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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk
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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
..
datasources Collapse the downsampling fork in the GATK engine 2013-01-28 01:50:30 -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
phonehome More aggressive checking of AWS key quality upon startup in the GATK 2013-01-31 09:08:38 -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 Temporarily back out the Picard team's patches to GATKBAMIndex from December 2013-02-01 13:51:31 -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