Output filtered reads should inherit input file type.

[cerebis]

https://github.com/Dreycey/PhageFilter/blob/963095238b15e163024ea98fc598cc89798961a4/src/main.rs#L301C17-L319

I see around here that PhageFilter is manually writing output as fasta format. It is likely that input reads will be fastq format, where the qualities are definitely relevant and should be maintained in the output. I would love to see the format inherited.

Otherwise, it might be simpler to write only IDs and pass the responsibility to read extraction to another tool, such as samtools.

[Dreycey]

These are both things that we discussed during development! I think keeping the output the same as the input file makes sense. Also adding this to the backlog