Releases: hartwigmedical/hmftools
Releases · hartwigmedical/hmftools
sage v3.4.3
Bugs:
- targeted panel (high-depth-mode) on v37 - set BAM header on fragment sync to ensure correct translocation check
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 theclf_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.