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Add tribble test data, clean up test suite
Fix bug in LinearIndex related to improper commenting/if-statement
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jacobbroad
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Jan 8, 2013
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,55 @@ | ||
| package org.broad.tribble; | ||
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| import org.broad.tribble.bed.BEDCodec; | ||
| import org.broad.tribble.example.ExampleBinaryCodec; | ||
| import org.testng.Assert; | ||
| import org.testng.annotations.DataProvider; | ||
| import org.testng.annotations.Test; | ||
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| import java.io.*; | ||
| import java.util.Iterator; | ||
| import java.util.List; | ||
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| public class BinaryFeaturesTest { | ||
| @DataProvider(name = "BinaryFeatureSources") | ||
| public Object[][] createData1() { | ||
| return new Object[][] { | ||
| { new File(TestUtils.DATA_DIR + "test.bed"), new BEDCodec() }, | ||
| { new File(TestUtils.DATA_DIR + "bed/Unigene.sample.bed"), new BEDCodec() }, | ||
| { new File(TestUtils.DATA_DIR + "bed/NA12878.deletions.10kbp.het.gq99.hand_curated.hg19_fixed.bed"), new BEDCodec() }, | ||
| }; | ||
| } | ||
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| @Test(enabled = true, dataProvider = "BinaryFeatureSources") | ||
| public void testBinaryCodec(final File source, final FeatureCodec<Feature> codec) throws IOException { | ||
| final File tmpFile = File.createTempFile("testBinaryCodec", ".binary.bed"); | ||
| ExampleBinaryCodec.convertToBinaryTest(source, tmpFile, codec); | ||
| tmpFile.deleteOnExit(); | ||
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| final FeatureReader<Feature> originalReader = AbstractFeatureReader.getFeatureReader(source.getAbsolutePath(), codec, false); | ||
| final FeatureReader<Feature> binaryReader = AbstractFeatureReader.getFeatureReader(tmpFile.getAbsolutePath(), new ExampleBinaryCodec(), false); | ||
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| // make sure the header is what we expect | ||
| final List<String> header = (List<String>)binaryReader.getHeader(); | ||
| Assert.assertEquals(header.size(), 1, "We expect exactly one header line"); | ||
| Assert.assertEquals(header.get(0), ExampleBinaryCodec.HEADER_LINE, "Failed to read binary header line"); | ||
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| final Iterator<Feature> oit = originalReader.iterator(); | ||
| final Iterator<Feature> bit = binaryReader.iterator(); | ||
| while ( oit.hasNext() ) { | ||
| final Feature of = oit.next(); | ||
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| Assert.assertTrue(bit.hasNext(), "Original iterator has items, but there's no items left in binary iterator"); | ||
| final Feature bf = bit.next(); | ||
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| Assert.assertEquals(bf.getChr(), of.getChr(), "Chr not equal between original and binary encoding"); | ||
| Assert.assertEquals(bf.getStart(), of.getStart(), "Start not equal between original and binary encoding"); | ||
| Assert.assertEquals(bf.getEnd(), of.getEnd(), "End not equal between original and binary encoding"); | ||
| } | ||
| Assert.assertTrue(! bit.hasNext(), "Original iterator is done, but there's still some data in binary iterator"); | ||
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| originalReader.close(); | ||
| binaryReader.close(); | ||
| } | ||
| } |
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src/tests/java/org/broad/tribble/FeatureReaderTest.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,163 @@ | ||
| package org.broad.tribble; | ||
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| import net.sf.samtools.seekablestream.SeekableFileStream; | ||
| import org.broad.tribble.bed.BEDCodec; | ||
| import org.broad.tribble.example.ExampleBinaryCodec; | ||
