Arun Ahuja
Arun Ahuja
Feature request: In the UI I'd like to at a failed job and then jump to the dependency that _actually_ failed. In the UI there is a filter `(and (is-failed)...
Very consistently seeing this when submitting many `epidisco` pipelines at once. It tends to happen when they all simultaneously hit the parallelized variant calling stage. ``` Lwt-async-exn: Unix.Unix_error(Unix.ENOMEM, "fork", "")...
More of a `DistributedShell` issue than `ketrew` but perhaps suggests moving away from `DistributedShell`. It makes a directory in the user's HDFS for homdir for _every_ container. For a ketrew...
I'm using scoverage:1.1.0 to generate a cobertura report and it is created in `target/cobertura.xml` Using coveralls maven plugin:3.1.0 ``` org.eluder.coveralls coveralls-maven-plugin 3.1.0 ${project.build.directory}/cobertura.xml ${basedir} ``` I get the following exception:...
The assumption for things like `SomaticStandardCaller` (or others that use `pileupFlatMap`) is that `--loci` controls the loci at which to examine pileups. However, when using `CappedRegionsPartitioner` this is not the...
It seems like this will involve: - removing/moving references `org.apache.spark.logging` - upgrading ADAM - upgrading `spark-testing-base` to `2.0.0_0.4.4` @ryan-williams have you tried this out already, I remember you were looking...
Possible contenders: 1) Scalameter http://scalameter.github.io/ Used by: http://scala-miniboxing.org/, but not sure how to connect to maven/build process 2) Google Caliper https://code.google.com/p/caliper/ Java, used by: https://github.com/scalanlp/breeze
We have many SAM files that used as gold sets for variant calling 1. Document/Log how each SAM file was created 2. Make this process reproducible
Follow on from #288, only retrieve allele counts at passing variants
Two issues here: 1. Estimate expected variant allele frequencies in the tumor sample 1. Estimate tumor contamination in normal sample for matched normals