Ensure bcftools liftover sorts VCF

bbimber · bbimber · commit 53eadbc46797 · 2024-06-18T14:33:23.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java
@@ -28,6 +28,7 @@
 import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome;
 import org.labkey.api.sequenceanalysis.pipeline.SequenceAnalysisJobSupport;
 import org.labkey.api.sequenceanalysis.pipeline.SequenceOutputHandler;
+import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
 import org.labkey.api.sequenceanalysis.pipeline.VariantProcessingStep;
 import org.labkey.api.sequenceanalysis.run.SelectVariantsWrapper;
 import org.labkey.api.util.FileType;
@@ -333,6 +334,8 @@ public void liftOverVcf(JobContext ctx, ReferenceGenome targetGenome, ReferenceG
         {
             LiftoverBcfToolsWrapper wrapper = new LiftoverBcfToolsWrapper(job.getLogger());
             wrapper.doLiftover(currentVCF, chain, sourceGenome.getWorkingFastaFile(), targetGenome.getWorkingFastaFile(), unmappedOutput, output);
+
+            SequencePipelineService.get().sortVcf(output, null, targetGenome.getSequenceDictionary(), ctx.getLogger());
         }
         else
         {

Original file line number	Diff line number	Diff line change
`@@ -28,6 +28,7 @@`
`28`	`28`	`import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome;`
`29`	`29`	`import org.labkey.api.sequenceanalysis.pipeline.SequenceAnalysisJobSupport;`
`30`	`30`	`import org.labkey.api.sequenceanalysis.pipeline.SequenceOutputHandler;`
	`31`	`+import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;`
`31`	`32`	`import org.labkey.api.sequenceanalysis.pipeline.VariantProcessingStep;`
`32`	`33`	`import org.labkey.api.sequenceanalysis.run.SelectVariantsWrapper;`
`33`	`34`	`import org.labkey.api.util.FileType;`
`@@ -333,6 +334,8 @@ public void liftOverVcf(JobContext ctx, ReferenceGenome targetGenome, ReferenceG`
`333`	`334`	`{`
`334`	`335`	`LiftoverBcfToolsWrapper wrapper = new LiftoverBcfToolsWrapper(job.getLogger());`
`335`	`336`	`wrapper.doLiftover(currentVCF, chain, sourceGenome.getWorkingFastaFile(), targetGenome.getWorkingFastaFile(), unmappedOutput, output);`
	`337`	`+`
	`338`	`+ SequencePipelineService.get().sortVcf(output, null, targetGenome.getSequenceDictionary(), ctx.getLogger());`
`336`	`339`	`}`
`337`	`340`	`else`
`338`	`341`	`{`