Commits on Oct 29, 2019

1. Addition of cnv data to oncoprint …

   - added optparse options to include `low_segmean_cutoff` and `high_segmean_cutoff` (both needed to distinguish amplifications, homozygous deletions, and hemizygous deletions)
   - changed the color for `Nonsense_Mutation` from black to dark blue in `oncoplot-palette.R`
   - changed `removeNonMutated` option in `oncoplot` function from FALSE to TRUE in order to make `Tumor_Sample_Barcodes`s more readable on the plot

   

   cbethell committed Oct 29, 2019
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2. Merge branch 'master' into add-cnv-oncoprint

   

   cbethell authored Oct 29, 2019
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3. Use lancet MAF file, it's smaller! …

   Also use CNVkit symlink

   

   jaclyn-taroni committed Oct 29, 2019
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