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hammerlab / guacamole

Spark-based variant calling, with experimental support for multi-sample somatic calling (including RNA) and local assembly
Apache License 2.0
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"upgrade" adam to forked "0.20.0" #581

Closed ryan-williams closed 7 years ago

ryan-williams commented 7 years ago

this ports us on to most of the non-trivial changes that have happened in ADAM since 0.19.0, using my forked "0.20.0".

ADAM's VCF-writing now requires Sample.sampleId to match Genotype.sampleId, and I am using the "sampleName" pulled from readsets.args.Base / ReadSets rather than the loaded-from-data sampleName on Read.

The latter is now unused so I removed it. It might make sense to keep it around explicitly in some way… seems like what ADAM now does with RecordGroups is the right thing, maybe we'll want to use that if we care about that data again.

This change is Reviewable

coveralls commented 7 years ago

Coverage Status

Coverage increased (+0.02%) to 78.593% when pulling 99caf8fb1e40058c552c9ef955d3ee3395121161 on ryan-williams:adam into a6771eeafed073e6858979e01b214b214d965a1f on hammerlab:master.

coveralls commented 7 years ago

Coverage Status

Coverage increased (+8.06%) to 86.628% when pulling bbad0c4ea3323db769e6f96a7f51ae5b66fd30be on ryan-williams:adam into a6771eeafed073e6858979e01b214b214d965a1f on hammerlab:master.

coveralls commented 7 years ago

Coverage Status

Coverage increased (+11.5%) to 90.123% when pulling d195e6e6693851f10a3972d7b5b4dea5148a2656 on ryan-williams:adam into a3018fd15952ccd65307bcd83ad92600072e109d on hammerlab:master.

arahuja commented 7 years ago

Coverage increased (+11.5%)

?? Does that seem right?

ryan-williams commented 7 years ago

No, coveralls is clearly confused on this PR.

It just occurred to me that it's likely to do with my caching target here; coverage-info from previous runs is hanging around.

Let me either make sure that doesn't happen, or remove that change.

In general I think zinc is reliable enough at this point that we could save a lot of time not recompiling everything every build, and only rarely (if ever) having to clear caches; having repros for such zinc bugs as cause us to need to clear caches could be useful anyway.

coveralls commented 7 years ago

Coverage Status

Coverage increased (+0.3%) to 78.953% when pulling 7e1a1143646b072b11387273c5b87a6a23528a87 on ryan-williams:adam into a3018fd15952ccd65307bcd83ad92600072e109d on hammerlab:master.

ryan-williams commented 7 years ago

OK, I think I fixed coveralls.

ryan-williams commented 7 years ago

I'd say just wait for/ask for a new ADAM release then managing one though

There's no "managing" to be done; we have the equivalent of a SNAPSHOT but that won't break under us.