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Java IOUtil.assertFilesEqual方法代码示例

本文整理汇总了Java中htsjdk.samtools.util.IOUtil.assertFilesEqual方法的典型用法代码示例。如果您正苦于以下问题：Java IOUtil.assertFilesEqual方法的具体用法？Java IOUtil.assertFilesEqual怎么用？Java IOUtil.assertFilesEqual使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类htsjdk.samtools.util.IOUtil的用法示例。


在下文中一共展示了IOUtil.assertFilesEqual方法的15个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Java代码示例。

示例1: testNonBarcoded

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@Test
public void testNonBarcoded() throws Exception {
    final String suffix = ".1.fastq";
    final File outputFastq1 = File.createTempFile("nonBarcoded.", suffix);
    outputFastq1.deleteOnExit();
    final String outputPrefix = outputFastq1.getAbsolutePath().substring(0, outputFastq1.getAbsolutePath().length() - suffix.length());
    final File outputFastq2 = new File(outputPrefix + ".2.fastq");
    outputFastq2.deleteOnExit();
    final int lane = 1;
    runPicardCommandLine(new String[]{
            "BASECALLS_DIR=" + BASECALLS_DIR,
            "LANE=" + lane,
            "READ_STRUCTURE=25T8B25T",
            "OUTPUT_PREFIX=" + outputPrefix,
            "RUN_BARCODE=HiMom",
            "MACHINE_NAME=machine1",
            "FLOWCELL_BARCODE=abcdeACXX",
            "MAX_READS_IN_RAM_PER_TILE=100" //force spill to disk to test encode/decode
    });
    IOUtil.assertFilesEqual(outputFastq1, new File(TEST_DATA_DIR, "nonBarcoded.1.fastq"));
    IOUtil.assertFilesEqual(outputFastq2, new File(TEST_DATA_DIR, "nonBarcoded.2.fastq"));
}
开发者ID:broadinstitute，项目名称:picard，代码行数:23，代码来源:IlluminaBasecallsToFastqTest.java

示例2: testWriteLaneMetrics

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@Test(dataProvider = "testLaneMetrics")
public void testWriteLaneMetrics(final String testRun) throws Exception {
    for (final boolean useReadStructure : Arrays.asList(true, false)) {
        final CollectIlluminaLaneMetrics clp = new CollectIlluminaLaneMetrics();
        clp.OUTPUT_DIRECTORY = IOUtil.createTempDir("illuminaLaneMetricsCollectorTest", null);
        clp.RUN_DIRECTORY = new File(TEST_DIRECTORY, testRun);
        clp.OUTPUT_PREFIX = "test";
        if (useReadStructure) clp.READ_STRUCTURE = new ReadStructure("101T8B101T");
        clp.doWork();

        final File laneMetricsFile = buildOutputFile(clp.OUTPUT_DIRECTORY, clp.OUTPUT_PREFIX, IlluminaLaneMetrics.getExtension());
        final File canonicalOutputFile = buildOutputFile(TEST_DIRECTORY, testRun, IlluminaLaneMetrics.getExtension());

        IOUtil.assertFilesEqual(canonicalOutputFile, laneMetricsFile);

        IOUtil.deleteDirectoryTree(clp.OUTPUT_DIRECTORY);
    }
}
开发者ID:broadinstitute，项目名称:picard，代码行数:19，代码来源:IlluminaLaneMetricsCollectorTest.java

