hanna 0982d35f5b Bug fixes in streaming in Tribble data via /dev/stdin. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4935 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-05 02:43:04 +00:00
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arguments	A significant refactoring of the ROD system, done largely to simplify the process of	2010-12-31 04:52:22 +00:00
contexts/variantcontext	Remove the extra trailing tab at the end of the VCF ## header line. Unfortunately, this meant updating every freaking integration test.	2010-12-08 17:22:29 +00:00
datasources	Bug fixes in streaming in Tribble data via /dev/stdin.	2011-01-05 02:43:04 +00:00
executive	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
filters	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00
iterators	Final version of BAQ calculation. default gap open is 1e-4, a good sensitive value. Useful timer class SimpleTimer added. BAQ is now live.	2010-12-10 19:35:12 +00:00
refdata	Update Picard / sam-jdk at Tim's request.	2011-01-03 02:17:25 +00:00
traversals	Update Picard / sam-jdk at Tim's request.	2011-01-03 02:17:25 +00:00
walkers	HaplotypeScore is revamped. It now uses reads' Cigar strings when building the haplotype blocks to skip over soft-clipped bases and factor in insertions and deletions. The statistic now uses only the reads from the filtered context to build the haplotypes but it scores all reads against the two best haplotypes. The score is now computed individually for each sample's reads and then averaged together. Bug fixes throughout. The math for the base quality and mapping quality rank sum tests is fixed. The annotations remain as ExperimentalAnnotations pending more investigation.	2011-01-05 00:28:05 +00:00
WalkerManagerUnitTest.java	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00