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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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	Re-enabled fastBAMindexing by replacing the FileChannel with a SeekableBufferedStream	2013-02-14 17:51:15 -05:00
test	Re-enabled fastBAMindexing by replacing the FileChannel with a SeekableBufferedStream	2013-02-14 17:51:15 -05:00