示例3: testCollectIlluminaLaneMetrics

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@Test(dataProvider = "testCollectIlluminaLaneMetrics")
public void testCollectIlluminaLaneMetrics(final String testRun, final ReadStructure readStructure, final boolean isNovaSeq) throws Exception {
    for (final boolean useReadStructure : Arrays.asList(true, false)) {
        final File runDirectory = new File(TILE_RUN_DIRECTORY, testRun);
        final CollectIlluminaLaneMetrics clp = new CollectIlluminaLaneMetrics();
        clp.OUTPUT_DIRECTORY = IOUtil.createTempDir("illuminaLaneMetricsCollectorTest", null);
        clp.RUN_DIRECTORY = runDirectory;
        clp.OUTPUT_PREFIX = "test";
        clp.IS_NOVASEQ = isNovaSeq;
        if (useReadStructure) clp.READ_STRUCTURE = readStructure;
        clp.doWork();

        final File phasingMetricsFile = buildOutputFile(clp.OUTPUT_DIRECTORY, clp.OUTPUT_PREFIX, IlluminaPhasingMetrics.getExtension());
        final File canonicalPhasingFile = buildOutputFile(runDirectory, testRun, IlluminaPhasingMetrics.getExtension());
        IOUtil.assertFilesEqual(canonicalPhasingFile, phasingMetricsFile);

        final File laneMetricsFile = buildOutputFile(clp.OUTPUT_DIRECTORY, clp.OUTPUT_PREFIX, IlluminaLaneMetrics.getExtension());
        final File canonicalLaneFile = buildOutputFile(runDirectory, testRun, IlluminaLaneMetrics.getExtension());
        IOUtil.assertFilesEqual(canonicalLaneFile, laneMetricsFile);
        IOUtil.deleteDirectoryTree(clp.OUTPUT_DIRECTORY);
    }
}
开发者ID:broadinstitute，项目名称:picard，代码行数:23，代码来源:IlluminaLaneMetricsCollectorTest.java

示例4: testMissingPhasingValuesSilent

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
/** Silently continue if we encounter a tile without phasing/pre-phasing metrics. */
@Test
public void testMissingPhasingValuesSilent() throws IOException {
    final ReadStructure readStructure = new ReadStructure("151T8B8B151T");
    for (final boolean useReadStructure : Arrays.asList(true, false)) {
        final File runDirectory = TEST_MISSING_PHASING_DIRECTORY;
        final CollectIlluminaLaneMetrics clp = new CollectIlluminaLaneMetrics();
        clp.OUTPUT_DIRECTORY = IOUtil.createTempDir("illuminaLaneMetricsCollectorTest", null);
        clp.RUN_DIRECTORY = runDirectory;
        clp.OUTPUT_PREFIX = "test";
        clp.VALIDATION_STRINGENCY = ValidationStringency.SILENT;
        if (useReadStructure) clp.READ_STRUCTURE = readStructure;
        clp.doWork();

        final File phasingMetricsFile = buildOutputFile(clp.OUTPUT_DIRECTORY, clp.OUTPUT_PREFIX, IlluminaPhasingMetrics.getExtension());
        final File canonicalPhasingFile = buildOutputFile(runDirectory, runDirectory.getName(), IlluminaPhasingMetrics.getExtension());
        IOUtil.assertFilesEqual(canonicalPhasingFile, phasingMetricsFile);

        final File laneMetricsFile = buildOutputFile(clp.OUTPUT_DIRECTORY, clp.OUTPUT_PREFIX, IlluminaLaneMetrics.getExtension());
        final File canonicalLaneFile = buildOutputFile(runDirectory, runDirectory.getName(), IlluminaLaneMetrics.getExtension());
        IOUtil.assertFilesEqual(canonicalLaneFile, laneMetricsFile);
        IOUtil.deleteDirectoryTree(clp.OUTPUT_DIRECTORY);
    }
}
开发者ID:broadinstitute，项目名称:picard，代码行数:25，代码来源:IlluminaLaneMetricsCollectorTest.java

示例5: testNonBarcoded

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@Test
public void testNonBarcoded() throws Exception {
    final File outputBam = File.createTempFile("nonBarcoded.", ".sam");
    outputBam.deleteOnExit();
    final int lane = 1;

