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Change Log

v0.1.0 / 2017-10-06

  • Successfully parse R1 file names
  • loaders.vcf: fixed imports
  • loaders.vcf.add_parsed_info_col: yank needless lambda
  • loaders.vcf: added cyvcf2 support and zygosity
  • multigene.snake: formatting
  • multigene.snake: added DEBUG metarule list
  • multigene.snake: rearranged imports
  • mulmultigene_LOF_search.snake: changed RUN.globals.input_vcfs
  • multigene.snake: added VCF_CHECK
  • added logging statements
  • added some metadata to multigene pipeline
  • set max mem in snpeff rules to 4g
  • multigene.snake: altered way config files treated
  • config.py: update replace_config
  • misc.py: yank DAG stuff, add load_csv/nan_to_str
  • errors.py remove logging
  • logging.yaml: use top_level_logs to store certain logs
  • update issue template
  • add vscode to ignore
  • switch to logzero
  • multigene: switch to ruamel.yaml
  • added explicit all lists for imports in init.py files
  • data.loaders.vcf: defined single identity func
  • data.loaders.vcf: formatting and docstrings
  • switched to snaketools
  • removed extraneous print
  • Snakefile: switch to logzero
  • Snakefile: switch to ruamel.yaml
  • updated requirements for tools in pipeline
  • switched to snaketools
  • Makefile: corrected install_python
  • docs/conf.py is now responsible for sphinx-api call
  • amended module docs title to 'Source Code Documentation'
  • allow files from sphinx-apidoc to be version controled.
  • configs cmd now supports prefixes to group yamls
  • docs/usage.rst: drafted demo "Register New Data"
  • Preliminary switch to logzero logging - currently ignores logging.yaml config vals
  • reorganized docs
  • updated docs/requirements.txt
  • pip install -e . succeeds (hopefully RTD will too)
  • setup.py is now pypi-able
  • Update for RTD
  • Merged pypackage goodies and updated README
  • merged Makefile with updated cookiecutter-data-science
  • add multiple binary file types to ignored
  • committed all from feature/sync-db

v0.0.4 / 2017-03-29

  • TeamSubjectDatabase(SubjectDatabase) is functional
  • ProjectSubjectDatabase(SubjectDatabase) is functional
  • added cli.sycdb skeleton

v0.0.3 / 2017-03-20

  • added rule "SNPSIFT_ANNOTATE"
  • added basic logging boilerplate
  • removed un-needed instantiation of synapse object in cli.push
  • Merge branch 'feature/CD55-filter' into develop
  • Merge branch 'feature/multigene-filter' into develop
  • added src/veoibd_synapse/data/preprocessing/variant_tables.py
  • Merge branch 'feature/multigene-filter' into develop
  • added preprocessing package
  • reorganized
  • Merge branch 'develop' into feature/CD55-filter
  • removed certain existing xls files from tracking
  • Merge branch 'feature/CD55-filter' into develop
  • ignore xls type files and libreoffice lock files
  • Filter is functional.
  • Merge branch 'feature/count-gene-variants' into develop
  • Functional minimal gtf parser
  • Added graph drawing rules to snakefile