Added reverse cycle and base dir lookup for tile metrics. (#1158)

* Added reverse cycle and base dir lookup for tile metrics.
Similar to https://github.com/broadinstitute/zamboni/blob/ccbfbd6e22b6eee65546ae612ce2626ed9f549f6/Client/src/scala/org/broadinstitute/zamboni/client/illumina/IlluminaRunConfigurationParser.scala#L425

src/main/java/picard/illumina/CollectIlluminaLaneMetrics.java

@@ -154,7 +154,7 @@ public static class IlluminaLaneMetricsCollector {
                                                                              final boolean isNovaSeq) {
             final Collection<Tile> tiles;
             try {
-                File tileMetricsOutFile = TileMetricsUtil.renderTileMetricsFileFromBasecallingDirectory(illuminaRunDirectory, isNovaSeq);
+                File tileMetricsOutFile = TileMetricsUtil.renderTileMetricsFileFromBasecallingDirectory(illuminaRunDirectory, readStructure.totalCycles, isNovaSeq);
                 if (isNovaSeq) {
                     tiles = TileMetricsUtil.parseTileMetrics(
                             tileMetricsOutFile,

src/main/java/picard/illumina/parser/TileMetricsUtil.java

@@ -36,6 +36,8 @@
 
 import java.io.File;
 import java.io.FileNotFoundException;
+import java.nio.file.Files;
+import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
@@ -56,10 +58,7 @@
 public class TileMetricsUtil {
 
     private static final Log log = Log.getInstance(TileMetricsUtil.class);
-    /**
-     * The cycle directory that contain the tile metrics output. (Cycle 25 for NovaSeq)
-     */
-    public static String CYCLE_CONTAINING_TILE_METRICS = "C25.1";
+
     /**
      * The path to the directory containing the tile metrics file relative to the basecalling directory.
      */
@@ -75,12 +74,31 @@ public class TileMetricsUtil {
     /**
      * Returns the path to the TileMetrics file given the basecalling directory.
      */
-    public static File renderTileMetricsFileFromBasecallingDirectory(final File illuminaRunDirectory, boolean isNovaSeq) {
+    public static File renderTileMetricsFileFromBasecallingDirectory(final File illuminaRunDirectory, Integer numCycles, boolean isNovaSeq) {
+        return fileTileMetricsFile(illuminaRunDirectory, numCycles, isNovaSeq);
+    }
+
+    private static File fileTileMetricsFile(File illuminaRunDirectory, Integer numCycles, boolean isNovaSeq) {
+        Path interOpDir = illuminaRunDirectory.toPath().resolve(INTEROP_SUBDIRECTORY_NAME);
+        final List<Path> pathsToTest = new ArrayList<>();
+
+        pathsToTest.add(interOpDir.resolve(TILE_METRICS_OUT_FILE_NAME));
+
         if (isNovaSeq) {
-            return new File(new File(illuminaRunDirectory, INTEROP_SUBDIRECTORY_NAME + File.separator + CYCLE_CONTAINING_TILE_METRICS), TILE_METRICS_OUT_FILE_NAME);
-        } else {
-            return new File(new File(illuminaRunDirectory, INTEROP_SUBDIRECTORY_NAME), TILE_METRICS_OUT_FILE_NAME);
+            // check cycles in reverse order.
+            for (int i = numCycles; i > 0; i--) {
+                pathsToTest.add(interOpDir.resolve(String.format("C%d.1/%s", i, TILE_METRICS_OUT_FILE_NAME)));
+            }
         }
+
+        return pathsToTest.stream().filter(Files::exists).findFirst().orElseThrow(() -> {
+            StringBuilder message = new StringBuilder(
+                    String.format("No %s file found in %s", INTEROP_SUBDIRECTORY_NAME, interOpDir));
+            if (isNovaSeq) {
+                message.append(" or any of its cycle directories.");
+            }
+            return new IllegalStateException(message.toString());
+        }).toFile();
     }
 
