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

esvee v1.0-rc.3

Description of release esvee v1.0-rc.3

Full Changelog: esvee-v1.0-rc.2...esvee-v1.0-rc.3

esvee v1.0-rc.2

Config:

• optionally set 'frag_length_file' for Assembly and Caller, otherwise continues to assume file is named TUMOR_ID.esvee.prep.fragment_length.tsv

sage v4.0-rc.2

Technical:

• expand BAM sampling for read length to test all panel regions with buffer

teal v1.3.2

Technical:

• uses BamMetrics summary file