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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net/sf/samtools	Delete unused FastaSequenceIndexBuilder class and accompanying test	2013-05-01 01:02:01 -04:00
org/broadinstitute/sting	Better GATK version and command line output	2013-06-20 11:19:13 -04:00