amplab/smash — pull request #21 by kwestbrooks (2014-07-23 19:42:52+00:00)
Title: Kelly's super cool java program for comparing variant sets

Hi Julie,

Per our previous discussion, here is my code i've written that diffs callsets. Please feel free to comment on any of the code that doesn't make sense. Here is a list of known deltas against your python code:

(1) This code is able to consume variant calls from both a VCF file and the GA4GH variants API.
(2) This code doesn't do any left-normalization or pre-rescue evaluation. (Per our discussion last friday, there exist cases that this code would fail to identify equivalent variation due to lack of normalization)
(3) This code explores *all* subsets of nonoverlapping variants during rescue and chooses the pair that maximizes the sum of cardinalities of the subsets of calls it rescues.
(4) This code generates all possible haplotypes during rescue (consequently, it also knows how to take advantage of the genotype information in conjunction with multiple alts)
(5) This code exploits phaseset information to reduce the set of possible haplotypes it needs to generate.
(6) This code doesn't distinguish SVs from indels like the python code does (per our discussion from friday, we acknowledge this is definitely something that needs to be done)
(7) This code only reports precision/recall - it doesn't produce any annotated VCF output.
(8) This algorithm is symmetric with respect to its inputs.