Release notes

v2.1.1 (March, 9th, 2020)

  • Recommended release.

  • Required: facets-suite v2.0.4 or higher

  • Required: facets_qc v1.0 or higher

  • parameterized mount names. no longer hard referencing juno

  • gracefully handing errors when user does not have write permissions to repo.

  • allowing refits when dipLogR is not provided.

  • (implemented functionality to validate .json config file against a schema. But disabled it due to issues with jsonvalidate on juno. Will be added back in next version)

v2.1.0 (March, 3rd, 2020)

  • Major release.

  • Required: facets-suite v2.0.4 or higher.

  • Required: facets_qc v1.0 or higher (that is already part of facets-preview package).

  • Introducing "repositories" (or "repo") that can be loaded into facets-preview. Quite simply, a "repo" is a folder with all facets runs/fits that be queried and loaded into the app through a "sample manifest" file.

  • QC script is now independent of the app and is versioned separately. Multiple versions of QC calls can now co-exist

  • Added new QC filters (therefore, require facets-suite v2.0.4 or higher)

  • Parameterized facets-preview to load options from a confg file (.json). Can be configured to load repositories, set QC scripts, specific version of facets-suite and also the refit watcher.

  • Allowing more expansive options for "refit".

v2.0.0a (December 2019)

  • Integration with IMPACT facets repository maintained by CCS.

  • QC criteria evaluating each fit

  • Migration to juno.

    • Now requires /juno to be mounted.

    • All refits now performed on juno

  • Enhanced features for detailed annotation of fits to enable downstream analyses (see screenshots below)

    • Choose fit at purity or hisens level. Useful when determining cancer cell fractions (CCFs)

    • Enable adjusting tcn or lcn for some segments. Especially useful to set lcn for segments where there are not enough het-snps to estimate allele-specific copy number.

    • Manually set purity estimate (where determinable) for fits with purity=NA/0.3

  • Allow refits to run both purity and hisens runs for a new dipLogR.

  • Forces refit to use the same facets version used as the default fit.

v1.0.0 (October 2017)

  • initial release (see version1.0.0 branch)

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