Prefer bcftools/liftover

BimberLab · Mar 1, 2025 · f21bfec · f21bfec
1 parent f83e55a
commit f21bfec
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Showing 2 changed files with 2 additions and 3 deletions.
diff --git a/...sis/run/util/LiftoverBcfToolsWrapper.java → ...analysis/run/LiftoverBcfToolsWrapper.java b/...sis/run/util/LiftoverBcfToolsWrapper.java → ...analysis/run/LiftoverBcfToolsWrapper.java
@@ -1,11 +1,10 @@
-package org.labkey.sequenceanalysis.run.util;
+package org.labkey.api.sequenceanalysis.run;
 
 import org.apache.logging.log4j.Logger;
 import org.jetbrains.annotations.Nullable;
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.sequenceanalysis.SequenceAnalysisService;
 import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService;
-import org.labkey.api.sequenceanalysis.run.PicardWrapper;
 
 import java.io.File;
 import java.io.IOException;

diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/LiftoverHandler.java
@@ -37,7 +37,7 @@
 import org.labkey.api.writer.PrintWriters;
 import org.labkey.sequenceanalysis.SequenceAnalysisModule;
 import org.labkey.sequenceanalysis.pipeline.ProcessVariantsHandler;
-import org.labkey.sequenceanalysis.run.util.LiftoverBcfToolsWrapper;
+import org.labkey.api.sequenceanalysis.run.LiftoverBcfToolsWrapper;
 import org.labkey.sequenceanalysis.run.util.LiftoverVcfWrapper;
 import org.labkey.sequenceanalysis.util.SequenceUtil;