Version 1.2.4

• Update convert.py @ljyanesm
  -- Fixes score output for bed formats when using portcullis table format as input

Full Changelog: Release-1.2.3...Release-1.2.4

Version 1.2.3

Fixes #51

Full Changelog: 1.2.2...Release-1.2.3

1.2.2

Date: Sun Aug 4 21:40:01 2019 +0100

Merge branch develop

Merging update to bump version.

1.2.0

• Junction Filtering:
  • Can control custom-defined rules for creating the initial training sets
  • Fixed an important bug which caused instability on some environments
• BAM Filtering: Fixed #42 which caused BAM filtering to fail when bam file path is to the current working directory
• CI: Switched from travis to jenkins
• Containers: Created docker and singularity containers
• Code: Removed boost from codebase

v1.1.2

IMPORTANT BUG FIX - Previous version had a bug which reduced sensitivity of portcullis filtering output. This release fixes that. We strongly recommend updating to this version.

Fixed a compilation bug that occurs with GCC7.

Updated junctools. Now the parser for tabular Portcullis junctions should be more stable, with dynamically calculated indices rather than brittle hard-coded ones

v1.1.0

• Using python3 pandas for rule-based filtering. This drastically improves performance for the filtering stage.

• During the junction analysis stage we also do a strand analysis. This looks at read counts (both R1 and R2) and whether they are detected on or off the transcript strand. From there we can determine what strandedness protocol was likely used.

• Improved build system, a subset of boost is included with portcullis and we also now require python3 to be available at both compile and runtime.

• Fixed a bug in the prepare stage which prevented samtools sort from working correctly.

• Added score to GFF notes in junctools

v1.0.2

Portcullis can now process BAM files that do not have the SEQ field populated.

junctools gtf now considers monoexonic transcripts.

v1.0.1

• Improved junctools to include a GTF comparison mode, including comparison of intron-chains.
• Improved handling of errors from portcullis
• Fixed a bug when trying to convert junction files in deduplicate mode.

v1.0.0

First official release of portcullis!

Changes from beta6:

• Added function to junctools to either filter or markup GTF transcripts that contain suspicious junctions

• Improved boost dependency configuration handling

• Changed unknown strand character in GFF output from '.' to '?'.

• Fail gracefully from filtering if no output is found when trying to build the positive set.

v1.0.0_beta6

Improved configuration, compilation and linking process. Added options to control whether or not to build junctools, and whether to dynamically link in boost. Improved the python detection.

Added column in tab output to handle sample number

Made GTF loading more flexible in junctools

Fixed a bug interpreting mapsplice junction files

Fixed a bug handling block sizes in bed files

Fixed several travis issues