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