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Cluster CCF Trace, Cluster Colors, and Cell Pop bug fixes #57

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Cluster CCF Trace, Cluster Colors, and Cell Pop bug fixes #57

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  • Allows output of the cluster CCF trace with option --cluster_ccf_trace when running BuildTree or CellPopulation
  • Allows for selecting the colors for non-consecutive clusters (if trying to match WES and WGS runs, for instance) by passing a comma-separated list to --cluster_order
  • Allows for selecting a certain tree number (--tree_number <iter_one_indexed>) when running CellPopulation, to get the CCF Trace for a specific tree iteration
  • Bug fixes in CellPopulation so it can run alone

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