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
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net/sf/picard/reference	A few minor modifications masquerading as significant changes according to	2011-02-03 17:59:19 +00:00
org/broadinstitute/sting	A checkpoint commit of two BAM reading projects going on simultaneously. These two projects	2011-02-25 17:50:32 +00:00