embed sample id in parquet filename

Author: mcovarr

scripts/variantstore/wdl/GvsImportGenomes.wdl

@@ -473,7 +473,7 @@ task LoadData {
       vet_parquet_file=`ls vet_*.parquet`
       ref_parquet_file=`ls ref_*.parquet`
 
-      # parse the table partition out of the file name
+      # parse the table superpartition out of the file name
       table_number=$(echo "$vet_parquet_file" | cut -d'_' -f2)
 
       # copy the vet and ref parquet files to the gcs bucket in the right place

src/main/java/org/broadinstitute/hellbender/tools/gvs/ingest/RefCreator.java

@@ -95,7 +95,10 @@ public RefCreator(String sampleIdentifierForOutputFileName, Long sampleId, Strin
 
         try {
             if (writeReferenceRanges) {
-                final File refOutputFile = new File(outputDirectory, REF_RANGES_FILETYPE_PREFIX + tableNumber + PREFIX_SEPARATOR + sampleIdentifierForOutputFileName + "." + outputType.toString().toLowerCase());
+                String[] sampleComponents = {tableNumber, sampleIdentifierForOutputFileName, sampleId.toString()};
+                String filename = REF_RANGES_FILETYPE_PREFIX + String.join(PREFIX_SEPARATOR, sampleComponents) + outputType.toString().toLowerCase();
+
+                final File refOutputFile = new File(outputDirectory, filename);
                 switch (outputType) {
                     case BQ:
                         if (projectId == null || datasetName == null) {

src/main/java/org/broadinstitute/hellbender/tools/gvs/ingest/VetCreator.java

@@ -65,7 +65,9 @@ public VetCreator(String sampleIdentifierForOutputFileName, Long sampleId, Strin
                     vetWriter.setHeaderLine(getHeaders());
                     break;
                 case PARQUET:
-                    final File parquetOutputFile = new File(outputDirectory, VET_FILETYPE_PREFIX + tableNumber + PREFIX_SEPARATOR + sampleIdentifierForOutputFileName + ".parquet");
+                    String[] sampleComponents = {tableNumber, sampleIdentifierForOutputFileName, sampleId.toString()};
+                    String filename = VET_FILETYPE_PREFIX + String.join(PREFIX_SEPARATOR, sampleComponents) + outputType.toString().toLowerCase();
+                    final File parquetOutputFile = new File(outputDirectory, filename);
                     vetParquetFileWriter = new GvsVariantParquetFileWriter(new Path(parquetOutputFile.toURI()), parquetSchema, CompressionCodecName.SNAPPY);
                     break;
             }