprecated, missing symbolic link for external program cd-hit
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also need to insert this code: # format and return exons my @tmp = shift @exons;...
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recommended hack to deal with mis-annotated references where ribosomal slippage significantly misplaced
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bug in subsequence subroutine (VIGOR3.pm)
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