Releases · andrej-fischer/cloneHD · GitHub

29 May 16:22

v1.17.8: bug fix patch Latest

Latest

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.

Assets 4

25 Apr 07:29

v1.17.7

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

Assets 5

24 Apr 12:34

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

Assets 5

22 Apr 06:44

v1.17.5

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

Assets 5

10 Apr 09:39

v1.17.4

fixed fatal bug in snv-mode with correlations

Assets 5

07 Apr 12:36

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]

Assets 5

10 Apr 09:42

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]

Assets 4