To better understand convergence issues, and outfit Freyja for spike-only sequencing, we need to add spike coverage read-outs alongside the coverage outputs in the freyja demix output files. Since these coordinates will be pathogen specific, we should allow the user to supply a file with start/end coordinates of key regions (here we'll just use the start/end of spike, but in principle we could have multiple such regions.
The input file should be csv formatted, like:
100,200
500,600
or potentially a json formatted with separate entries for each region with name and start/end.
To better understand convergence issues, and outfit Freyja for spike-only sequencing, we need to add spike coverage read-outs alongside the coverage outputs in the
freyja demixoutput files. Since these coordinates will be pathogen specific, we should allow the user to supply a file with start/end coordinates of key regions (here we'll just use the start/end of spike, but in principle we could have multiple such regions.The input file should be csv formatted, like:
or potentially a json formatted with separate entries for each region with name and start/end.