Version 0.7.8

New features in the call command make it more amenable to analyzing tumor heterogeneity, and also make the rescale command redundant. Documentation is updated with more methodological background info.

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, export 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.