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gatk-3.8/java/test/org/broadinstitute/sting/gatk
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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
..
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 A checkpoint commit of two BAM reading projects going on simultaneously. These two projects 2011-02-25 17:50:32 +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 A few minor modifications masquerading as significant changes according to 2011-02-03 17:59:19 +00:00
refdata Oops...forgot to commit the changes that allow primitive VCF streaming. 2011-01-12 21:54:51 +00:00
traversals A few minor modifications masquerading as significant changes according to 2011-02-03 17:59:19 +00:00
walkers Elegant solution to the determinism problem: force testNG to run tests in the order that I want it to. 2011-02-24 21:32:35 +00:00
WalkerManagerUnitTest.java Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00