History¶
v1.0.0 (April 3rd, 2017)¶
This is the first major release of outrigger
!!!
v1.0.0 New features¶
- Parallelized event across chromosomes
- Added
--low-memory
flag forindex
,validate
, andpsi
commands to use a smaller memory footprint when reading CSV files. - Added
--splice-types
option to specify only one kind of splicing you’d like to find - So the user can double-check the Psi calculation, create a
summary.csv
file 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 howoutrigger
judged it. - Added functions to extract constitutive and alternative exons separately
v1.0.0 Bug fixes¶
- Fixed a bug that stalled on
.bam
files while counting the junctions
v1.0.0 Miscellaneous¶
- Added
GC/AG
to valid splice sites
v0.2.9 (November 11th, 2016)¶
This is a non-breaking release with many speed improvements, and upgrade is recommended.
v0.2.9 New features¶
- Add
bam
alignment files as input option
Miscellaneous¶
- Parallelized Psi calculation, the exact number of processors can be specified
with
--n-jobs
, and by default,--n-jobs
is-1
, which means use as many processors as are available.
v0.2.8 (October 23rd, 2016)¶
Updated README/HISTORY files
v0.2.7 (October 23rd, 2016)¶
v0.2.7 New features¶
- Added
outrigger validate
command 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.
v0.2.7 API changes¶
- Added
--resume
and--force
options tooutrigger index
to prevent the overwriting of interrupted indexing operations, or to force overwriting. By default,outrigger
complains and cowardly exits.
v0.2.7 Bug fixes¶
- Support ENSEMBL gtf files which specify chromsome names with a number, e.g.
4
instead ofchr4
. Thank you to lcscs12345 for pointing this out!
v0.2.7 Miscellaneous¶
- Added version info with
outrigger --version
- Sped up gffutils queries and event finding by running
ANALYZE
on SQLite databases.
v0.2.6 (September 15th, 2016)¶
This is a non-breaking patch release
v0.2.6 Bug fixes¶
- Wasn’t concatenating exons properly after parallelizing
v0.2.6 Miscellaneous¶
- Clarified
.gtf
file example for directory output
v0.2.4 (September 14th, 2016)¶
This is a non-breaking patch release of outrigger
.
v0.2.4 New features¶
- Actually parallelized exon finding for novel exons. Before had written the code and tested the non-parallelized version but now using actually parallelized version!
v0.2.4 Bug fixes¶
- Don’t need to turn on
--debug
command for outrigger to even run
v0.2.3 (September 13th, 2016)¶
This is a patch release of outrigger, with non-breaking changes from the previous one.
Bug fixes¶
- Subfolders get copied when installing
- Add test for checking that
outrigger -h
command works
v0.2.2 (September 12th, 2016)¶
This is a point release which includes the index
submodule in the __all__
statement.
v0.2.1 (September 12th, 2016)¶
This is a point release which actually includes the requirements.txt
file that specifies which packages outrigger
depends on.
v0.2.0 (September 9th, 2016)¶
This is the second release of outrigger
!
New features¶
- Parallelized exon finding for novel exons
- Added
outrigger validate
command 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)
v0.1.0 (May 25, 2016)¶
This is the initial release of outrigger