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Remove Beta label from some Spark tools #5991

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Jul 29, 2019
Merged

Remove Beta label from some Spark tools #5991

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2dc7733
Remove Beta label from some Spark tools
tomwhite Jun 10, 2019
4f2d842
Take PrintReadsSpark and PrintVariantsSpark out of beta
tomwhite Jun 11, 2019
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2 changes: 0 additions & 2 deletions src/main/java/org/broadinstitute/hellbender/tools/spark/pipelines/CountBasesSpark.java
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import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.broadinstitute.barclay.argparser.Argument;
import org.broadinstitute.barclay.argparser.BetaFeature;
import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
import org.broadinstitute.barclay.help.DocumentedFeature;
import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
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programGroup = CoverageAnalysisProgramGroup.class
)
@DocumentedFeature
@BetaFeature
public final class CountBasesSpark extends GATKSparkTool {

private static final long serialVersionUID = 1L;
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2 changes: 0 additions & 2 deletions src/main/java/org/broadinstitute/hellbender/tools/spark/pipelines/CountReadsSpark.java
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import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.broadinstitute.barclay.argparser.Argument;
import org.broadinstitute.barclay.argparser.BetaFeature;
import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
import org.broadinstitute.barclay.help.DocumentedFeature;
import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
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* </pre>
*/
@DocumentedFeature
@BetaFeature
@CommandLineProgramProperties(
summary = "Counts reads in the input SAM/BAM",
oneLineSummary = "Counts reads in the input SAM/BAM",
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2 changes: 0 additions & 2 deletions src/main/java/org/broadinstitute/hellbender/tools/spark/pipelines/CountVariantsSpark.java
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import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.broadinstitute.barclay.argparser.Argument;
import org.broadinstitute.barclay.argparser.BetaFeature;
import org.broadinstitute.barclay.argparser.CommandLinePluginDescriptor;
import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
import org.broadinstitute.barclay.help.DocumentedFeature;
Expand All @@ -22,7 +21,6 @@
oneLineSummary = "CountVariants on Spark",
programGroup = VariantEvaluationProgramGroup.class)
@DocumentedFeature
@BetaFeature
public final class CountVariantsSpark extends GATKSparkTool {

private static final long serialVersionUID = 1L;
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2 changes: 0 additions & 2 deletions src/main/java/org/broadinstitute/hellbender/tools/spark/pipelines/FlagStatSpark.java
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import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.JavaSparkContext;
import org.broadinstitute.barclay.argparser.Argument;
import org.broadinstitute.barclay.argparser.BetaFeature;
import org.broadinstitute.barclay.argparser.CommandLineProgramProperties;
import org.broadinstitute.barclay.help.DocumentedFeature;
import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
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* -O statistics.txt
* </pre>
*/
@BetaFeature
@DocumentedFeature
@CommandLineProgramProperties(
summary = "Spark tool to accumulate flag statistics given a BAM file, e.g. total number of reads with QC failure flag set," +
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1 change: 0 additions & 1 deletion src/main/java/org/broadinstitute/hellbender/tools/spark/pipelines/PrintReadsSpark.java
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Expand Up @@ -15,7 +15,6 @@

@CommandLineProgramProperties(summary = "Print reads from the input BAM", oneLineSummary = "PrintReads on Spark", programGroup = ReadDataManipulationProgramGroup.class)
@DocumentedFeature
@BetaFeature
public final class PrintReadsSpark extends GATKSparkTool {

private static final long serialVersionUID = 1L;
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1 change: 0 additions & 1 deletion src/main/java/org/broadinstitute/hellbender/tools/spark/pipelines/PrintVariantsSpark.java
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Expand Up @@ -43,7 +43,6 @@
oneLineSummary = "Prints out variants from the input VCF.",
programGroup = VariantManipulationProgramGroup.class)
@DocumentedFeature
@BetaFeature
public final class PrintVariantsSpark extends VariantWalkerSpark {

private static final long serialVersionUID = 1L;
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