Eric Banks 530e0e5ea6 Added a fix for combining/genotyping positions over spanning deletions. ... Previously, if a SNP occurred in sample A at a position that was in the middle of a deletion for sample B, sample B would be genotyped as homozygous reference there (but it's NOT reference - there's a deletion). Now, sample B is genotyped as having a symbolic DEL allele. Minor cleanup added. Note that I also removed Laura's previous fix for this problem. Existing integration tests change because I've added a new header line to the VCF being output. I also added several tests for the new functionality showing: 1. genotyping from separate and already combined gvcfs give the same output 2. genotyping over multiple spanning deletions works 3. combining works too Existing unit tests also cover this case.		2015-05-11 15:11:16 -04:00
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src	Added a fix for combining/genotyping positions over spanning deletions.	2015-05-11 15:11:16 -04:00
pom.xml	Faster builds, with updates to documentation generation.	2014-11-05 00:32:23 +08:00