Add validation of existence of input directories (#1673)

broadinstitute · Apr 28, 2021 · b675e57 · b675e57
1 parent 0fd4218
commit b675e57
Show file tree

Hide file tree

Showing 2 changed files with 9 additions and 0 deletions.
diff --git a/src/main/java/picard/illumina/IlluminaBasecallsToFastq.java b/src/main/java/picard/illumina/IlluminaBasecallsToFastq.java
@@ -226,6 +226,11 @@ protected int doWork() {
     protected String[] customCommandLineValidation() {
         final LinkedList<String> errors = new LinkedList<>();
 
+        IOUtil.assertDirectoryIsReadable(BASECALLS_DIR);
+        if (BARCODES_DIR != null) {
+            IOUtil.assertDirectoryIsReadable(BARCODES_DIR);
+        }
+
         if (NUM_PROCESSORS == 0) {
             NUM_PROCESSORS = Runtime.getRuntime().availableProcessors();
         } else if (NUM_PROCESSORS < 0) {

diff --git a/src/main/java/picard/illumina/IlluminaBasecallsToSam.java b/src/main/java/picard/illumina/IlluminaBasecallsToSam.java
@@ -275,6 +275,10 @@ protected int doWork() {
      * Prepares loggers, initiates garbage collection thread, parses arguments and initialized variables appropriately/
      */
     private void initialize() {
+        IOUtil.assertDirectoryIsReadable(BASECALLS_DIR);
+        if (BARCODES_DIR != null) {
+            IOUtil.assertDirectoryIsReadable(BARCODES_DIR);
+        }
         if (OUTPUT != null) {
             IOUtil.assertFileIsWritable(OUTPUT);
         }