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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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add `partition-loci` cmd #603

Closed ryan-williams closed 7 years ago

ryan-williams commented 7 years ago

reuses all the same arguments, partitions loci (optionally writing it to --loci-partitioning path), and exits

coveralls commented 7 years ago

Coverage Status

Coverage decreased (-0.05%) to 78.932% when pulling deb4b5efd08ce22db0e6a13b0504ac6d2e7d4ec2 on ryan-williams:plc into 4afd15011eb01576ca3789ce77ea03a526515ebe on hammerlab:master.

ryan-williams commented 7 years ago

Yea, they're somewhat debug-y, but the logical things they do make sense to expose downstream, e.g. to workflow managers that might be interested in finer-grained composition of these pieces, or QC/viz tools that might do analytics on the data they generate; keeping several logical workflow-stages coupled within larger Spark apps starts to push workflow-management into Spark, which is not where we want to be.

Plus, we don't have a ton of Commands bearing out the space of possibilities atm, so I think a couple composable proof-of-concept units in there is reasonable.