| import org.broad.tribble.index.Block; | ||
| import org.broad.tribble.index.Index; | ||
| import org.broad.tribble.index.IndexFactory; | ||
| import org.broad.tribble.util.ParsingUtils; | ||
| import org.testng.Assert; | ||
| import org.testng.annotations.AfterClass; | ||
| import org.testng.annotations.BeforeClass; | ||
| import org.testng.annotations.DataProvider; | ||
| import org.testng.annotations.Test; | ||
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| import java.io.File; | ||
| import java.io.IOException; | ||
| import java.util.Arrays; | ||
| import java.util.Iterator; | ||
| import java.util.List; | ||
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| public class FeatureReaderTest { | ||
| private final static File asciiBedFile = new File(TestUtils.DATA_DIR + "test.bed"); | ||
| private final static File binaryBedFile = new File(TestUtils.DATA_DIR + "test.binary.bed"); | ||
| private final static File tabixBedFile = new File(TestUtils.DATA_DIR + "test.tabix.bed.gz"); | ||
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| @BeforeClass | ||
| public void setup() throws IOException { | ||
| ExampleBinaryCodec.convertToBinaryTest(asciiBedFile, binaryBedFile, new BEDCodec()); | ||
| } | ||
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| @AfterClass | ||
| public void teardown() throws Exception { | ||
| // binaryBedFile.delete(); | ||
| } | ||
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| @DataProvider(name = "indexProvider") | ||
| public Object[][] createData1() { | ||
| return new Object[][]{ | ||
| {asciiBedFile, IndexFactory.IndexType.LINEAR, new BEDCodec()}, | ||
| {asciiBedFile, IndexFactory.IndexType.INTERVAL_TREE, new BEDCodec()}, | ||
| {tabixBedFile, IndexFactory.IndexType.TABIX, new BEDCodec()}, | ||
| {binaryBedFile, IndexFactory.IndexType.LINEAR, new ExampleBinaryCodec()}, | ||
| {binaryBedFile, IndexFactory.IndexType.INTERVAL_TREE, new ExampleBinaryCodec()}, | ||
| }; | ||
| } | ||
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| @Test(dataProvider = "indexProvider") | ||
| public void testBedQuery(final File featureFile, IndexFactory.IndexType indexType, FeatureCodec<Feature> codec) throws IOException { | ||
| final AbstractFeatureReader<Feature> reader = getReader(featureFile, indexType, codec); | ||
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| // Query | ||
| testQuery(reader, "chr1", 1, 500, 3); | ||
| testQuery(reader, "chr1", 1, 200, 1); | ||
| testQuery(reader, "chr1", 1, 201, 2); | ||
| testQuery(reader, "chr1", 500, 600, 0); | ||
| testQuery(reader, "chr1", 100000, 100010, 1); | ||
| testQuery(reader, "chr1", 100000, 100000, 0); | ||
| testQuery(reader, "chr1", 100001, 100001, 1); | ||
| testQuery(reader, "chr1", 100005, 100006, 1); | ||
| testQuery(reader, "chr1", 100009, 100011, 1); | ||
| testQuery(reader, "chr1", 100010, 100010, 1); | ||
| testQuery(reader, "chr1", 100011, 100011, 0); | ||
| testQuery(reader, "chr2", 1, 100, 2); | ||
| testQuery(reader, "chr2", 1, 10, 1); | ||
| testQuery(reader, "chr2", 15, 16, 0); | ||
| testQuery(reader, "chr3", 1, 201, 0); | ||
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| // Close reader | ||
| reader.close(); | ||
| } | ||
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| @Test(dataProvider = "indexProvider") | ||
| public void testLargeNumberOfQueries(final File featureFile, IndexFactory.IndexType indexType, FeatureCodec<Feature> codec) throws IOException { | ||
| final AbstractFeatureReader<Feature> reader = getReader(featureFile, indexType, codec); | ||
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| final List<Integer> sites = Arrays.asList(500, 200, 201, 600, 100000); | ||
| for (int i = 0; i < 2000; i++) { | ||
| for (int start : sites) { | ||
| int end = start + 1; // query so we find something | ||
| if (start < end) { | ||
| for (final String chr : Arrays.asList("chr1", "chr2", "chr3")) { | ||
| CloseableTribbleIterator<Feature> iter = reader.query(chr, start, end); | ||
