Support common user-defined file extension

• geneLevel.R - support for user-defined .tsv output file as well as .txt (#22)

Remove troublesome genes in WES

geneLevel.R - For exomes only, skip troublesome pseudogenes, and those that map to multiple chromosomes. Also retain only genes in autosomes and chrX.

Incorporates mafAnno, geneLevel, armLevel, WGD-related updates

• incorporates updates from Philip and Sam from 22 May 2018 to 24 May 2019, including adding t_var_freq
  #16
  #17

• incorporates armLevel.R and geneLevel.R changes from Allison, Shweta, Cyriac et al:
  #18
  #20

• WGD cases:
  #19

That’s pretty descriptive, imho

Generate portal-ready files

doFacets.R

• Added optional tumor_id argument that will be used as the ID instead of the TAG (which is typically the file path and name).
• Use input cvals only for CN fits. Use fixed cval 25 for segmentation.

geneLevel.R

• Added optional method argument to allow scna output and a corresponding -m/--method command line argument to call it (-m scna).
• Genes within segments longer than 25Mbp or with cell-fraction <0.6 are now reported as diploid (or as tetraploid if WGD).

PRETEND FAILURES DONT EXIST

• optionally set an env value to ignore doFacets return code for IMPACT samples with unreliable input

With pooled normals, use --unmatched TRUE

merge

Merge branch 'master' of github.com:mskcc/facets-suite

fix return codes in facets wrapper

1.5.1

more better return code fixing

Simultaneous support for version < 0.5.2 and > 0.5.2

This release should allow one to use the "--R_lib" argument in facets to correctly use "old-style" facets, or new style.

supplying nothing currently defaults to 0.5.5 in the main R-3.2.2 tree.

Version 1.0.1

BIC Pipeline Freeze - before facets lib refactor

Version 0.9.7 (BIC Freeze)

Checkpoint release for importing FACETS into BIC pipeline (postProcessing)