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"));
}
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);
}
}
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);
}
}
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);
}
}
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"));
}
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"));
}
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"));
}
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"));
}
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"));
}
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"));
}
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);
}
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);
}
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);
}
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);
}
}
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);
}