When running GenotypeGVCFs by interval, add --only-output-calls-starting-in-intervals

bbimber · bbimber · commit e63356feea0a · 2020-08-10T08:45:54.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GenotypeGVCFHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/GenotypeGVCFHandler.java
@@ -368,6 +368,8 @@ private File runGenotypeGVCFs(PipelineJob job, JobContext ctx, ProcessVariantsHa
                     toolParams.add("-L");
                     toolParams.add(interval.getContig() + ":" + interval.getStart() + "-" + interval.getEnd());
                 });
+
+                toolParams.add("--only-output-calls-starting-in-intervals");
             }
 
             if (ctx.getParams().optBoolean("variantCalling.GenotypeGVCFs.disableFileLocking", false))

Original file line number	Diff line number	Diff line change
`@@ -368,6 +368,8 @@ private File runGenotypeGVCFs(PipelineJob job, JobContext ctx, ProcessVariantsHa`
`368`	`368`	`toolParams.add("-L");`
`369`	`369`	`toolParams.add(interval.getContig() + ":" + interval.getStart() + "-" + interval.getEnd());`
`370`	`370`	`});`
	`371`	`+`
	`372`	`+ toolParams.add("--only-output-calls-starting-in-intervals");`
`371`	`373`	`}`
`372`	`374`
`373`	`375`	`if (ctx.getParams().optBoolean("variantCalling.GenotypeGVCFs.disableFileLocking", false))`