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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src/org/broadinstitute/sting	Fixed the logic of the @Output annotation and its interaction with 'required'.	2013-03-14 11:58:51 -04:00
test/org/broadinstitute/sting	New GATKSAMRecord concept of a strandless read, update to FS	2013-03-13 11:16:36 -04:00