    Assert.assertEquals(runPicardCommandLine(new String[]{
            "BASECALLS_DIR=" + BASECALLS_DIR,
            "LANE=" + lane,
            "READ_STRUCTURE=25S8S25T",
            "OUTPUT=" + outputBam,
            "RUN_BARCODE=HiMom",
            "SAMPLE_ALIAS=HiDad",
            "LIBRARY_NAME=Hello, World"
    }), 0);
    IOUtil.assertFilesEqual(outputBam, new File(TEST_DATA_DIR, "nonBarcoded.sam"));
}
开发者ID:broadinstitute，项目名称:picard，代码行数:18，代码来源:IlluminaBasecallsToSamTest.java

示例6: testNonBarcodedWithMolecularIndex

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@Test
public void testNonBarcodedWithMolecularIndex() throws Exception {
    final File outputBam = File.createTempFile("nonBarcodedWithMI.", ".sam");
    outputBam.deleteOnExit();
    final int lane = 1;

    Assert.assertEquals(runPicardCommandLine(new String[]{
            "BASECALLS_DIR=" + BASECALLS_DIR,
            "LANE=" + lane,
            "READ_STRUCTURE=25S8M25T",
            "OUTPUT=" + outputBam,
            "RUN_BARCODE=HiMom",
            "SAMPLE_ALIAS=HiDad",
            "LIBRARY_NAME=Hello, World"
    }), 0);
    IOUtil.assertFilesEqual(outputBam, new File(TEST_DATA_DIR, "nonBarcodedWithMolecularIndex8M.sam"));
}
开发者ID:broadinstitute，项目名称:picard，代码行数:18，代码来源:IlluminaBasecallsToSamTest.java

示例7: testNonBarcodedWithTagPerMolecularIndexIsNUll

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@Test
public void testNonBarcodedWithTagPerMolecularIndexIsNUll() throws Exception {
    final File outputBam = File.createTempFile("nonBarcodedWithMI.", ".sam");
    outputBam.deleteOnExit();
    final int lane = 1;

    Assert.assertEquals(runPicardCommandLine(new String[]{
            "BASECALLS_DIR=" + BASECALLS_DIR,
            "LANE=" + lane,
            "READ_STRUCTURE=25S8M25T",
            "OUTPUT=" + outputBam,
            "RUN_BARCODE=HiMom",
            "SAMPLE_ALIAS=HiDad",
            "LIBRARY_NAME=Hello, World",
            "TAG_PER_MOLECULAR_INDEX=null"
    }), 0);
    IOUtil.assertFilesEqual(outputBam, new File(TEST_DATA_DIR, "nonBarcodedWithMolecularIndex8M.sam"));
}
开发者ID:broadinstitute，项目名称:picard，代码行数:19，代码来源:IlluminaBasecallsToSamTest.java

示例8: testNonBarcodedWithDualMoleclarIndex

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@Test
public void testNonBarcodedWithDualMoleclarIndex() throws Exception {
    final File outputBam = File.createTempFile("nonBarcodedWithDualMI.", ".sam");
    outputBam.deleteOnExit();
    final int lane = 1;

    Assert.assertEquals(runPicardCommandLine(new String[]{
            "BASECALLS_DIR=" + BASECALLS_DIR,
            "LANE=" + lane,
            "READ_STRUCTURE=25S4M4M25T",
            "OUTPUT=" + outputBam,
            "RUN_BARCODE=HiMom",
            "SAMPLE_ALIAS=HiDad",
            "LIBRARY_NAME=Hello, World"
    }), 0);
    IOUtil.assertFilesEqual(outputBam, new File(TEST_DATA_DIR, "nonBarcodedWithMolecularIndex4M4M.sam"));
}
开发者ID:broadinstitute，项目名称:picard，代码行数:18，代码来源:IlluminaBasecallsToSamTest.java

示例9: testNonBarcodedWithTagPerMolecularIndexDual

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@Test
public void testNonBarcodedWithTagPerMolecularIndexDual() throws Exception {
    final File outputBam = File.createTempFile("nonBarcodedWithDualMI.", ".sam");
    outputBam.deleteOnExit();
    final int lane = 1;

