Create FileType for GenomicsDB

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ProcessVariantsHandler.java

@@ -859,7 +859,7 @@ private static Collection<String> getSamples(File input) throws PipelineJobExcep
                 throw new PipelineJobException(e);
             }
         }
-        else if (input.getName().toLowerCase().endsWith(".tdb"))
+        else if (AbstractGenomicsDBImportHandler.TILE_DB_FILETYPE.isType(input))
         {
             return AbstractGenomicsDBImportHandler.getSamplesForWorkspace(input.getParentFile());
         }

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/AbstractGenomicsDBImportHandler.java

@@ -45,6 +45,8 @@
 abstract public class AbstractGenomicsDBImportHandler extends AbstractParameterizedOutputHandler<SequenceOutputHandler.SequenceOutputProcessor> implements SequenceOutputHandler.TracksVCF, SequenceOutputHandler.HasCustomVariantMerge
 {
     protected FileType _gvcfFileType = new FileType(Arrays.asList(".g.vcf"), ".g.vcf", false, FileType.gzSupportLevel.SUPPORT_GZ);
+    public static final FileType TILE_DB_FILETYPE = new FileType(Arrays.asList(".tdb"), ".tdb", false, FileType.gzSupportLevel.NO_GZ);
+
     public static final String CATEGORY = "GenomicsDB Workspace";
     public static final String EXISTING_WORKSPACE = "existingWorkspaceId";
 

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/GenotypeGVCFsWrapper.java

@@ -47,6 +47,10 @@ public void execute(File referenceFasta, File outputFile, @Nullable List<String>
         {
             args.add(inputFile.getPath());
         }
+        else if (AbstractGenomicsDBImportHandler.TILE_DB_FILETYPE.isType(inputFile))
+        {
+            args.add("gendb://" + inputFile.getParentFile().getPath());
+        }
         else if (inputFile.isDirectory())
         {
             args.add("gendb://" + inputFile.getPath());