[FEATURE] Support generating a pooled reference in cnvkit/reference

Is your feature request related to a problem? Please describe

Currently the cnvkit/reference module only seems to support generating a flat reference as you cannot provide coverage files to generate a pooled normal reference e.g

cnvkit.py reference normal1_coverage.cnn normal2coverage.cnn ... -f hg38.fa -o reference.cnn

Describe the solution you'd like

The module should be extended by adding an input for the normal-sample coverage .cnn files and passing those files positionally to cnvkit.py reference. That is the mechanism CNVkit itself uses to distinguish a pooled reference from a flat reference. The current module only supplies --fasta, --targets, and --antitargets, so CNVkit has no normal coverage profiles to pool and therefore builds a flat reference.

Describe alternatives you've considered

No response

Additional context

No response

Locate the module entry point that wraps cnvkit.py reference and inspect how its current --fasta, --targets, and --antitargets arguments are assembled. Add support for positional normal-sample .cnn inputs, then verify the generated command pools those files while retaining flat-reference behavior when none are supplied.