v3.11.1

Handle edge case error

v3.11.0

Use pybedtools instead of bedtools cli interface to call bedtools.
Plus some code and documentation maintenance.

v3.10.0

Accepts complex variants from VCF files but convert them into snvs and indels.

v3.9.1

Bug fix

• Fixed a misplaced , that broke the --help function in somaticseq_run_workflows. The script was still functional but the --help message could not print.
• Fixed links in README due to example moving to tests/example.

v3.9.0

Mostly for maintenance

• Add pyproject.toml to modernize build scripts for pip install . as ./setup.py install is being deprecated by python.
  • Additional entrypoints for scripts shown in pyproject.toml. Scripts in setup.py are kept to be backward-compatible to previous command line interface.
• Extra packages for development can be installed via pip install '.[dev]'.
• Add an initial test in tests and moved example there.
• Refactored some functions

v3.8.0

Mostly maintenance

• A lot of coding stylistic changes to make things more modern and easier to maintain
• Enforce versioning for some dependencies in setup.py, including python>=3.10
• For XGBoost model, additionally output json file (i.e., decision trees)
• Updated some docker files for 3rd party tools
• remove -d dbsnp.vcf.gz parameter from tumor-only LoFreq command (that param is only meaningful for tumor-normal pair)

Full Changelog: v3.7.4...v3.8.0

Restrict xgboost to >=1.4

ntree_limit is replaced with iteration_range in xgboost.predict in xgboost >=1.4. This release uses iteration_range=(0, iterations) instead of ntree_limit=iterations.

Allow custom hyperparameters be passed into somaticseq_parallel.py

Allow xgboost hyperparameters be passed into somaticseq_parallel.py, e.g., somaticseq_parallel.py --somaticseq-train --extra-hyperparameters scale_pos_weight:0.1 seed:100. Previously, they could only be passed into somatic_xgboost.py. Beware, however, multi-argument options like --extra-hyperparameters and --features-excluded cannot be placed immediately before paired or single, because otherwise it'll try to include paired or single as an argument instead of invoking paired or single mode.

Check VCF file sorting order

• More robustly check sorting order when VCF files are being read. Raise Exception when they are not sorted according to the reference file.
• Change -u $UID to -u $(id -u):$(id -g) when invoking docker command in somaticseq.utilities.dockered_pipelines.container_option.

minor bug fix in docker workflow

• Fixed three bugs where dbsnp and cosmic VCF and exclusion-region BED files did not pass properly in makeSomaticScripts.py.
• No change in SomaticSeq code otherwise.