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TODO.md

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TODO

  • Check how themes are handled & use theme_get() as default if none supplied
  • Ensure factor levels are correct for Before_filtering and After_filtering
  • Add line plot to plotInsertSize()
  • Add options to facet by base for plotBaseQuals() for a FastpDataList object
  • Add Overrepresented Sequences for FastpData and FastpDataList
  • Build more plotting/reporting functions for fastp reports
  • Add methylation logs from SammyB
  • Add samtools stats as a new S4 class