Version 2.3

Fixes a bug where spanning pairs are calculated as 0 when input reads end in /1 or /2

Version 2.2

This version adds support for JAFFAL (the long read fusion finder) to detect three or more gene fusions. These are reported in a separate summary file for each sample processed.

Version 2.1

Fixes issue with version 2.0 where memory consumption would blow out for some larger datasets.

Version 2.00

This is major new version of JAFFA which includes:

• Support of fusion finding in noising long reads such as from Nanopore or PacBio (use the JAFFAL.groovy mode)
• Substantial rewrite for speed and multi-thread support now means JAFFA can be run substantially faster.
• Slight improvement in sensitivity.
• New ranking category ("PotentialTransSplicing") for single read supported fusions. Formally most of these were ranked as "Medium".

Note: This release will only work with the Hg38 V2 JAFFA reference files.

version-1.09

This release fixes bugs related to compatibility with:

• the latest R/bioconductor (3.5/3.4.0)
• the mouse transcriptome

version-1.08

Minor update to fix to links in the installation script

version-1.07

Updates the default reference from hg19 to hg38

version-1.06

This version fixes a bug from 1.05, where recurrent fusions in the Mitelman database weren't being flagged correctly