This is a minor release to `outrigger.
- Fixed UNIQUE ID error that happened somewhat stochastically when adding new exons to the database
- Explicitly added Python 3.6 compatibility
- Change logo location to logo/ instead of logo/v1 since there's only one version anyway...
This is the first major release of outrigger!!!
- Parallelized event across chromosomes
- Added
--low-memoryflag forindex,validate, andpsicommands to use a smaller memory footprint when reading CSV files. - Added
--splice-typesoption to specify only one kind of splicing you'd like to find - So the user can double-check the Psi calculation, create a
summary.csvfile indicating the number of reads found at each junction, for all samples - This also shows which "Case" corresponds to each event in each sample, so you can see whether there were sufficient or insufficient reads on the junctions of each event, and howoutriggerjudged it. - Added functions to extract constitutive and alternative exons separately
- Fixed a bug that stalled on
.bamfiles while counting the junctions
- Added
GC/AGto valid splice sites
This is a non-breaking release with many speed improvements, and upgrade is recommended.
- Add
bamalignment files as input option
- Parallelized Psi calculation, the exact number of processors can be specified
with
--n-jobs, and by default,--n-jobsis-1, which means use as many processors as are available.
Updated README/HISTORY files
- Added
outrigger validatecommand to check for canonical splice sites by default:GT/AG(U1, major spliceosome) andAT/AC(U12, minor spliceosome). Both of these are user-adjustable as they are only the standard for mammalian genomes.
- Added
--resumeand--forceoptions tooutrigger indexto prevent the overwriting of interrupted indexing operations, or to force overwriting. By default,outriggercomplains and cowardly exits.
- Support ENSEMBL gtf files which specify chromsome names with a number, e.g.
4instead ofchr4. Thank you to lcscs12345 for pointing this out!
- Added version info with
outrigger --version - Sped up gffutils queries and event finding by running
ANALYZEon SQLite databases.
This is a non-breaking patch release
- Wasn't concatenating exons properly after parallelizing
- Clarified
.gtffile example for directory output
- Added
joblibto requirements
This is a non-breaking patch release of outrigger.
- Actually parallelized exon finding for novel exons. Before had written the code and tested the non-parallelized version but now using actually parallelized version!
- Don't need to turn on
--debugcommand for outrigger to even run
This is a patch release of outrigger, with non-breaking changes from the previous one.
- Subfolders get copied when installing
- Add test for checking that
outrigger -hcommand works
This is a point release which includes the index submodule in the __all__ statement.
This is a point release which actually includes the requirements.txt file that specifies which packages outrigger depends on.
This is the second release of outrigger!
- Parallelized exon finding for novel exons
- Added
outrigger validatecommand to check that your new exons have proper splice sites (e.g. GT/AG and AT/AC) - Added more test data for other event types (even though we don't detect them yet)
This is the initial release of outrigger