Release 0.5 requirements

iqbal-lab-org / gramtools

Genome inference from a population reference graph

MIT License

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Release 0.5 requirements #72

Closed iqbal-lab closed 6 years ago

iqbal-lab commented 6 years ago

[x] 1) Build from VCF
[ ] 2) Works for Release 0.5 datasets (https://github.com/iqbal-lab-org/gramtools/issues/74)
[x] 3) Indexing kmers takes <2 days with 24 cores for Release 0.5 datasets
[x] 4) Handle mapping of fwd and rev comp reads (naive sufficient)
[x] 5) Outputs mosaic fasta and VCF at graph sites
[ ] 6) Tube map support? (optional)
[x] 7) Merge with master, update README

Item 2 is the biggest, as far as I can see. Item 5 is optional.

ffranr commented 6 years ago

@iqbal-lab Can we close this issue?

iqbal-lab commented 6 years ago

I think the answer is very nearly yes. I've changed the release 0.5 datasets to something more sensible. We now have all of those datasets l. So if we look at the criteria mentioned on the release 5 datasets the only open issue is

Benchmark build, quasimap, infer for a single fastq

We should be able to do all this now!

iqbal-lab commented 6 years ago

I've updated the previous comment, and removed another dataset from the release list. It's just tb and pf now

ffranr commented 6 years ago

@iqbal-lab I would like to close this issue. I've reorganized everything as a project. Is that ok with you?

iqbal-lab commented 6 years ago

Yep