Arun Ahuja

Is there an alternative to using multiValued in there, or a reason it was taken out? Is there interest a contribution to add it back in?

The link above is implying something different than implemented in #286. While they gather the individual statistics in a parallel manner, there is a reduce step to create a single...

@trautonen Thanks for the reply - this is a single module project and I don't believe package names should overlap at all - but I can double check in case...

Thanks for the update - I had to add to it `pluginRepositories` actually. Running that says ``` Build error: Line number 292 is greater than the source file src/main/scala/org/hammerlab/guacamole/LociSet.scala size...

Another option is http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0151664 I've contacted the authors for access to the data as there were no details with the paper, hopefully this will be easier to obtain than the...

Hi @car2008 The error is actually "ContigNotFound: Contig 19". I believe the files you are using are aligned to b37 where the chromosomes don't have the `chr` prefix. The file...

That is actually not something we have tested, we typically run on Yarn or locally, but interested to hear if there are issues. In that stacktrace at least, it is...

@car2008 Is the BAM very large? In local mode, by default, we use `samtools` to read in the BAM which loads them all into memory. This is useful if you...

For those that might be interested (likely no one else) `scalariform` does not need to run through maven but can also run as a command line tool: https://github.com/scala-ide/scalariform/ Some properties...

The `fold` and `map+getOrElse` are not necessarily interchangeable. I think I'd prefer `map+getOrElse` in most cases, but in the case referenced at #569, it would required a chainable `.map`. >...