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gatk-3.8/public/java/test/org/broadinstitute/sting
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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
..
commandline Fixed the logic of the @Output annotation and its interaction with 'required'. 2013-03-14 11:58:51 -04:00
gatk Increase timeout for a test in the EngineFeaturesIntegrationTest 2013-03-12 23:53:26 -04:00
jna Fix more tests that fail when run in parallel on the farm 2013-03-12 16:53:30 -04:00
utils New GATKSAMRecord concept of a strandless read, update to FS 2013-03-13 11:16:36 -04:00
BaseTest.java Replace org.broadinstitute.variant with jar built from the Picard repo 2013-02-05 17:24:25 -05:00
ExampleToCopyUnitTest.java Replace org.broadinstitute.variant with jar built from the Picard repo 2013-02-05 17:24:25 -05:00
MD5DB.java Encrypt GATK AWS keys using the GATK private key, and decrypt as needed as a resource when uploading to AWS logs 2013-01-30 16:42:23 -05:00
MD5Mismatch.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
StingTextReporter.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
TestNGTestTransformer.java Fix tests that were consistently or intermittently failing when run in parallel on the farm 2013-03-06 13:56:54 -05:00
WalkerTest.java Replace org.broadinstitute.variant with jar built from the Picard repo 2013-02-05 17:24:25 -05:00