David Roazen 32dee7ed9b Avoid buffer underflow in GATKBAMIndex by detecting premature EOF in BAM indices ... GATKBAMIndex would allow an extremely confusing BufferUnderflowException to be thrown when a BAM index file was truncated or corrupt. Now, a UserException is thrown in this situation instructing the user to re-index the BAM. Added a unit test for this case as well.		2012-03-08 15:30:44 -05:00
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broadinstitute/sting	Avoid buffer underflow in GATKBAMIndex by detecting premature EOF in BAM indices	2012-03-08 15:30:44 -05:00