feat: preparation for somatic cnv

[ericblanc20]

Adds several (fairly simple & simple-minded) steps required for proper CNV calling:

• guess_sex: simple inference of sex for autosome & sex chromosome coverage
• germline_snvs: simple identification of well-supported germline SNPs. The variant_calling step unfortunately cannot be used for this task, as it is designed for trios.
• somatic_variants_for_cnv: creates input for cnv tools using B-allele fractions to improve/verify CNV calls based on coverage alone. The somatic_variant_calling step cannot be used, as the somatic variants from mutect2 differ greatly when germline variants are included or not.

The current code is OK, but can certainly be improved:

• Pipes could be extended, but it needs more clever choices in germline_snvs/__init__.py
• The problems with model serialization & validation should be understood & fixed: at the moment, automatic alias generation in bcftools models seems to work in isolation, when only the step model is considered. But validation fails during registration of sub-steps.
• Better design of the snappy_wrapper is probably possible. Also, the derived BcftoolsWrapper is a first attempt at streamlining UNIX-like tools (such as bcftools, bedtools, bedops, samtools, rnaqc, ...). Its design should be critically reviewed, before similar wrappers are built.
• The treatment of ignored_chroms should also be seen as a first attempt to be critically reviewed. The code in genome_windows is exercised in the ignored_chroms wrapper, called from the germline_snvs & somatic_variants_for_cnv snakefiles.

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