Releases: mskcc/facets-suite
Version 2.0.9
This version incorporates several small bug fixes and changes the way that . seg files are produced. DipLogR correction until now has always been performed, however, this is not clear in the file naming convention and leaves uncorrected data unavailable. From this release, _diplogR.adjusted.seg and _diplogR.unadjusted.seg files will be generated, and no .seg file will be created. Changes to the impact repository have been made to retroactively reflect this difference.
Specific details are located here: #54
Additionally, several small bug fixes have been incorporated:
#53
#49
#45
#38
Version 2.0.8
Added FGA to facets.qc.txt output. fixed syntax errors in previous version. deprecating 2.0.7 version.
Version 2.0.6
bug fixes to gene and arm level scripts.
Version 2.0.5
updated annotate-maf-wrapper.R to use purity from the fit corresponding to the Rdata/cncf provided (instead of using 'purity' fit's purity);
fixed logic to correctly call AMPs in gene-level;
removed normalization for dipLogR to 0;
fixed plotting issue with y-axis for icn;
fixed issue with calculating discordant tcn;
Version 2.0.4
Added new QC metrics in check_fit() function to work with new QC criteria in facets-preview v2.1.0 (Facets QC v1.0). Fixed several bugs with CCF annotation and plotting.
Version 2
Version 2 of facets-suite replaces prior version and is a complete structural revamp.
The essential functionality remains unchanged. This new version of the facets-suite repository contains an R package (facetsSuite) which contains standalone functions that individual wrapper scripts use for the core usage cases. The motivation for these changes was to remove code redundancy and improve stability and reproducibility. Additionally, this new repository aims to better document both usage and functionality.
Old releases remain accessible through the release page: https://github.com/mskcc/facets-suite/releases
hacky emcncf workaround
Brute forcing preprocsample RNG (up to three times) until emcncf works.
Bugfix
gene-level script
incorporates #24 changes
Arm- and gene-level script and output modifications
The incorporates PR #26, changes prompted by functionality in Vaporware.