mark-dups v1.1.5

Technical:

• clear any previous duplicate flags (eg set from prior runs or other tools)

orange v3.4.0

Changes:

• Produce ORANGE datamodel v2.4.0 (including max copy number for gene copy numbers)

Bugfixes:

• Bugfix: ORANGE can now map stomach and esophageal squamous cell carcinomas to their rightful cohort.

mark-dups v1.1.4

Technical:

• call system GC prior to final BAM sort and merge

cuppa v2.1.1

Bug fixes:

• PredictionRunner now has the clf_group arg that can be either 'all' or 'dna'. This is useful when a sample had RNA data during training, but only has DNA input data at runtime (and hence we don't expect to have RNA predictions)
• Fixed CV performance data not properly being added to cuppa.vis_data.tsv and hence not being shown in the visualization

Other:

• Refactored/clean-up of constants and code related to predictions

cuppa v2.1.0

Changes:

• Various improvements to visualization
• Training set (cross-validation) predictions can now be passed to CUPPA. When CUPPA is run on a training sample the cross-validation prediction for that sample will be returned instead
• Added option to run CuppaDataPrep in multi-sample mode

mark-dups v1.1.3

Bugs:

• remove unmapping coord delim from alt contig to avoid crash

orange v3.3.1

Bugfix:

• ORANGE can now map the doid combinations for stomach and esophageal squamous cell carcinoma to their proper cohorts.

sage v3.4.2

Technical:

• allow adjacent indel to SNV in NovaseqX artefact logic

orange v3.3.0

Changes:

• Clonal likelihood is set to 0 or 1 based on variant copy number when converting germline variants to somatic
• Bugfix: Fix bug in germline MVLH parsing that caused them to be underestimated by a factor 100.
• Restrict germline MVLH table on PDF and related field in JSON to genes handled by SAGE germline.

mark-dups v1.1.2

Bugs:

• only unmap supplementaries if their primary satisfies standard primary-mate criteria