fromer a7af1a164b Updated MNP merging to merge VC records if any sample has a haplotype of ALT-ALT, since this could possibly change annotations. Note that, besides the "interesting" case of an ALT-ALT MNP in a pair of HET sites, this could even occur if two records are hom-var (irrespective of using phasing). Note also that this procedure may generate more than one ALT allele. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4577 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-27 01:50:36 +00:00
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MergeSegregatingAlternateAllelesIntegrationTest.java	Updated MNP merging to merge VC records if any sample has a haplotype of ALT-ALT, since this could possibly change annotations. Note that, besides the "interesting" case of an ALT-ALT MNP in a pair of HET sites, this could even occur if two records are hom-var (irrespective of using phasing). Note also that this procedure may generate more than one ALT allele.	2010-10-27 01:50:36 +00:00
ReadBackedPhasingIntegrationTest.java	Trivially phases any hom site (since it is always correct to continue the previous haplotypes by appending the same allele onto both haplotypes)	2010-10-25 16:58:41 +00:00