redux v1.1-rc.2

Technical:

• Replace sambamba with samtools in Dockerfile

redux v1.1-rc.1

Bugs:

• fixes a couple of minor & rare issues which could result in either dropped or duplicate reads

Technical:

• has significantly lower memory usage

Config:

• requires samtools instead of sambamba for final BAM concatenation

esvee v1.0-rc.5

Functional:

• cap frag distribution output by max observer read length, to avoid use of short adapter-trimmed reads

Technical:

• load disc stats file from prep dir instead of output dir

cuppa v2.3.1-rc.3

Technical:

• Fix bug where RNA classifier probs were shown when RNA data is missing. This was due to MissingFeaturesHandler erroneously filling in NAs for samples with no RNA data

sage v4.0-rc.3

Bugs:

• minor fix to extending lower repeats in variant context building

Technical:

• close BAM reads in Sage Append once region finished

cuppa v2.3.1-rc.2

Functional:

• Added arg --force_plot to allow cuppa vis plotting when there are too many samples

cuppa v2.3.1-rc.1

Technical:

• Handle alt splices junction with duplicate coordinates (and added test data for this case)
• Improved progress and error logging

purple v4.1-rc.2

Technical:

• Fix PURPLE clonality plot breaking on empty input data

patient-db v6.0-rc.1

Added Peach table

Update for Linx fusions

esvee v1.0-rc.4

Functional:

• Prep write more detail on discordant stats and write max remote group frags for discordant-only junctions
• Assembly adjusts min fragment rates to load junctions: +1 for split junctions, +3 or discordant-only junctions per discordant rate percentage

Technical:

• optionally specify 'esvee_prep_dir' for inputs for assembly and caller
• removed config 'fragment_length_file' config