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gatk3的最后一个经典版本3.8
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Java 95.8%
Scala 3.8%
R 0.2%
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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
licensing Removing the symlink from the private license file 2013-02-09 12:57:44 -05:00
protected Better GATK version and command line output 2013-06-20 11:19:13 -04:00
public Better GATK version and command line output 2013-06-20 11:19:13 -04:00
settings Rev picard, sam-jdk, tribble, and variant to version 1.91.1453 2013-05-07 14:21:15 -04:00
.gitignore Detect stuck lock-acquisition calls, and disable file locking for tests 2013-04-24 22:49:02 -04:00
README.md Create README.md 2013-06-17 16:03:45 -03:00
build.xml Restore scala compilation by default in build.xml 2013-05-31 11:28:29 -04:00
intellij_example.tar.bz2 Removed the intellij files from the root and made an example package for new users. This allows users to start at the same page and then change it as they see fit without interfering with the repo (thanks guillermo!) 2012-09-27 11:04:56 -04:00
ivy.xml Brought all of ReduceReads to fastutils 2013-02-23 22:53:23 -05:00

README.md

gsa-unstable

See http://www.broadinstitute.org/gatk/