add somatic-standard end-to-end test

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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Closed ryan-williams closed 8 years ago

ryan-williams commented 8 years ago

Individual commits stand alone, but a couple of additional notes:

fold common genotype/variant logic into GenotypeOutputCaller, implemented by SomaticStandard and GermlineAssembly
add hook in SparkCommand for validating arguments
remove superfluous inheritance of "args" types from e.g. DebugLogHelpers
remove tumor/normal API from ReadSets, per discussion on #575

This change is

coveralls commented 8 years ago

Changes Unknown when pulling da2d453dd5bdae5aa73146fb6c649e0607460ebb on ryan-williams:args into \ on hammerlab:master**.

ryan-williams commented 8 years ago

Hm sort of lame that coveralls says "unknown" here, as this PR increases coverage ~3% (previously 76%), which is one of its selling points…

arahuja commented 8 years ago

LGTM - would prefer it if we kept Concordance

coveralls commented 8 years ago

Changes Unknown when pulling 6711f4adb203d96fa14ba7403b1a4ba68ad0ba37 on ryan-williams:args into \ on hammerlab:master**.