Prefer bcftools/liftover

Author: bbimber

…is/run/util/LiftoverBcfToolsWrapper.java …nalysis/run/LiftoverBcfToolsWrapper.javaSequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/LiftoverBcfToolsWrapper.java renamed to SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/LiftoverBcfToolsWrapper.java SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/LiftoverBcfToolsWrapper.java renamed to SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/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;

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;