This pull request performs quality checks and displays an error/warning icon and a list of possible issues.
Open issues:
[x] Sample Africa02 has now a warning: The sample contains 4 global private mutation(s) that are not known by Phylotree (QUAL). What could be wrong? Problems with hotspots? Could this be solved merging with #13 @seppinho
[x] Check the following, after merging with #13: Fasta import calls sampleFile. applyNomenclatureRules(..). This creates an instance of qualityAssitant and adds a rule. Applying quality rules does the same. TODO: check if quality rules are working with fasta, because qualityAssitant is not null in this case. @seppinho
[x] Add a flag ----write-qc that writes a csv file with sample ids and detected issues
This pull request performs quality checks and displays an error/warning icon and a list of possible issues.
Open issues:
Africa02has now a warning:The sample contains 4 global private mutation(s) that are not known by Phylotree (QUAL). What could be wrong? Problems with hotspots? Could this be solved merging with #13 @seppinhosampleFile. applyNomenclatureRules(..). This creates an instance ofqualityAssitantand adds a rule. Applying quality rules does the same. TODO: check if quality rules are working with fasta, becausequalityAssitantis not null in this case. @seppinho----write-qcthat writes a csv file with sample ids and detected issues