    Assert.assertEquals(runPicardCommandLine(new String[]{
            "BASECALLS_DIR=" + BASECALLS_DIR,
            "LANE=" + lane,
            "READ_STRUCTURE=25S4M4M25T",
            "OUTPUT=" + outputBam,
            "RUN_BARCODE=HiMom",
            "SAMPLE_ALIAS=HiDad",
            "LIBRARY_NAME=Hello, World",
            "TAG_PER_MOLECULAR_INDEX=ZA",
            "TAG_PER_MOLECULAR_INDEX=ZB"

    }), 0);
    IOUtil.assertFilesEqual(outputBam, new File(TEST_DATA_DIR, "nonBarcodedWithTagPerMolecularIndex4M4M.sam"));
}
开发者ID:broadinstitute，项目名称:picard，代码行数:21，代码来源:IlluminaBasecallsToSamTest.java

示例10: testNonBarcodedWithTagPerMolecularIndexDualFourMolecularIndexes

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@Test
public void testNonBarcodedWithTagPerMolecularIndexDualFourMolecularIndexes() throws Exception {
    final File outputBam = File.createTempFile("nonBarcodedWithDualMI.", ".sam");
    //outputBam.deleteOnExit();
    final int lane = 1;

    Assert.assertEquals(runPicardCommandLine(new String[]{
            "BASECALLS_DIR=" + BASECALLS_DIR,
            "LANE=" + lane,
            "READ_STRUCTURE=25S2M2M2M2M25T",
            "OUTPUT=" + outputBam,
            "RUN_BARCODE=HiMom",
            "SAMPLE_ALIAS=HiDad",
            "LIBRARY_NAME=Hello, World",
            "TAG_PER_MOLECULAR_INDEX=ZA",
            "TAG_PER_MOLECULAR_INDEX=ZB",
            "TAG_PER_MOLECULAR_INDEX=ZC",
            "TAG_PER_MOLECULAR_INDEX=ZD"
    }), 0);
    IOUtil.assertFilesEqual(outputBam, new File(TEST_DATA_DIR, "nonBarcodedWithTagPerMolecularIndex2M2M2M2M.sam"));
}
开发者ID:broadinstitute，项目名称:picard，代码行数:22，代码来源:IlluminaBasecallsToSamTest.java

示例11: testContaminationDetection

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@Test(dataProvider = "UnmappedReadStrategies")
public void testContaminationDetection(final AbstractAlignmentMerger.UnmappingReadStrategy strategy, final String basename) throws IOException {
    final File unmappedSam = new File(TEST_DATA_DIR, "contam.unmapped.sam");
    final File alignedSam = new File(TEST_DATA_DIR, "contam.aligned.sam");
    final File expectedSam = new File(TEST_DATA_DIR, basename);
    final File refFasta = new File(TEST_DATA_DIR, "cliptest.fasta");
    final File mergedSam = File.createTempFile("merged", ".sam");
    mergedSam.deleteOnExit();

    doMergeAlignment(unmappedSam, Collections.singletonList(alignedSam),
            null, null, null, null,
            false, true, false, 1,
            "0", "1.0", "align!", "myAligner",
            true, refFasta, mergedSam,
            null, null, null, null, true, SAMFileHeader.SortOrder.coordinate, strategy);

    assertSamValid(mergedSam);
    IOUtil.assertFilesEqual(expectedSam, mergedSam);
}
开发者ID:broadinstitute，项目名称:picard，代码行数:20，代码来源:MergeBamAlignmentTest.java

