Allow for no barcode files case. (#1675)

This PR fixes an error case that can happen when the NewIlluminaDataProvider is used in ExtractIlluminaBarcodes which makes the barcode files. Add an explicit check for the presence of a lane directory in CheckIlluminaDirectory Modify an EIB test to check for the condition where NewIlluminaDataProvider was expecting to find barcode files in the basecalls directory.
broadinstitute · May 1, 2021 · e6a2827 · e6a2827
1 parent 949d7f9
commit e6a2827
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Showing 3 changed files with 14 additions and 5 deletions.
diff --git a/src/main/java/picard/illumina/CheckIlluminaDirectory.java b/src/main/java/picard/illumina/CheckIlluminaDirectory.java
@@ -128,6 +128,8 @@ protected int doWork() {
         log.info("Expected cycles: " + StringUtil.intValuesToString(outputCycles));
 
         for (final Integer lane : LANES) {
+            IOUtil.assertDirectoryIsReadable(new File(BASECALLS_DIR, IlluminaFileUtil.longLaneStr(lane)));
+
             if (IlluminaFileUtil.hasCbcls(BASECALLS_DIR, lane)) {
                 final List<Integer> tiles = new ArrayList<>();
 

diff --git a/src/main/java/picard/illumina/parser/NewIlluminaDataProvider.java b/src/main/java/picard/illumina/parser/NewIlluminaDataProvider.java
@@ -77,11 +77,6 @@ class NewIlluminaDataProvider extends BaseIlluminaDataProvider {
                 ParameterizedFileUtil.makeBarcodeRegex(lane)));
 
         final File[] barcodeFiles = getTiledFiles(barcodesDirectory, barcodeRegex);
-        if (Arrays.stream(barcodeFiles).noneMatch(Objects::nonNull)) {
-            throw new PicardException("No barcode files found in the barcodesDirectory " + barcodesDirectory.getAbsolutePath());
-        }
-
-        IOUtil.assertFilesAreReadable(Arrays.asList(barcodeFiles));
         this.barcodeFileMap = new HashMap<>();
         for (File barcodeFile : barcodeFiles) {
             barcodeFileMap.put(fileToTile(barcodeFile.getName()), new BarcodeFileReader(barcodeFile));

diff --git a/src/test/java/picard/illumina/ExtractIlluminaBarcodesTest.java b/src/test/java/picard/illumina/ExtractIlluminaBarcodesTest.java
@@ -25,6 +25,7 @@
 
 import htsjdk.samtools.metrics.MetricsFile;
 import htsjdk.samtools.util.IOUtil;
+import org.apache.commons.io.FileUtils;
 import org.testng.Assert;
 import org.testng.annotations.AfterTest;
 import org.testng.annotations.BeforeTest;
@@ -85,10 +86,12 @@ private void setUp() throws Exception {
         Assert.assertTrue(basecallsDir.delete());
         Assert.assertTrue(basecallsDir.mkdir());
         IOUtil.copyDirectoryTree(SINGLE_DATA_DIR, basecallsDir);
+
         dual = File.createTempFile("eib_dual", ".tmp");
         Assert.assertTrue(dual.delete());
         Assert.assertTrue(dual.mkdir());
         IOUtil.copyDirectoryTree(DUAL_DATA_DIR, dual);
+
         qual = File.createTempFile("eib_qual", ".tmp");
         Assert.assertTrue(qual.delete());
         Assert.assertTrue(qual.mkdir());
@@ -103,6 +106,14 @@ private void setUp() throws Exception {
         Assert.assertTrue(cbcl.delete());
         Assert.assertTrue(cbcl.mkdir());
         IOUtil.copyDirectoryTree(CBCL_DATA_DIR, cbcl);
+        // For the cbcl test, we are deleting the '*barcode.txt.gz' files that exist in the test Basecalls directory
+        // This is to prevent the error conditon that was briefly introduced which expected to find such files in that
+        // directory before EIB was run on it.
+        final File basecallsDir = new File(cbcl, "BaseCalls");
+        Collection<File> barcodeFiles = FileUtils.listFiles(basecallsDir, new String[]{"txt.gz"}, false);
+        for (final File barcodeFile : barcodeFiles) {
+            Assert.assertTrue(barcodeFile.delete());
+        }
     }
 
     @AfterTest
@@ -111,6 +122,7 @@ private void tearDown() {
         IOUtil.deleteDirectoryTree(dual);
         IOUtil.deleteDirectoryTree(qual);
         IOUtil.deleteDirectoryTree(noSymlink);
+        IOUtil.deleteDirectoryTree(cbcl);
     }
 
     @Test