| Assert.assertTrue(iter != null, "Failed to create non-null iterator"); | ||
| iter.close(); | ||
| } | ||
| } | ||
| } | ||
| } | ||
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| // Close reader | ||
| reader.close(); | ||
| } | ||
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| private void testQuery(AbstractFeatureReader<Feature> reader, final String chr, int start, int stop, int expectedNumRecords) throws IOException { | ||
| Iterator<Feature> iter = reader.query(chr, start, stop); | ||
| int count = 0; | ||
| while (iter.hasNext()) { | ||
| final Feature f = iter.next(); | ||
| Assert.assertTrue(f.getEnd() >= start && f.getStart() <= stop); | ||
| count++; | ||
| } | ||
| Assert.assertEquals(count, expectedNumRecords); | ||
| } | ||
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| @Test(dataProvider = "indexProvider") | ||
| public void testBedNames(final File featureFile, IndexFactory.IndexType indexType, FeatureCodec<Feature> codec) throws IOException { | ||
| final AbstractFeatureReader<Feature> reader = getReader(featureFile, indexType, codec); | ||
| String[] expectedSequences = {"chr1", "chr2"}; | ||
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| List<String> seqNames = reader.getSequenceNames(); | ||
| Assert.assertEquals(seqNames.size(), expectedSequences.length, | ||
| "Expected sequences " + ParsingUtils.join(",", expectedSequences) + " but saw " + ParsingUtils.join(",", seqNames)); | ||
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| for (String s : expectedSequences) { | ||
| Assert.assertTrue(seqNames.contains(s)); | ||
| } | ||
| } | ||
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| private AbstractFeatureReader<Feature> getReader(final File featureFile, | ||
| IndexFactory.IndexType indexType, | ||
| FeatureCodec<Feature> codec) | ||
| throws IOException { | ||
| if (indexType.canCreate()) { | ||
| // for types we can create make a new index each time | ||
| File idxFile = Tribble.indexFile(featureFile); | ||
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| // delete an already existing index | ||
| if (idxFile.exists()) { | ||
| idxFile.delete(); | ||
| } | ||
| Index idx = IndexFactory.createIndex(featureFile, codec, indexType); | ||
| IndexFactory.writeIndex(idx, idxFile); | ||
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| idxFile.deleteOnExit(); | ||
| } // else let's just hope the index exists, and if so use it | ||
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| return AbstractFeatureReader.getFeatureReader(featureFile.getAbsolutePath(), codec); | ||
| } | ||
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| @Test() | ||
| public void testReadingBeyondIntSizedBlock() throws IOException { | ||
| final Block block = new Block(0, ((long) Integer.MAX_VALUE) * 2); | ||
| final SeekableFileStream stream = new SeekableFileStream(new File("/dev/zero")); | ||
| final TribbleIndexedFeatureReader.BlockStreamWrapper blockStreamWrapper = new TribbleIndexedFeatureReader.BlockStreamWrapper(stream, block); | ||
| final int chunkSize = 100000; // 10 Mb | ||
| final int chunksToRead = (int) Math.ceil(block.getSize() / (chunkSize * 1.0)); | ||
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| final byte[] bytes = new byte[chunkSize]; | ||
| long totalRead = 0; | ||
| for (int chunk = 0; chunk < chunksToRead; chunk++) { | ||
| //System.out.println("Reading chunk " + chunk + " of " + chunkSize + " total read " + totalRead); | ||
| final int nRead = blockStreamWrapper.read(bytes); | ||
| Assert.assertTrue(nRead != -1, "Prematurely got EOF after " + totalRead + " bytes"); | ||
| totalRead += nRead; | ||
| } | ||
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| Assert.assertEquals(totalRead, block.getSize(), "Failed to read all bytes from a block with size > 2B = " + block.getSize()); | ||
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| } | ||
| } | ||
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