Add estimator flag to include zero-mutation groups

[Copilot]

Estimator currently skips groups with 0 observed mutations, preventing omega values for those cases. This adds a CLI option to control whether those zero-mutation groups are ignored or included.

• CLI surface

  • Adds a paired flag to toggle zero-mutation handling for the estimator.

• Estimator data flow

  • Threads the flag through estimator preparation and assembler input generation to conditionally skip or keep zero-mutation groups.

• Documentation

  • Notes the new flag in the estimator options section.

Example usage:

omega estimator \
  --observed-mutations-file observed.tsv \
  --mutability-file mutability.tsv \
  --depths-file depths.tsv \
  --vep-annotation-file vep.tsv \
  --grouping-folder grouping/ \
  --output-fn results.tsv \
  --include-zero-mutations