Add --doubleRun to tell ReMatCh to run a second time using as reference the noMatter consensus sequence produced in the first run.
Add --debug to not remove temporary files
Clean sequence headers (replace "|", " ", ",", ".", "(", ")", "'" and "/" for "_")
Change variants determination
Add
--doubleRunto tell ReMatCh to run a second time using as reference the noMatter consensus sequence produced in the first run. Add--debugto not remove temporary files Clean sequence headers (replace "|", " ", ",", ".", "(", ")", "'" and "/" for "_") Change variants determination