gatk3的最后一个经典版本3.8

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
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected/java	Merge pull request #32 from broadinstitute/yf_per-sample-downsampling_GSA_765	2013-02-13 10:08:11 -08:00
public	Re-enabled fastBAMindexing by replacing the FileChannel with a SeekableBufferedStream	2013-02-14 17:51:15 -05:00
settings	Replace org.broadinstitute.variant with jar built from the Picard repo	2013-02-05 17:24:25 -05:00
.gitignore	Fixing the licensing scripts	2013-01-26 13:42:49 -05:00
build.xml	Minor build.xml cleanup post-variant-migration	2013-02-06 11:16:52 -05:00
intellij_example.tar.bz2	Removed the intellij files from the root and made an example package for new users. This allows users to start at the same page and then change it as they see fit without interfering with the repo (thanks guillermo!)	2012-09-27 11:04:56 -04:00
ivy.xml	Replace org.broadinstitute.variant with jar built from the Picard repo	2013-02-05 17:24:25 -05:00