Implement DELETE_INPUTS

Author: alecw

src/java/org/broadinstitute/dropseqrna/beadsynthesis/CorrectScrnaReadPairs.java

@@ -42,6 +42,7 @@
 import picard.nio.PicardHtsPath;
 
 import java.io.File;
+import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.util.List;
@@ -161,6 +162,24 @@ protected int doWork() {
         if (METRICS != null) {
             barcodeCorrector.writeMetrics(METRICS, getMetricsFile());
         }
+
+        try {
+            if (DELETE_INPUTS) {
+                inputPaths.stream().forEach(p -> Files.delete(p));
+            }
+            if (DELETE_INPUT_INDICES) {
+                for (final Path inputBam : inputPaths) {
+                    final Path index = SamFiles.findIndex(inputBam);
+                    if (index != null && index.toFile().exists()) {
+                        Files.delete(index);
+
+                    }
+                }
+            }
+        } catch (IOException e) {
+            throw new RuntimeIOException(e);
+        }
+
         return 0;
     }
     /** Stock main method, for testing. */