Rebase on RANS branch and use common methods from CRAMInteropTestUtil…

…s class
samtools · Jan 2, 2024 · 2ac2b83 · 2ac2b83
1 parent 2233b02
commit 2ac2b83
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Showing 2 changed files with 9 additions and 78 deletions.
diff --git a/src/test/java/htsjdk/samtools/cram/CRAMInteropTestUtils.java b/src/test/java/htsjdk/samtools/cram/CRAMInteropTestUtils.java
@@ -33,17 +33,8 @@ public static Path getInteropTestDataLocation() {
         return Paths.get(INTEROP_TEST_FILES_PATH);
     }
 
-    // Given a test file name and the codec, map it to the corresponding compressed file path
-    public static final Path getCompressedCodecPath(final String codecType, final Path uncompressedInteropPath, int formatFlags) {
-
-        // Example uncompressedInteropPath: q4, codecType: r4x16, formatFlags: 193  => compressedFileName: r4x16/q4.193
-        // the substring after "." in the compressedFileName is the formatFlags or the first byte of the compressed stream
-        final String compressedFileName = String.format("%s/%s.%s", codecType, uncompressedInteropPath.getFileName(), formatFlags);
-        return uncompressedInteropPath.getParent().resolve(compressedFileName);
-    }
-
     // the input files have embedded newlines that the test remove before round-tripping...
-    public static final byte[] filterEmbeddedNewlines(final byte[] rawBytes) throws IOException {
+    protected static final byte[] filterEmbeddedNewlines(final byte[] rawBytes) throws IOException {
         // 1. filters new lines if any.
         // 2. "q40+dir" file has an extra column delimited by tab. This column provides READ1 vs READ2 flag.
         //     This file is also new-line separated. The extra column, '\t' and '\n' are filtered.

diff --git a/src/test/java/htsjdk/samtools/cram/RangeInteropTest.java b/src/test/java/htsjdk/samtools/cram/RangeInteropTest.java
@@ -10,7 +10,6 @@
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
-import java.io.ByteArrayOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.nio.ByteBuffer;
@@ -20,6 +19,11 @@
 import java.util.ArrayList;
 import java.util.List;
 
+import static htsjdk.samtools.cram.CRAMInteropTestUtils.filterEmbeddedNewlines;
+import static htsjdk.samtools.cram.CRAMInteropTestUtils.getInteropCompressedFilePaths;
+import static htsjdk.samtools.cram.CRAMInteropTestUtils.getParamsFormatFlags;
+import static htsjdk.samtools.cram.CRAMInteropTestUtils.getUnCompressedFilePath;
+
 public class RangeInteropTest extends HtsjdkTest  {
     public static final String COMPRESSED_RANGE_DIR = "arith";
 
@@ -30,13 +34,13 @@ public Object[][] getRoundTripTestCases() throws IOException {
         // compressed testfile path, uncompressed testfile path,
         // Range encoder, Range decoder, Range params
         final List<Object[]> testCases = new ArrayList<>();
-        for (Path path : getInteropRangeCompressedFilePaths(COMPRESSED_RANGE_DIR)) {
+        for (Path path : getInteropCompressedFilePaths(COMPRESSED_RANGE_DIR)) {
             Object[] objects = new Object[]{
                     path,
-                    getRangeUnCompressedFilePath(path),
+                    getUnCompressedFilePath(path),
                     new RangeEncode(),
                     new RangeDecode(),
-                    getRangeParams(path)
+                    new RangeParams(getParamsFormatFlags(path))
             };
             testCases.add(objects);
         }
@@ -109,68 +113,4 @@ public void testDecodeOnly(
         }
     }
 
-    // the input files have embedded newlines that the test remove before round-tripping...
-    private final byte[] filterEmbeddedNewlines(final byte[] rawBytes) throws IOException {
-        // 1. filters new lines if any.
-        // 2. "q40+dir" file has an extra column delimited by tab. This column provides READ1 vs READ2 flag.
-        //     This file is also new-line separated. The extra column, '\t' and '\n' are filtered.
-        try (final ByteArrayOutputStream baos = new ByteArrayOutputStream()) {
-            int skip = 0;
-            for (final byte b : rawBytes) {
-                if (b == '\t'){
-                    skip = 1;
-                }
-                if (b == '\n') {
-                    skip = 0;
-                }
-                if (skip == 0 && b !='\n') {
-                    baos.write(b);
-                }
-            }
-            return baos.toByteArray();
-        }
-    }
-
-    // return a list of all encoded test data files in the htscodecs/tests/dat/<compressedDir> directory
-    private List<Path> getInteropRangeCompressedFilePaths(final String compressedDir) throws IOException {
-        final List<Path> paths = new ArrayList<>();
-        Files.newDirectoryStream(
-                        CRAMInteropTestUtils.getInteropTestDataLocation().resolve("dat/"+compressedDir),
-                        path -> Files.isRegularFile(path))
-                .forEach(path -> paths.add(path));
-        return paths;
-    }
-
-    // Given a compressed test file path, return the corresponding uncompressed file path
-    public static final Path getRangeUnCompressedFilePath(final Path compressedInteropPath) {
-        String uncompressedFileName = getUncompressedFileName(compressedInteropPath.getFileName().toString());
-        // Example compressedInteropPath: ../dat/r4x8/q4.1 => unCompressedFilePath: ../dat/q4
-        return compressedInteropPath.getParent().getParent().resolve(uncompressedFileName);
-    }
-
-    public static final String getUncompressedFileName(final String compressedFileName) {
-        // Returns original filename from compressed file name
-        int lastDotIndex = compressedFileName.lastIndexOf(".");
-        if (lastDotIndex >= 0) {
-            return compressedFileName.substring(0, lastDotIndex);
-        } else {
-            throw new CRAMException("The format of the compressed File Name is not as expected. " +
-                    "The name of the compressed file should contain a period followed by a number that" +
-                    "indicates the order of compression. Actual compressed file name = "+ compressedFileName);
-        }
-    }
-
-    public static final RangeParams getRangeParams(final Path compressedInteropPath){
-        // Returns RangeParams from compressed file path
-        final String compressedFileName = compressedInteropPath.getFileName().toString();
-        final int lastDotIndex = compressedFileName.lastIndexOf(".");
-        if (lastDotIndex >= 0 && lastDotIndex < compressedFileName.length() - 1) {
-            return new RangeParams(Integer.parseInt(compressedFileName.substring(lastDotIndex + 1)));
-        } else {
-            throw new CRAMException("The format of the compressed File Name is not as expected. " +
-                    "The name of the compressed file should contain a period followed by a number that" +
-                    "indicates the order of compression. Actual compressed file name = "+ compressedFileName);
-        }
-    }
-
 }