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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
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R Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs) 2013-03-12 10:57:14 -04:00
c At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings. 2012-01-17 14:47:53 -05:00
chainFiles
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doc Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs) 2013-03-12 10:57:14 -04:00
java Fixed the logic of the @Output annotation and its interaction with 'required'. 2013-03-14 11:58:51 -04:00
keys Public-key authorization scheme to restrict use of NO_ET 2012-03-06 00:09:43 -05:00
packages ValidatingPileup was renamed to CheckPileup 2013-02-15 11:56:19 -05:00
perl Split out contig names from Reference .fai file on white space (to support the GATK resource bundle's file human_g1k_v37.fasta.fai.gz, which does not use tab delimiters) 2012-06-07 16:56:32 -04:00
scala Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs) 2013-03-12 10:57:14 -04:00
testdata Reverting move of BQSR tests to public, as per DR's email 2012-07-19 10:02:05 -04:00