Yossi Farjoun 3a7c8c13e2 Re-enabled fastBAMindexing by replacing the FileChannel with a SeekableBufferedStream ... This helps a lot since FileChannel is very low-level and traversing the BAMIndex involves lots of short reads. - Fixed a deterioration in BAMIndex due to rev'ed picard (see below) - Added unit tests for SeekableBufferedStream - Added integrationTests for GATKBAMIndex (in PileupWalkerIntegrationTest) - Added a runtime-test to verify that the amount read equals the amount requested. - Added failing tests with expectedExceptions - Used a DataProvider to make code nicer		2013-02-14 17:51:15 -05:00
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datasources	Re-enabled fastBAMindexing by replacing the FileChannel with a SeekableBufferedStream	2013-02-14 17:51:15 -05:00
downsampling	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
executive	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
filters	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
iterators	Refactor LIBS into utils.locusiterator before refactoring	2013-01-11 15:17:16 -05:00
refdata	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
report	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
samples	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
traversals	Collapse the downsampling fork in the GATK engine	2013-01-28 01:50:30 -05:00
walkers	Re-enabled fastBAMindexing by replacing the FileChannel with a SeekableBufferedStream	2013-02-14 17:51:15 -05:00
CommandLineGATKUnitTest.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
EngineFeaturesIntegrationTest.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
GenomeAnalysisEngineUnitTest.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
MaxRuntimeIntegrationTest.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
WalkerManagerUnitTest.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00