2.0

The Ship of Theseus edition

This is an almost complete (>98%) rewrite of the simulator such that it can be considered something entirely different from the source material and inspiration, XENIA.

Breaking Changes

• somehow, none
  • the file outputs are a little different, so that would be considered breaking if Mimick was part of a pipeline with specific output expectations

Non-breaking changes

• output is now one pair of FASTQ files, rather than a pair for each haplotype

New

• molecules sharing a barcode can now span contigs and haplotypes
  • process described here
• singular GFF output file for mutations
• outputs a molecule manifest file that lists all molecules that were simulated and some important details about them

Internal

• completely rewritten simulator
• significantly improved multithreading
• one thread always reserved for writing final output files

PRs closed @pdimens in #1

Full Changelog: 1.3...2.0