Version 0.7.8 call: - Put absolute copy number in a new "cn" column. When rescaling log2 ratios for purity, do not round to integer absolute copy number values. (#83) - New `-v`/`--vcf` option: Calculate b-allele frequency (BAF) average for each segment and output as a new column "baf". Rescale BAFs if `--purity` is specified. Then, using BAF and total copy number (CN, the "cn" column), assign major and minor allele copy number to each segment and output as new columns "cn1" and "cn2". These values can indicate allelic imbalance, including loss of heterozygosity (LOH). (#84) - New "--center" option that works the same as in "rescale". - New method "-m none" to perform any specified transformations (rescaling, re-centering, adding b-allele frequencies), but do not call integer copy numbers. rescale: - Deprecated in favor of "call" with the "-m none" option, which does the same thing. - If recentering is specified with `--center`, do it before, not after, rescaling log2 values for tumor sample purity. export bed, vcf: - Take absolute copy number from "cn" column if present (#83) antitarget: - Whitelist chromosomes X and Y along with integer chromosome names for inclusion as canonical mammalian chromosomes. Keep the fallback to "short" chromosome names if no such canonical chromosome names are detected. (#37) reference: - Expose bias corrections (GC, RepeatMasker, targeting density) as command-line options `--no-gc`, `--no-rmask`, and `--no-edge`, similar to the `fix` command. (#80) Internal: - VariantArray.read_vcf: somatic mask was the opposite of what it should have been, i.e. skip_somatic was skipping germline and retaining only somatic SNVs.