v1.0.0_beta5

This release contains a significant change to portcullis: the tab format has been overhauled to better group the metrics. In additional we add additional metrics that are only calculated in the filtering stage back into the tab format in order to keep all useful junction data in one place. Junctools has been updated accordingly.

In addition, we have fixed a number of bugs in junctools related to set operations and split mode.

v1.0.0_beta4

Beta release for portcullis. (Betas 1, 2 and 3, where internal releases).

Portcullis scripts have been condensed into a single python program called "junctools", this is a one stop shop for handling all kinds of file formats containing junctions. The user can use this to (amongst other things):

• compare junction files
• convert between one file format and another
• perform set operations between junction files

Runtime improvement to rule-based filtering. This has an impact on runtimes in the filtering stage.

Improvement to selection of initial positive and negative sets for training our filtering model. This should make portcullis slightly more precise than before.

Added an extra option so the user can perform coverage filtering on the junctions after all other filtering has taken place. This is useful if the user is more interested in precision than sensitivity.

v0.17.3

First public release