Hi all! I started upgrading to the latest ADAM in commit https://github.com/fnothaft/cloud-scale-bwamem/commit/998aec98ca261d3534470641e7905d3abd6a9253 from this PR, and noticed a bit of code in CS-bwamem that duplicated some other code in ADAM. Anyways, that got me started refactoring, and I did a variety of cleanup (ran a code style tool over the codebase, changed the package names to more closely match Java conventions, moved to the bigdatagenomics utils command line classes, etc). In the end, this wound up being a pretty big refactor. I'm testing this right now. Single end mode works. I'm running paired end mode right now. I'll make an end-to-end variant calling pass in the morning.
Resolves #8.
Hi all! I started upgrading to the latest ADAM in commit https://github.com/fnothaft/cloud-scale-bwamem/commit/998aec98ca261d3534470641e7905d3abd6a9253 from this PR, and noticed a bit of code in CS-bwamem that duplicated some other code in ADAM. Anyways, that got me started refactoring, and I did a variety of cleanup (ran a code style tool over the codebase, changed the package names to more closely match Java conventions, moved to the bigdatagenomics utils command line classes, etc). In the end, this wound up being a pretty big refactor. I'm testing this right now. Single end mode works. I'm running paired end mode right now. I'll make an end-to-end variant calling pass in the morning.