v1.2.3

• Major Update: Update simulation to use sequential sampling - instead of creating hypothetical gene clusters of equivalent size to the focal region of interest by randomly grouping together genes from across the genome, the simulation samples real genomic loci of similar size to the focal region. This makes the simulation more realistic (preserves spatial structure of the genome) and makes inferences more robust to artifacts due to focal region size.
• Major Update: Instead of an "empirical p-value" to assess codon usage discordance to the background genome, we now report a "discordance percentile".
• Introduce: Introduced run_simulations.py to perform simulations of running codoff on random regions of a certain length for any input genome to validate the percentile/p-value distribution is uniform as expected.

What's Changed

• Update to v1.2.3 by @raufs in #5

Full Changelog: v1.2.2...v1.2.3