Remove POSIX ceil dep from Downstream

[stekaz]

I'm not sure if this is really all that helpful, I hope that it is so I thought I'd submit a PR anyway. I refactored the Downstream plugin a few months ago but got busy with other projects. It removes the dependency on POSIX ceil and simplifies how the sequence "to translate" is obtained. In my limited testing, it produced the same results as the current version (v2.3). I found this PR helpful when I was debugging pVACtools (please see #342). I wonder if this could be helpful for you @at7?

[aparton]

Hi @stekaz,

Thank you for submitting this PR, we always welcome plugin submissions from users. We'll review it in the coming weeks and let you know if we have any questions.

Thanks,
Andrew

[at7]

The PR presents a cleaner organisation of the code and simplifies updating CDS sequence with TVA sequence and retrieving CDS sequence after last codon which doesn't overlap the variant allele. It also removes the POSIX dependency. PR adds check that FASTA file is provided in offline mode.
Major code restructure relates to:
-- replaces CDS sequence with TVA sequence, handling insertions correctly
-- computes last_complete_codon end position using modulo, replacing the dependency on ceil function which also works if CDS start overlaps the first codon
-- gets the downstream sequence starting after the last complete codon

-- following steps haven't changed
-- Updated plugin returns same results as it did before the updates. Plugin versions were tested with all frameshift variants for COL7A1 (on reverse strand) and BRCA2 (forward strand)