gatk-3.8/public/java/test/org/broadinstitute/sting
David Roazen 0702ee1587 Public-key authorization scheme to restrict use of NO_ET
-Running the GATK with the -et NO_ET or -et STDOUT options now
 requires a key issued by us. Our reasons for doing this, and the
 procedure for our users to request keys, are documented here:
 http://www.broadinstitute.org/gsa/wiki/index.php/Phone_home

-A GATK user key is an email address plus a cryptographic signature
 signed using our private key, all wrapped in a GZIP container.
 User keys are validated using the public key we now distribute with
 the GATK. Our private key is kept in a secure location.

-Keys are cryptographically secure in that valid keys definitely
 came from us and keys cannot be fabricated, however keys are not
 "copy-protected" in any way.

-Includes private, standalone utilities to create a new GATK user key
 (GenerateGATKUserKey) and to create a new master public/private key
 pair (GenerateKeyPair). Usage of these tools will be documented on
 the internal wiki shortly.

-Comprehensive unit/integration tests, including tests to ensure the
 continued integrity of the GATK master public/private key pair.

-Generation of new user keys and the new unit/integration tests both
 require access to the GATK private key, which can only be read by
 members of the group "gsagit".
2012-03-06 00:09:43 -05:00
..
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 Getting rid of redundant methods in MathUtils. Adding unit tests for approximateLog10SumLog10 and normalizeFromLog10. Increasing the precision of the Jacobian approximation used by approximateLog10SumLog which changes the UG+HC integration tests ever so slightly. 2012-03-05 12:28:32 -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 Public-key authorization scheme to restrict use of NO_ET 2012-03-06 00:09:43 -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