     public static Collection<Tile> parseTileMetrics(final File tileMetricsOutFile,

src/test/java/picard/illumina/parser/TileMetricsUtilTest.java

@@ -0,0 +1,83 @@
+package picard.illumina.parser;
+
+import htsjdk.samtools.util.IOUtil;
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.stream.IntStream;
+
+public class TileMetricsUtilTest {
+    @Test
+    public void testFindTileMetrics() throws IOException {
+        Path baseDir = createTestDirs(0, true);
+        File tileMetricsFile = TileMetricsUtil.renderTileMetricsFileFromBasecallingDirectory(
+                baseDir.toFile(), 0, false);
+
+        Assert.assertEquals(tileMetricsFile.getAbsolutePath(),
+                baseDir.resolve(TileMetricsUtil.INTEROP_SUBDIRECTORY_NAME)
+                        .resolve(TileMetricsUtil.TILE_METRICS_OUT_FILE_NAME).toString());
+
+        IOUtil.deleteDirectoryTree(baseDir.toFile());
+    }
+
+    @Test(expectedExceptions = IllegalStateException.class)
+    public void testMissingTileMetrics() throws IOException {
+        Path baseDir = createTestDirs(0, false);
+        TileMetricsUtil.renderTileMetricsFileFromBasecallingDirectory(
+                baseDir.toFile(), 0, false);
+
+        IOUtil.deleteDirectoryTree(baseDir.toFile());
+    }
+
+    // put tile metrics file in 1 random cycle dir and interop based ensure we get the one in base
+    @Test
+    public void testFindTileMetricsNovaSeqInBaseInterOp() throws IOException {
+        Path baseDir = createTestDirs(1, true);
+        File tileMetricsFile = TileMetricsUtil.renderTileMetricsFileFromBasecallingDirectory(
+                baseDir.toFile(), 1, true);
+
+        Assert.assertEquals(tileMetricsFile.getAbsolutePath(),
+                baseDir.resolve(TileMetricsUtil.INTEROP_SUBDIRECTORY_NAME)
+                        .resolve(TileMetricsUtil.TILE_METRICS_OUT_FILE_NAME).toString());
+
+        IOUtil.deleteDirectoryTree(baseDir.toFile());
+    }
+
+    // put a file named tile metrics in 2 cycle directories and ensure that we get the one in the highest cycle
+    @Test
+    public void testFindTileMetricsNovaSeqInCycleDirs() throws IOException {
+        Path baseDir = createTestDirs(2, false);
+        File tileMetricsFile = TileMetricsUtil.renderTileMetricsFileFromBasecallingDirectory(
+                baseDir.toFile(), 2, true);
+
+        Assert.assertEquals(tileMetricsFile.getAbsolutePath(),
+                baseDir.resolve(TileMetricsUtil.INTEROP_SUBDIRECTORY_NAME).resolve("C2.1")
+                        .resolve(TileMetricsUtil.TILE_METRICS_OUT_FILE_NAME).toString());
+
+        IOUtil.deleteDirectoryTree(baseDir.toFile());
+    }
+
+    private Path createTestDirs(int numCycleMetricsFiles, boolean baseMetricsFile) throws IOException {
+        Path baseDir = Files.createTempDirectory("TileMetricsUtilTest");
+        // create 10 cycle dirs put tile metrics in the last one.
+        Path baseOpDir = Files.createDirectory(baseDir.resolve(TileMetricsUtil.INTEROP_SUBDIRECTORY_NAME));
+        IntStream.range(1, numCycleMetricsFiles + 1).forEach(i -> {
+            try {
+                Path cycleDir = Files.createDirectory(baseOpDir.resolve("C" + i + ".1"));
+                if (i == numCycleMetricsFiles) {
+                    Files.createFile(cycleDir.resolve(TileMetricsUtil.TILE_METRICS_OUT_FILE_NAME));
+                }
+            } catch (IOException e) {
+                e.printStackTrace();
+            }
+        });
+        if (baseMetricsFile) {
+            Files.createFile(baseOpDir.resolve(TileMetricsUtil.TILE_METRICS_OUT_FILE_NAME));
+        }
+        return baseDir;
+    }
+}