Michael L Heuer

[AVOCADO] Update ADAM dependency to 0.26.0.

3

Fixes #306 #225

The following issue for oscP5 has been closed Remove runtime dependency on Processing by adding no-parent-argument OscP5 constructor http://code.google.com/p/oscp5/issues/detail?id=1 and a new version of oscP5 has been released http://code.google.com/p/oscp5/downloads/detail?name=oscP5-0.9.8.zip Thus...

Per https://www.nature.com/articles/s41587-023-01773-0 Foldseek is GPLv3-licensed free open-source software. There is no license defined in this repository, is it also GPL version 3? In any case, I would appreciate if you...

get_valid_interaction fails with exitcode 137 with --digestion arima

6

There isn't much context provided with the following error ``` $ nextflow run main.nf \ -profile docker \ --genome GRCh38 \ --digestion arima \ --input '/home/ec2-user/*{1,2}.fastq.gz' ... Error executing process...

Fixes #145 Currently expected to fail.

Updating maven-failsafe-plugin to 3.0.0-M5 fails CI integration tests under openjdk11

1

Not sure about this one ... something wrong with the classpath definition wrt JDK11 modules? ``` [INFO] --- maven-failsafe-plugin:3.0.0-M5:integration-test (default) @ disq --- [INFO] [INFO] ------------------------------------------------------- [INFO] T E S...

Migrate end-to-end tests from Travis CI to Github Actions

1

The end-to-end tests in the Travis CI build have yet to be migrated over to Github Actions.

Investigate performance implications of using Java serialization for genotypes

1

Pull request #52 uses `JavaSerializer` for `htsjdk.variant.variantcontext.LazyGenotypesContext` to workaround issues with serializing transient fields. Java binary serialization is demonstratively worse than Kryo, in both read/write speed and size in memory,...