chartl 88a06ad81f Changes to Depth of Coverage: ... - For speedup in large number of samples, base counts are done on a per read group level, then merged into counts on larger partitions (samples, libraries, etc) + passed all integration tests before next item - Added additional summary item, a coverage threshold. Set by (possibly multiple) -ct flags, the summary outputs will have columns for "%_bases_covered_to_X"; both per sample, and per sample per interval summary files are effected (thus md5s changed for these) NOTE: This is the last revision that will include the per-gene summary files. Once DesignFileGenerator is sufficiently general, and has integration tests, it will be moved to core and the per-gene summary from Depth of Coverage will be retired. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3437 348d0f76-0448-11de-a6fe-93d51630548a		2010-05-26 03:39:22 +00:00
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alignment	Forgot to uncomment the AlignerIntegrationTest before committing. And yes, matt, commenting it out is, in fact, easier than just setting my classpath.	2010-04-01 17:17:16 +00:00
commandline	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +00:00
gatk	Changes to Depth of Coverage:	2010-05-26 03:39:22 +00:00
playground	commenting out this test until I can figure out what the hell is going on with the codecs.	2010-05-26 01:12:10 +00:00
utils	Genotyper now is using bytes not chars. Passes all tests.	2010-05-20 21:02:44 +00:00
BaseTest.java	Walkers and integration tests that calculate and compare callable bases	2010-05-07 21:33:47 +00:00
WalkerTest.java	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +00:00