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Ground work for processing additional sites sampled from the pool of multinomial negatives

Louis Duchemin requested to merge pelican-scan into master

This addresses the need for running AAModel on specific sites, e.g sampled sites from the pool of multinomial negatives. To achieve it, following changes were made :

  • Clean up Alignment_run module from legacy functions and move functions specifically related to multinomial scan into their own module Multinomial. Introduce Multinomial.result type that wrap Multinomial_test.result with info about the site (Constant | Variable), to avoid redondant computation of the site state.
  • Store site state (Constant | Variable) in the cache alongside scan results
  • Implement a conductor to define specific sites to be processed ; also refactor the conductors (see Scan_cmd.Conductor and AAModel). Constant site detection is now delegated to the conductor to take advantage of cached data / multinomial scan.
  • Add a flag to the CLI to specify a number of multinomial negatives to be sampled and processed by AAModel

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