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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alignment	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
commandline	Added ability to specify arguments in files via -args/--arg_file	2011-10-24 15:58:34 -04:00
gatk	Avoid buffer underflow in GATKBAMIndex by detecting premature EOF in BAM indices	2012-03-08 15:30:44 -05:00
jna	When using bam list mode in HSP deriving VCF name from bam list instead of requiring an additional parameter.	2011-12-16 18:09:25 -05:00
utils	Do not fail tests that require the GATK private key if the user does not have permission to read it	2012-03-06 15:57:02 -05:00
BaseTest.java	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
MD5DB.java	Merged bug fix from Stable into Unstable	2011-10-13 18:02:06 -04:00
MedianUnitTest.java	Adding more unit tests and contracts to PairHMM util class. Updating HaplotypeCaller to use the new PairHMM util class. Now that the HMM result isn't dependent on the length of the haplotype there is no reason to ensure all haplotypes have the save length which simplifies the code considerably.	2012-03-05 08:28:42 -05:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00