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gatk3的最后一个经典版本3.8
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Eric Banks 7cab709a88 Fixed the logic of the @Output annotation and its interaction with 'required'. 
ALL GATK DEVELOPERS PLEASE READ NOTES BELOW:

I have updated the @Output annotation to behave differently and to include a 'defaultToStdout' tag.
  * The 'defaultToStdout' tags lets walkers specify whether to default to stdout if -o is not provided.
  * The logic for @Output is now:
    * if required==true then -o MUST be provided or a User Error is generated.
    * if required==false and defaultToStdout==true then the output is assigned to stdout if no -o is provided.
      * this is the default behavior (i.e. @Output with no modifiers).
    * if required==false and defaultToStdout==false then the output object is null.
      * use this combination for truly optional outputs (e.g. the -badSites option in AssessNA12878).

  * I have updated walkers so that previous behavior has been maintained (as best I could).
    * In general, all @Outputs with default long/short names have required=false.
    * Walkers with nWayOut options must have required==false and defaultToStdout==false (I added checks for this)
  * I added unit tests for @Output changes with David's help (thanks!).
  * #resolve GSA-837
 		2013-03-14 11:58:51 -04:00
licensing Removing the symlink from the private license file 2013-02-09 12:57:44 -05:00
protected Fixed the logic of the @Output annotation and its interaction with 'required'. 2013-03-14 11:58:51 -04:00
public Fixed the logic of the @Output annotation and its interaction with 'required'. 2013-03-14 11:58:51 -04:00
settings Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs) 2013-03-12 10:57:14 -04:00
.gitignore Fixing the licensing scripts 2013-01-26 13:42:49 -05:00
build.xml Fix tests that were consistently or intermittently failing when run in parallel on the farm 2013-03-06 13:56:54 -05:00
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