v1.17.0

changed the way SNV priors are computed:

• if CNA given: SNV prior informed by CNA posterior
• if CNA+BAF given, SNV prior informed by BAF+CNA posterior
• if SNV only and --max-tcn not given, assumes all chr to be all-normal, mean total c.n. to be normal; SNV prior parameters can be learned with --learn-priors 1.
• if SNV only and --max-tcn [int/file] is given, this data is used to fix the total c.n. per chr and subclone; mean total c.n. is calculated on the fly; SNV prior parameters can be learned with --learn-priors 1.
• if SNV only and --max-tcn [int/file] and --avail-cn [file] are given, SNV prior is calculated according to c.n. availability.

more changes

• changed option --copynumber [file] to --mean-tcn [file]
• new option --avail-cn [file]
• changed option --maxcn [int:4] to --max-tcn [file/int]
• changed option --snv-err [double] to --snv-fpfreq [double]
• changed option --snv-fpr [double] to --snv-fprate [double]
• output file *used-tcn.txt to *used_mean_tcn.txt
• output file *copynumber.txt to *mean_tcn.txt
• new output file *available_cn.txt
• changed sample to chr in cloneHD output files
• slimmed down output of --print-options.
• split clone.cpp into components clone-*.cpp
• split off cloneHD-inference.cpp
• new Makefile