updated ur submodule to 5b23eae
Re-use the flagstat file in the IntermediateAlignmentResult if we can.
updated ur submodule to b8303e2
updated workflow submodule to 945d332
new tumor type
Changed get to get_with_lock
Add filtering for overlap fraction in dbsnp
Refine dbsnp and segdup annotations
Refine segdup annotation and add dbvar annotation
Natural sort for chromosomes
Look at a different column for the name of the segmental duplication
Move functionality to Base and Combine
Refactor annotate-sv so each annotator is a stand-alone command
updated ur submodule to 5422c81
test cases for four convergers