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Unit Tests and fixes for a few classes in samtools.cram.io (#1198)
* Additional roundtrips for ExternalCompressionTest + moved inside samtools * Rename CramArray to CramIntArray and add tests - add IOTestCases and CramIntTest - rename RamInt.read to readInt32 - byte[] and ByteBuffer tests and fixes
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27 changes: 27 additions & 0 deletions
27
src/test/java/htsjdk/samtools/cram/io/CramIntArrayTest.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,27 @@ | ||
| package htsjdk.samtools.cram.io; | ||
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| import htsjdk.HtsjdkTest; | ||
| import org.testng.Assert; | ||
| import org.testng.annotations.Test; | ||
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| import java.io.ByteArrayInputStream; | ||
| import java.io.ByteArrayOutputStream; | ||
| import java.io.IOException; | ||
| import java.util.List; | ||
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| public class CramIntArrayTest extends HtsjdkTest { | ||
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| @Test(dataProvider = "testInt32Arrays", dataProviderClass = IOTestCases.class) | ||
| public void runTest(List<Integer> ints) throws IOException { | ||
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| int[] inputArray = ints.stream().mapToInt(Integer::intValue).toArray(); | ||
| try (ByteArrayOutputStream baos = new ByteArrayOutputStream()) { | ||
| CramIntArray.write(inputArray, baos); | ||
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| try (ByteArrayInputStream bais = new ByteArrayInputStream(baos.toByteArray())) { | ||
| int[] outputArray = CramIntArray.array(bais); | ||
| Assert.assertEquals(inputArray, outputArray, "Arrays did not match"); | ||
| } | ||
| } | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,106 @@ | ||
| package htsjdk.samtools.cram.io; | ||
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| import htsjdk.HtsjdkTest; | ||
| import org.testng.Assert; | ||
| import org.testng.annotations.Test; | ||
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| import java.io.ByteArrayInputStream; | ||
| import java.io.ByteArrayOutputStream; | ||
| import java.io.IOException; | ||
| import java.nio.ByteBuffer; | ||
| import java.util.ArrayList; | ||
| import java.util.List; | ||
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| public class CramIntTest extends HtsjdkTest { | ||
| private byte[] streamWritten(List<Integer> ints) throws IOException { | ||
| try (ByteArrayOutputStream baos = new ByteArrayOutputStream()) { | ||
| for (int value : ints) { | ||
| CramInt.writeInt32(value, baos); | ||
| } | ||
| return baos.toByteArray(); | ||
| } | ||
| } | ||
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| private byte[] byteArrayWritten(List<Integer> ints) { | ||
| final int bufSize = 4; | ||
| final int arraySize = bufSize * ints.size(); | ||
| byte[] array = new byte[arraySize]; | ||
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| int offset = 0; | ||
| byte[] arrayBuffer; | ||
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| for (int value : ints) { | ||
| arrayBuffer = CramInt.writeInt32(value); | ||
| System.arraycopy(arrayBuffer, 0, array, offset, bufSize); | ||
| offset += bufSize; | ||
| } | ||
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| return array; | ||
| } | ||
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| @Test(dataProvider = "littleEndianTests32", dataProviderClass = IOTestCases.class) | ||
| public void checkStreamLittleEndian(Integer testInt, byte[] expected) throws IOException { | ||
| List<Integer> ints = new ArrayList<>(); | ||
| ints.add(testInt); | ||
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| byte[] actual = streamWritten(ints); | ||
| Assert.assertEquals(actual, expected); | ||
| } | ||
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| @Test(dataProvider = "littleEndianTests32", dataProviderClass = IOTestCases.class) | ||
| public void checkByteArrayLittleEndian(Integer testInt, byte[] expected) { | ||
| List<Integer> ints = new ArrayList<>(); | ||
| ints.add(testInt); | ||
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| byte[] actual = byteArrayWritten(ints); | ||
| Assert.assertEquals(actual, expected); | ||
| } | ||
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| // Combinatorial tests of 2 CramInt write methods x 3 CramInt read methods | ||
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| @Test(dataProvider = "testInt32Arrays", dataProviderClass = IOTestCases.class) | ||
| public void matchStreamRead(List<Integer> ints) throws IOException { | ||
