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changelog.md

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changelog for cloneHD/filterHD

v1.17.9 / to come

  • bug fix for sparse data with singletons in a chr (bug-001)

v1.17.8 / 29.05.2014

  • 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 / 25.04.2014

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

v1.17.6 / 24.04.2014

  • 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 / 22.04.2014

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

v1.17.4 / 10.04.2014

  • fixed fatal bug in snv-mode with correlations

v1.17.3 / 04.04.2014

  • 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 / 27.03.2014

  • 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]

v1.17.1 / 01.03.2014

  • BAF posterior symmetrized for output
  • CNA transition matrix penalizes clones with zero copies of a segment
  • fixed bug in SNV prior computation
  • added pre-processor directives for conditional openMP compilation

v1.17.0 / 25.02.2014 major release

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

v1.16.7 / 19.02.2014

  • fixed bug in SNV w/ corr mode when --bulk-fix is used
  • introduced different grid sizes for CNA, BAF and SNV
  • fixed bug in Clone::get_interpolation(), at the boundaries
  • fixed bug in Clone::trapezoidal() (affected --bulk-prior vs --bulk-mean consistency)

v1.16.6 / 12.02.2014

  • fixed major bug for SNV false positive emission rate and prior
  • introduced new functions: Clone::update_snv_site_ncorr/fixed/nfixed()
  • fixed bug in SNV prior from CNA/BAF posterior computation (BAF normalization)
  • false positive SNV prior now includes P(c=all-zero)
  • fixed bug in used cn output
  • all-zero "observations" in SNV input (w/o corr) are ignored (and not printed!)
  • fixed bug in filterHD: all-zero observations are always retained.

v1.16.5 / 07.04.2014

  • fixed major bug when CNA, BAF and SNV data used with males (X,Y with only one copy)
  • fixed bug in Clone::snv_prior_from_cna_baf_post()
  • fixed bug in posterior output for BAF and SNV
  • introduced prior masking for all update functions
  • introduced --maxcn_mask [file] option to limit total c.n. per chromosome
  • static linking of both libgcc and libstdc++ for increased portability

v1.16.4 / 30.01.2014

  • filterHD: if --reflect 1, use only posterior in [0,0.5] for mean/std-dev
  • fixed bug with --bulk-fix 0.0

v1.16.3 / 13.01.2014

  • introduced the option --mass-gauging [0/1:1] to switch off the mass gauging for cna data.

v1.16.2 / 12.01.2104

  • snp -> snv and cnv -> cna in all code
  • introduced --chr [file], candidate masses are computed via majority normal copy number

v1.16.1 / 10.01.2014

  • cnv to cna for all command line options
  • cnv to cna in all output file names and content
  • filterHD stdout modified

v1.16 / 03.01.2014

  • first stable release of cloneHD