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Currently, read counts aligned to each of the reference sequences in the packaging FASTA file are reported as either "repcap", if the reference sequence name matches the user-provided repcap_name, otherwise "helper". If reference sequences other than the RepCap and helper plasmids are included in the packaging FASTA, they are mis-labeled as "helper", too.
Tasks:
- Add
helper_nameandlambda_nameinput fields, similar torepcap_name, and use them similarly to label the helper plasmid and lambda spike-in reference sequences (from the packaging FASTA file) as such, if given and present. - Create another "source type" category, e.g. "unidentified" or "extra", to label the remaining packaging sequences that are not repcap, helper or lambda. Use this label in the intermediate TSVs. Don't clobber the original sequence names. (Relates to Consolidate output TSVs and remove .Rdata output #29)
- In the report's first summary table (Table 1), report vector/host/repcap/helper/lambda as usual using their source type categories, but for the unidentified/extra sequences, display their original sequence names.
- Retitle Table 1 to: "Percentage of reads by reference sequence"
FYI @alphabdiallo & @Magdoll
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