Restore original ClinVar annotation code

Author: bbimber

mGAP/src/org/labkey/mgap/pipeline/AnnotationStep.java

@@ -60,6 +60,7 @@
 public class AnnotationStep extends AbstractCommandPipelineStep<CassandraRunner> implements VariantProcessingStep
 {
     public static final String GRCH37 = "genome37";
+    private static final String CLINVAR_VCF = "clinvar37";
     private static final String DBNSFP_FILE = "dbnsfpFile";
 
     public static final String CHAIN_FILE = "CHAIN_FILE";
@@ -74,6 +75,10 @@ public static class Provider extends AbstractVariantProcessingStepProvider<Annot
         public Provider()
         {
             super("AnnotateVariants", "Annotate VCF for mGAP", "VCF Annotation", "This will annotate an input NHP VCF using human annotations including funcotator and SnpSift.  This jobs will automatically look for chain files based on the source VCF genome and GRCh37/38 targets and will fail if these are not found.", Arrays.asList(
+                    ToolParameterDescriptor.createExpDataParam(CLINVAR_VCF, "Clinvar 2.0 VCF (GRCh37)", "This is the DataId of the VCF containing human Clinvar variants, which should use the GRCh37 genome. After liftover of the rhesus data, any matching variants are annotated.", "ldk-expdatafield", new JSONObject()
+                    {{
+                        put("allowBlank", false);
+                    }}, null),
                     ToolParameterDescriptor.createExpDataParam(DBNSFP_FILE, "dbNSFP Database (GRCh37)", "This is the DataId of the dbNSFP database (txt.gz file) using the GRCh37 genome.", "ldk-expdatafield", new JSONObject()
                     {{
                         put("allowBlank", false);
@@ -205,6 +210,12 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
     {
         VariantProcessingStepOutputImpl output = new VariantProcessingStepOutputImpl();
 
+        File clinvarVCF = getPipelineCtx().getSequenceSupport().getCachedData(getProvider().getParameterByName(CLINVAR_VCF).extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Integer.class));
+        if (!clinvarVCF.exists())
+        {
+            throw new PipelineJobException("Unable to find file: " + clinvarVCF.getPath());
+        }
+
         ReferenceGenome grch37Genome = getPipelineCtx().getSequenceSupport().getCachedGenome(getProvider().getParameterByName(GRCH37).extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Integer.class));
         Integer chainFileId = getPipelineCtx().getSequenceSupport().getCachedObject(CHAIN_FILE, Integer.class);
         File chainFile = getPipelineCtx().getSequenceSupport().getCachedData(chainFileId);
@@ -370,6 +381,38 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
         output.addIntermediateFile(liftedToGRCh37);
         output.addIntermediateFile(new File(liftedToGRCh37.getPath() + ".tbi"));
 
+        //annotate with clinvar
+        getPipelineCtx().getLogger().info("annotating with ClinVar 2.0");
+        File clinvarAnnotated = new File(outputDirectory, SequenceAnalysisService.get().getUnzippedBaseName(liftedToGRCh37.getName()) + ".cv.vcf.gz");
+        if (forceRecreate || !indexExists(clinvarAnnotated))
+        {
+            ClinvarAnnotatorRunner cvRunner = new ClinvarAnnotatorRunner(getPipelineCtx().getLogger());
+            cvRunner.execute(liftedToGRCh37, clinvarVCF, clinvarAnnotated);
+        }
+        else
+        {
+            getPipelineCtx().getLogger().info("resuming with existing file: " + clinvarAnnotated.getPath());
+        }
+        output.addOutput(clinvarAnnotated, "VCF Annotated With ClinVar2.0");
+        output.addIntermediateFile(clinvarAnnotated);
+        output.addIntermediateFile(new File(clinvarAnnotated.getPath() + ".tbi"));
+
+        //backport ClinVar
+        getPipelineCtx().getLogger().info("backport ClinVar 2.0 to source genome");
+        File clinvarAnnotatedBackport = new File(outputDirectory, SequenceAnalysisService.get().getUnzippedBaseName(clinvarAnnotated.getName()) + ".bp.vcf.gz");
+        if (forceRecreate || !indexExists(clinvarAnnotatedBackport ))
+        {
+            BackportLiftedVcfRunner bpRunner = new BackportLiftedVcfRunner(getPipelineCtx().getLogger());
+            bpRunner.execute(clinvarAnnotated, originalGenome.getWorkingFastaFile(), grch37Genome.getWorkingFastaFile(), clinvarAnnotatedBackport);
+        }
+        else
+        {
+            getPipelineCtx().getLogger().info("resuming with existing file: " + clinvarAnnotatedBackport.getPath());
+        }
+        output.addOutput(clinvarAnnotatedBackport, "VCF Annotated With Clinvar, Backported");
+        output.addIntermediateFile(clinvarAnnotatedBackport);
+        output.addIntermediateFile(new File(clinvarAnnotatedBackport.getPath() + ".tbi"));
+
         //annotate with SnpSift
         getPipelineCtx().getLogger().info("annotating with SnpSift/dbnsfp");
         File snpSiftAnnotated = new File(outputDirectory, SequenceAnalysisService.get().getUnzippedBaseName(liftedToGRCh37.getName()) + ".snpSift.vcf.gz");
@@ -543,7 +586,7 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
             addToolFieldNames("SnpSift", "-ssf", options, multiAnnotated.getParentFile(), output, liftFields, SOURCE_FIELDS);
             addToolFieldNames("SnpSift", "-rssf", options, multiAnnotated.getParentFile(), output, liftFields, TARGET_FIELDS);
 
-            maRunner.execute(inputVCF, cassandraAnnotatedBackport, liftoverRejects, funcotatorAnnotatedBackport, snpSiftAnnotatedBackport, multiAnnotated, options);
+            maRunner.execute(inputVCF, cassandraAnnotatedBackport, clinvarAnnotatedBackport, liftoverRejects, funcotatorAnnotatedBackport, snpSiftAnnotatedBackport, multiAnnotated, options);
         }
         else
         {

mGAP/src/org/labkey/mgap/pipeline/MultiSourceAnnotatorRunner.java

@@ -15,7 +15,7 @@ public MultiSourceAnnotatorRunner(Logger log)
         super(log);
     }
 
-    public File execute(File inputVcf, @Nullable File cassandraVcf, File liftoverRejects, @Nullable File funcotator, @Nullable File snpSift, File outputVcf, @Nullable List<String> options)  throws PipelineJobException
+    public File execute(File inputVcf, @Nullable File cassandraVcf, File clinvarAnnotatedBackport, File liftoverRejects, @Nullable File funcotator, @Nullable File snpSift, File outputVcf, @Nullable List<String> options)  throws PipelineJobException
     {
         List<String> args = getBaseArgs("MultiSourceAnnotator");
 
@@ -31,6 +31,9 @@ public File execute(File inputVcf, @Nullable File cassandraVcf, File liftoverRej
         args.add("-lr");
         args.add(liftoverRejects.getPath());
 
+        args.add("-cv");
+        args.add(clinvarAnnotatedBackport.getPath());
+
         if (funcotator != null)
         {
             args.add("-f");