feat: PureCN implementation

[ericblanc20]

Attempted to implement purity & ploidy, but restricted to PureCN implementation of CNV calling & segmentation

Remaining tasks

• PureCN ploidy & purity in complex_biomarkers step (with TMB & mutational signatures)
• Complete sequenza purity & ploidy CNV calling and segmentation
• Add sequenza purity & ploidy to the complex_biomarkers step
• Add scarHRD to the complex_biomarkersstep and remove thehomologous_recombination_deficiency` step
• Add GATK4 CNV calling
• Unify CNV segmentation output (no more bed file, use DNAcopy format)

[coveralls]

coverage: 85.904% (+0.3%) from 85.642% when pulling 3f89ac7 on 414-defining-tumor-purityploidy into 55146c7 on main.