hanna 600f73cbd6 A checkpoint commit of two BAM reading projects going on simultaneously. These two projects ... are works in progress, and this checkin will provide a baseline against which to gauge improvements to both projects. Low-memory BAM protoshards (disabled by default): - Currently passing ValidatingPileupIntegrationTest. - Gets progressively slower throughout the traversal, but should run at least as fast as original implementation. - Uses 10+ file handles per BAM, but should use 3. BAM performance microbenchmark test system: - Currently tests performance of BAM reading using SAM-JDK vs. GATK - Tests do not hit all GATK performance hotspots. - New tests that require input data in a slightly different form are hard to implement. - Output of test results is not easily parseable (investigating Google Caliper for possible improvements). git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5317 348d0f76-0448-11de-a6fe-93d51630548a		2011-02-25 17:50:32 +00:00
..
alignment	Quick fix for Danny Lieber: flesh out the additional functionality required	2011-01-31 05:28:37 +00:00
commandline	Fixed long-standing bug reported by Mauricio where @Arguments assigned to	2011-01-12 22:18:24 +00:00
datasources/pipeline	Removed deprecated getDbsnpFile.	2011-02-08 21:12:15 +00:00
gatk	A checkpoint commit of two BAM reading projects going on simultaneously. These two projects	2011-02-25 17:50:32 +00:00
jna	Added pipeline for calling FCP in batches called MultiFullCallingPipeline.	2011-02-15 18:26:14 +00:00
oneoffprojects/walkers	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
playground/gatk/walkers	Committing the fragment-based calling code. Results look great in all datasets (will show this at 1000G this week with Ryan). Note that this is an intermediate commit. The code needs to be cleaned up and the fragmentation code needs to be moved up into LocusIteratorByState. This should all happen later this week, but I don't want Ryan to have to keep running from my own personal Sting directory. The current crappy implementation adds ~10% to the runtime, but that should all go away in the next iteration.	2011-01-23 05:04:17 +00:00
utils	Oops, old local paths committed on accident.	2011-02-04 23:35:56 +00:00
BaseTest.java	Added pipeline for calling FCP in batches called MultiFullCallingPipeline.	2011-02-15 18:26:14 +00:00
StingTextReporter.java	Cleanup testng listener configuration.	2010-11-15 23:43:14 +00:00
WalkerTest.java	When subsetting by sample, need to take extra care that hom-ref sites don't accidentally get treated as variant sites in CompOverlap. Renamed convenience method for creating command-lines in integration tests.	2011-02-18 06:26:38 +00:00