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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
..
config Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
src Temporarily back out the Picard team's patches to GATKBAMIndex from December 2013-02-01 13:51:31 -05:00
test Temporarily back out the Picard team's patches to GATKBAMIndex from December 2013-02-01 13:51:31 -05:00