Mark DePristo fdfe4e41d5 Better GATK version and command line output ... -- Previous version emitted command lines that look like: ##HaplotypeCaller="analysis_type=HaplotypeCaller input_file=[private/testdata/reduced.readNotFullySpanningDeletion.bam] ..." the new version provides additional information on when the GATK was run and the GATK version in a nicer format: ##GATKCommandLine=<ID=HaplotypeCaller,Version=2.5-206-gbc7be2b,Date="Thu Jun 20 11:09:01 EDT 2013",Epoch=1371740941197,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[private/testdata/reduced.readNotFullySpanningDeletion.bam] read_buffer_size=null phone_home=AWS ..."> -- Additionally, the command line options are emitted sequentially in the file, so you can see a running record of how a VCF was produced, such as this example from the integration test: ##GATKCommandLine=<ID=HaplotypeCaller,Version=2.5-206-gbc7be2b,Date="Thu Jun 20 11:09:01 EDT 2013",Epoch=1371740941197,CommandLineOptions="lots of stuff"> ##GATKCommandLine=<ID=SelectVariants,Version=2.5-206-gbc7be2b,Date="Thu Jun 20 11:16:23 EDT 2013",Epoch=1371741383277,CommandLineOptions="lots of stuff"> -- Removed the ProtectedEngineFeaturesIntegrationTest -- Actual unit tests for these features!		2013-06-20 11:19:13 -04:00
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datasources	Implement ActiveRegionTraversal RefMetaDataTracker for map call; HaplotypeCaller now annotates ID from dbSNP	2013-06-10 16:20:31 -04:00
downsampling	Exclude reduced reads from elimination during downsampling	2013-06-11 16:16:26 -04:00
executive	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
filters	This commit addresses JIRA issue GSA-948: Prevent users from doing the wrong thing with RNA-Seq data and the GATK.	2013-06-10 10:44:42 -04:00
iterators	SAMDataSource: always consolidate cigar strings into canonical form	2013-06-19 13:29:01 -04:00
refdata	Detect stuck lock-acquisition calls, and disable file locking for tests	2013-04-24 22:49:02 -04:00
report	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
samples	Trivial update to ceutrio.ped file to make it really the CEU trio sample names	2013-05-14 17:08:13 -04:00
traversals	Exclude reduced reads from elimination during downsampling	2013-06-11 16:16:26 -04:00
walkers	SAMDataSource: always consolidate cigar strings into canonical form	2013-06-19 13:29:01 -04:00
CommandLineGATKUnitTest.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
EngineFeaturesIntegrationTest.java	Better GATK version and command line output	2013-06-20 11:19:13 -04:00
GenomeAnalysisEngineUnitTest.java	Added the functionality to impose a relative ordering on ReadTransformers in the GATK engine.	2013-03-06 12:38:59 -05:00
MaxRuntimeIntegrationTest.java	Subshard timeouts in the GATK	2013-05-15 07:00:39 -04:00
ReadMetricsUnitTest.java	Implement ActiveRegionTraversal RefMetaDataTracker for map call; HaplotypeCaller now annotates ID from dbSNP	2013-06-10 16:20:31 -04:00
WalkerManagerUnitTest.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00