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 for index, validate, and psi 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 how outrigger 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


  • 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) and AT/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 to outrigger 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 of chr4. 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

v0.2.5 (September 14th, 2016)

v0.2.5 Bug fixes

  • Added joblib to requirements

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