gatk-3.8/public/java/test/org/broadinstitute/sting/utils
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
..
R No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path. 2011-10-27 14:17:07 -04:00
baq Putative fix for BAQ array out of bounds 2011-09-21 11:25:08 -04:00
clipping Add support for reads starting with insertion 2012-01-03 09:29:45 -05:00
codecs Adding test for reading samtools VCF file 2012-02-27 17:05:50 -05:00
collections Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
crypt Public-key authorization scheme to restrict use of NO_ET 2012-03-06 00:09:43 -05:00
fasta Reduced the number of combinations being tested here, which was overkill 2011-09-01 10:42:43 -04:00
fragments GATKSAMRecord refactor 2011-11-03 15:43:26 -04:00
genotype/vcf Change interface to getNegLog10PError to getLog10PError 2011-11-18 21:07:30 -05:00
interval make the size of a GenomeLoc int instead of long 2012-02-03 17:12:42 -05:00
io Public-key authorization scheme to restrict use of NO_ET 2012-03-06 00:09:43 -05:00
pileup GATKSAMRecord refactor 2011-11-03 15:43:26 -04:00
report Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
runtime No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path. 2011-10-27 14:17:07 -04:00
sam BQSR with indels integrated! 2012-02-09 18:46:45 -05:00
text GATKReport v0.2: 2011-08-03 00:24:47 -04:00
threading Removed GATK use of distributed parallelism framework. 2011-07-20 16:26:09 -04:00
variantcontext Bug fix for incorrect logic in subsetSamples 2011-12-14 16:14:26 -05:00
BaseUtilsUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
GenomeLocParserUnitTest.java During flanking interval creation merging overlapping flanks so that on scatter the list doesn't accidentally genotype the same site twice. 2011-11-17 13:56:42 -05:00
GenomeLocSortedSetUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
GenomeLocUnitTest.java Support for list of known CNVs in VariantEval 2011-11-30 17:05:16 -05:00
HaplotypeUnitTest.java Adding Unit test for Haplotype class. Used in HC's genotype given alleles mode. 2012-03-05 21:08:07 -05:00
MWUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
MathUtilsUnitTest.java 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
PathUtilsUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
ReservoirDownsamplerUnitTest.java Moving reduced read functionality into GATKSAMRecord 2011-10-21 13:28:05 -04:00
SimpleTimerUnitTest.java The right fix for this test is just to delete it. 2011-11-15 14:53:27 -05:00
UtilsUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00