chartl 6759acbdef Coverage statistics now fully implements DepthOfCoverage functionality, including the ability to print base counts. Minor changes to BaseUtils to support 'N' and 'D' characters. PickSequenomProbes now has the option to not print the whole window as part of the probe name (e.g. you just see PROJECT_NAME|CHR_POS and not PROJECT_NAME|CHR_POS_CHR_PROBESTART-PROBEND). Full integration tests for CoverageStatistics are forthcoming. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2924 348d0f76-0448-11de-a6fe-93d51630548a		2010-03-04 15:00:02 +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	Coverage statistics now fully implements DepthOfCoverage functionality, including the ability to print base counts. Minor changes to BaseUtils to support 'N' and 'D' characters. PickSequenomProbes now has the option to not print the whole window as part of the probe name (e.g. you just see PROJECT_NAME|CHR_POS and not PROJECT_NAME|CHR_POS_CHR_PROBESTART-PROBEND). Full integration tests for CoverageStatistics are forthcoming.	2010-03-04 15:00:02 +00:00
test/org/broadinstitute/sting	a little clean-up: move setting the bases of generated reads into Artificial SAM Utils now that the clean read injector test is gone.	2010-03-03 16:31:45 +00:00