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David Roazen c4b0ba4d45 Temporarily back out the Picard team's patches to GATKBAMIndex from December 
These patches to GATKBAMIndex are causing massive BAM index reading errors in
combination with the latest version of Picard. The bug is either in the patches
themselves or in the underlying SeekableBufferedStream class they rely on. Until
the cause can be identified, we are temporarily backing out these changes so that
we can continue to run with the latest Picard/Tribble.

This reverts commits:
81483ec21e528790dfa719d18cdee27d577ca98e
68cf0309db490b79eecdabb4034987ff825ffea8
54bb68f28ad5fe1b3df01702e9c5e108106a0176
 		2013-02-01 13:51:31 -05:00
..
commandline Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
gatk Temporarily back out the Picard team's patches to GATKBAMIndex from December 2013-02-01 13:51:31 -05:00
jna Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
utils Cleanup unused utils functions, and add unit test for one (append) 2013-02-01 13:51:31 -05:00
BaseTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ExampleToCopyUnitTest.java UnitTesting example for copying 2013-01-30 11:19:08 -05:00
MD5DB.java Encrypt GATK AWS keys using the GATK private key, and decrypt as needed as a resource when uploading to AWS logs 2013-01-30 16:42:23 -05:00
MD5Mismatch.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
StingTextReporter.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
TestNGTestTransformer.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
WalkerTest.java Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00