Enable gzipped FastA input as reference genome

[apeltzer]

Adds support for gzipped FastA reference genome input.

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[apeltzer]

Should add support following on #91

[apeltzer]

@jfy133 please review this, then you may request changes and/or merge it :-)

[apeltzer]

Would like to stick to review / merge pattern from now on to keep things protected here :-)

[jfy133]

Only potential issue I see is, if we are assuming one wants to have compressed FASTAs in the first place, when the --saveReference flag is used - we would want to re-compress the saved FASTA once the reference files not needed anymore in the pipeline.

This would then save disk space when that particular file is not being used - which I guess was my motivation for that feature request.

[apeltzer]

Hm, I don#t get what you mean with this:

• Input FastA.gz (solved by this already)
• Index creation
• Usage in the pipeline
• ... ?

Zipping the index doesn't make that much sense, as we'd have to uncompress everytime we use the index again before running something in a pipeline (which is too much overhead ...) .

Or do you mean we should save the indexed reference genome as compressed zip archive as well?

[jfy133]

Hm, I don#t get what you mean with this:

• Input FastA.gz (solved by this already)
• Index creation
• Usage in the pipeline
• ... ?

Zipping the index doesn't make that much sense, as we'd have to uncompress everytime we use the index again before running something in a pipeline (which is too much overhead ...) .

Or do you mean we should save the indexed reference genome as compressed zip archive as well?

The latter. But this is still a rare case I imagine.

Just accepting a gzipped reference the first time the reference is used would be a sufficient purpose of this functionality as implmented here (e.g. genomes downloaded from NCBI are gzipped).

Maybe keep this commit as it is for the moment. If someone else requests a recompressed indexed FASTA we can consider that later.