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)