gatk-3.8

History

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
..
java	Fixed the logic of the @Output annotation and its interaction with 'required'.	2013-03-14 11:58:51 -04:00
scala/test/org/broadinstitute/sting/queue/pipeline/examples	Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest	2013-02-27 04:45:53 -05:00

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

java

Fixed the logic of the @Output annotation and its interaction with 'required'.

2013-03-14 11:58:51 -04:00

scala/test/org/broadinstitute/sting/queue/pipeline/examples

Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest

2013-02-27 04:45:53 -05:00