v1.17.8: bug fix patch

• added checks whether files are open for writing
• changed to new defaults: --(cna/baf/snv)-rnd [double:1.0e-6] (nan)
• allowed --cna-jump -1 and --baf-jump -1 (no jumps)
• --cna-jumps [baf-jumps-file] and vice versa enabled (useful for exome data)
• jumps read and integrated with new function match_jumps() (not get_track()).
• fixed bug when chromosomes have no non-zero observations.

v1.17.7

• fixed range error in pre-filter pick-from/match-to mode

v1.17.6

• fixed nan bug in GOF, when N==0 (missing data).
• fixed bugs in pre-filter, when --window-size is greater than length
• fixed bug in pre-filter in pick-from-match-to mode

v1.17.5

• fixed memory alloc bug in pre-filter
• abandon ftp site for releases, used only for backup and beta

v1.17.4

• fixed fatal bug in snv-mode with correlations

v1.17.3

• new program pre-filter
• --snv-pen to --snv-pen-high and --snv-pen-mult
• --baf-pen to --baf-pen-compl
• --cna-pen to --cna-pen-zero, --cna-pen-diff and cna-pen-norm
• split README
• fixed bug in SNV transition matrix in combination with --max-tcn [file]

v1.17.2

• new output: posterior per subclone, goodness of fit (GOF) per
  segment
• changed file name *clonal.txt -> *summary.txt
• filterHD STDOUT includes now GOF per sample
• cloneHD *summary.txt includes now GOF per sample
• changed _ to - in all file names
• fixed bug: BAF now symmetrized only in per-subclone-posterior
• new CNA prior to penalize homozygous deletions --cna-pen [double:0.9]