| byte[][] inputs = {streamWritten(ints), byteArrayWritten(ints)}; | ||
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| for (byte[] byteArray : inputs) { | ||
| try (ByteArrayInputStream bais = new ByteArrayInputStream(byteArray)) { | ||
| for (int value : ints) { | ||
| int fromStream = CramInt.readInt32(bais); | ||
| Assert.assertEquals(fromStream, value, "Value did not match"); | ||
| } | ||
| } | ||
| } | ||
| } | ||
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| @Test(dataProvider = "testInt32Arrays", dataProviderClass = IOTestCases.class) | ||
| public void matchBufferRead(List<Integer> ints) throws IOException { | ||
| byte[][] inputs = {streamWritten(ints), byteArrayWritten(ints)}; | ||
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| for (byte[] byteArray : inputs) { | ||
| ByteBuffer bb = ByteBuffer.wrap(byteArray); | ||
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| for (int value : ints) { | ||
| int fromBuffer = CramInt.readInt32(bb); | ||
| Assert.assertEquals(fromBuffer, value, "Value did not match"); | ||
| } | ||
| } | ||
| } | ||
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| @Test(dataProvider = "testInt32Arrays", dataProviderClass = IOTestCases.class) | ||
| public void matchByteArrayRead(List<Integer> ints) throws IOException { | ||
| byte[][] inputs = {streamWritten(ints), byteArrayWritten(ints)}; | ||
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| for (byte[] inputArray : inputs) { | ||
| final int bufSize = 4; | ||
| byte[] outBuf = new byte[bufSize]; | ||
| int offset = 0; | ||
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| for (int value : ints) { | ||
| System.arraycopy(inputArray, offset, outBuf, 0, bufSize); | ||
| int fromBuffer = CramInt.readInt32(outBuf); | ||
| Assert.assertEquals(fromBuffer, value, "Value did not match"); | ||
| offset += bufSize; | ||
| } | ||
| } | ||
| } | ||
| } |
54 changes: 54 additions & 0 deletions
54
src/test/java/htsjdk/samtools/cram/io/ExternalCompressionTest.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,54 @@ | ||
| package htsjdk.samtools.cram.io; | ||
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| import htsjdk.HtsjdkTest; | ||
| import htsjdk.samtools.cram.encoding.rans.RANS; | ||
| import org.testng.Assert; | ||
| import org.testng.annotations.Test; | ||
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| import java.io.File; | ||
| import java.io.IOException; | ||
| import java.nio.file.Files; | ||
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| public class ExternalCompressionTest extends HtsjdkTest { | ||
| public static final File BZIP2_FILE = new File("src/test/resources/htsjdk/samtools/cram/io/bzip2-test.bz2"); | ||
| public static final byte[] TEST_BYTES = "This is a simple string to test compression".getBytes(); | ||
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| @Test | ||
| public void testBZip2Decompression() throws IOException { | ||
| final byte [] input = Files.readAllBytes(BZIP2_FILE.toPath()); | ||
| final byte [] output = ExternalCompression.unbzip2(input); | ||
| Assert.assertEquals(output, "BZip2 worked".getBytes()); | ||
| } | ||
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| @Test | ||
| public void testGZipRoundtrip() throws IOException { | ||
| final byte [] compressed = ExternalCompression.gzip(TEST_BYTES); | ||
| final byte [] restored = ExternalCompression.gunzip(compressed); | ||
| Assert.assertEquals(TEST_BYTES, restored); | ||
| } | ||
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| @Test | ||
| public void testBZip2Roundtrip() throws IOException { | ||
| final byte [] compressed = ExternalCompression.bzip2(TEST_BYTES); | ||
| final byte [] restored = ExternalCompression.unbzip2(compressed); | ||
| Assert.assertEquals(TEST_BYTES, restored); | ||
| } | ||
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| @Test | ||
| public void testRANSRoundtrip() { | ||
| for(RANS.ORDER order : RANS.ORDER.values()) { | ||
| final byte[] compressed = ExternalCompression.rans(TEST_BYTES, order); | ||
| final byte[] restored = ExternalCompression.unrans(compressed); | ||
| Assert.assertEquals(TEST_BYTES, restored); | ||
| } | ||
| } | ||
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| @Test | ||
| public void testXZRoundtrip() throws IOException { | ||
| final byte [] compressed = ExternalCompression.xz(TEST_BYTES); | ||
| final byte [] restored = ExternalCompression.unxz(compressed); | ||
| Assert.assertEquals(TEST_BYTES, restored); | ||
| } | ||
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| } |
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