示例12: testMergeHeaderMappedAndReference

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@Test
public void testMergeHeaderMappedAndReference() throws IOException {
    final File unmappedSam = new File(TEST_DATA_DIR, "specialHeader.unmapped.sam");
    final File alignedSam = new File(TEST_DATA_DIR, "specialHeader.aligned.sam");
    final File expectedSam = new File(TEST_DATA_DIR, "specialHeader.expected.sam");
    final File refFasta = new File(TEST_DATA_DIR, "specialHeader.fasta");
    final File mergedSam = File.createTempFile("merged", ".sam");
    mergedSam.deleteOnExit();

    doMergeAlignment(unmappedSam, Collections.singletonList(alignedSam),
            null, null, null, null,
            false, true, false, 1,
            "0", "1.0", "align!", "myAligner",
            true, refFasta, mergedSam,
            null, null, null, null, true, null);

    assertSamValid(mergedSam);
    IOUtil.assertFilesEqual(expectedSam, mergedSam);
}
开发者ID:broadinstitute，项目名称:picard，代码行数:20，代码来源:MergeBamAlignmentTest.java

示例13: runFixVcfHeader

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
private void runFixVcfHeader(final int checkFirstNRecords,
                             final File replacementHeader,
                             final boolean enforceSampleSamples) throws IOException {
    final FixVcfHeader program = new FixVcfHeader();
    final File outputVcf = VcfTestUtils.createTemporaryIndexedVcfFile("output.", ".vcf");

    program.INPUT      = INPUT_VCF;
    program.OUTPUT     = outputVcf;
    if (replacementHeader == null) {
        program.CHECK_FIRST_N_RECORDS = checkFirstNRecords;
    }
    else {
        program.HEADER = replacementHeader;
        program.ENFORCE_SAME_SAMPLES = enforceSampleSamples;
    }

    Assert.assertEquals(program.instanceMain(new String[0]), 0);

    IOUtil.assertFilesEqual(OUTPUT_VCF, outputVcf);
}
开发者ID:broadinstitute，项目名称:picard，代码行数:21，代码来源:FixVcfHeaderTest.java

示例14: testMultiplexWithIlluminaReadNameHeaders

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@Test
public void testMultiplexWithIlluminaReadNameHeaders() throws Exception {
    final File outputDir = File.createTempFile("testMultiplexRH.", ".dir");
    try {
        outputDir.delete();
        outputDir.mkdir();
        outputDir.deleteOnExit();

        final String filePrefix = "testMultiplexRH";
        final File outputPrefix = new File(outputDir, filePrefix);

        runPicardCommandLine(new String[]{
                "BASECALLS_DIR=" + BASECALLS_DIR,
                "LANE=" + 1,
                "RUN_BARCODE=HiMom",
                "READ_STRUCTURE=" + "25T8B25T",
                "OUTPUT_PREFIX=" + outputPrefix.getAbsolutePath(),
                "MACHINE_NAME=machine1",
                "FLOWCELL_BARCODE=abcdeACXX",
                "READ_NAME_FORMAT=" + IlluminaBasecallsToFastq.ReadNameFormat.ILLUMINA,
                "MAX_READS_IN_RAM_PER_TILE=100" //force spill to disk to test encode/decode
        });

        final String[] filenames = new String[]{
                filePrefix + ".1.fastq",
                filePrefix + ".barcode_1.fastq"
        };
        for (final String filename : filenames) {
            IOUtil.assertFilesEqual(new File(outputDir, filename), new File(TEST_DATA_DIR, filename));
        }

    } finally {
        TestUtil.recursiveDelete(outputDir);
    }
}
开发者ID:broadinstitute，项目名称:picard，代码行数:36，代码来源:IlluminaBasecallsToFastqTest.java

示例15: testCopyLocal

import htsjdk.samtools.util.IOUtil; //导入方法依赖的package包/类
@Test
public void testCopyLocal() throws IOException {
    final String src = publicTestDir+"empty.vcf";
    File dest = createTempFile("copy-empty",".vcf");

    BucketUtils.copyFile(src, dest.getPath());
    IOUtil.assertFilesEqual(new File(src), dest);
}
开发者ID:broadinstitute，项目名称:gatk，代码行数:9，代码来源:BucketUtilsTest.java


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