delangel a1653f0c83 Another major redo for indel genotyper: this time, add ability to do allele and variant discovery, and don't rely necessarily on external vcf's to provide candidate variants and alleles (e.g. by using IndelGenotyperV2). This has two major advantages: speed, and more fine-grained control of discovery process. Code is still under test and analysis but this version should be hopefully stable. ... Ability to genotype candidate variants from input vcf is retained and can be turned on by command line argument but is disabled by default. Code, by default, will build a consensus of the most common indel event at a pileup. If that consensus allele has a count bigger than N (=5 by default), we proceed to genotype by computing probabilistic realigmment, AF distribution etc. and possibly emmiting a call. Needed for this, also added ability to build haplotypes from list of alleles instead of from a variant context. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4893 348d0f76-0448-11de-a6fe-93d51630548a		2010-12-22 02:38:06 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src	Another major redo for indel genotyper: this time, add ability to do allele and variant discovery, and don't rely necessarily on external vcf's to provide candidate variants and alleles (e.g. by using IndelGenotyperV2). This has two major advantages: speed, and more fine-grained control of discovery process. Code is still under test and analysis but this version should be hopefully stable.	2010-12-22 02:38:06 +00:00
test	Now I call BeforeMethod correctly	2010-12-17 22:45:45 +00:00