This PR introduces parsing of analysis results and updating the corresponding Charon fields. Currently, the fields that will be set on the sample level in Charon are total_reads (from QualiMap), autosomal_coverage (calculated from QualiMap) and percent_duplication (from MarkDuplicates).
In addition, there are some major refactorizations to the Sarek-handling code. In particular, the rather large models.py has been broken apart into submodules (mostly just moving the code without changing anything).
This PR introduces parsing of analysis results and updating the corresponding Charon fields. Currently, the fields that will be set on the sample level in Charon are
total_reads(from QualiMap),autosomal_coverage(calculated from QualiMap) andpercent_duplication(from MarkDuplicates).In addition, there are some major refactorizations to the Sarek-handling code. In particular, the rather large
models.pyhas been broken apart into submodules (mostly just moving the code without changing anything).