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gatk-3.8/java/test/org/broadinstitute/sting/gatk
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aaron cba436fa2f small fix for the table codec; if you see a header line, you know you've finished parsing the header. Also also some changes to return the ref ordered data pool test to using MappedStreamSegment instead of EntireStream 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4942 348d0f76-0448-11de-a6fe-93d51630548a
 		2011-01-05 21:20:26 +00:00
..
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 small fix for the table codec; if you see a header line, you know you've finished parsing the header. Also also some changes to return the ref ordered data pool test to using MappedStreamSegment instead of EntireStream 2011-01-05 21:20:26 +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