本文整理匯總了Java中htsjdk.samtools.SamFileValidator.validateSamFileVerbose方法的典型用法代碼示例。如果您正苦於以下問題:Java SamFileValidator.validateSamFileVerbose方法的具體用法?Java SamFileValidator.validateSamFileVerbose怎麽用?Java SamFileValidator.validateSamFileVerbose使用的例子?那麽, 這裏精選的方法代碼示例或許可以為您提供幫助。您也可以進一步了解該方法所在類htsjdk.samtools.SamFileValidator
的用法示例。
在下文中一共展示了SamFileValidator.validateSamFileVerbose方法的3個代碼示例,這些例子默認根據受歡迎程度排序。您可以為喜歡或者感覺有用的代碼點讚,您的評價將有助於係統推薦出更棒的Java代碼示例。
示例1: testCleanSam
import htsjdk.samtools.SamFileValidator; //導入方法依賴的package包/類
@Test(dataProvider = "testCleanSamDataProvider")
public void testCleanSam(final String samFile, final String expectedCigar) throws IOException {
final File cleanedFile = File.createTempFile(samFile + ".", ".sam");
cleanedFile.deleteOnExit();
final String[] args = new String[]{
"INPUT=" + new File(TEST_DATA_DIR, samFile).getAbsolutePath(),
"OUTPUT=" + cleanedFile.getAbsolutePath()
};
Assert.assertEquals(runPicardCommandLine(args), 0);
final SamFileValidator validator = new SamFileValidator(new PrintWriter(System.out), 8000);
validator.setIgnoreWarnings(true);
validator.setVerbose(true, 1000);
validator.setErrorsToIgnore(Arrays.asList(SAMValidationError.Type.MISSING_READ_GROUP));
SamReader samReader = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.LENIENT).open(cleanedFile);
final SAMRecord rec = samReader.iterator().next();
samReader.close();
Assert.assertEquals(rec.getCigarString(), expectedCigar);
samReader = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.LENIENT).open(cleanedFile);
final boolean validated = validator.validateSamFileVerbose(samReader, null);
samReader.close();
Assert.assertTrue(validated, "ValidateSamFile failed");
}
示例2: test
import htsjdk.samtools.SamFileValidator; //導入方法依賴的package包/類
protected void test() {
try {
final SamFileValidator validator = new SamFileValidator(new PrintWriter(System.out), 8000);
// Validate it has the expected cigar
validator.setIgnoreWarnings(true);
validator.setVerbose(true, 1000);
validator.setErrorsToIgnore(Arrays.asList(SAMValidationError.Type.MISSING_READ_GROUP));
SamReaderFactory factory = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.LENIENT);
SamReader samReader = factory.open(getOutput());
final SAMRecordIterator iterator = samReader.iterator();
while (iterator.hasNext()) {
final SAMRecord rec = iterator.next();
Assert.assertEquals(rec.getCigarString(), expectedCigar);
if (SAMUtils.hasMateCigar(rec)) {
Assert.assertEquals(SAMUtils.getMateCigarString(rec), expectedCigar);
}
}
CloserUtil.close(samReader);
// Run validation on the output file
samReader = factory.open(getOutput());
final boolean validated = validator.validateSamFileVerbose(samReader, null);
CloserUtil.close(samReader);
Assert.assertTrue(validated, "ValidateSamFile failed");
} finally {
TestUtil.recursiveDelete(getOutputDir());
}
}
示例3: assertSamValid
import htsjdk.samtools.SamFileValidator; //導入方法依賴的package包/類
/**
* causes an exception if the given sam isn't valid
* @param reference is allowed to be null
*/
public static void assertSamValid(final File sam, final ValidationStringency validationStringency, final File reference) throws IOException {
assertCRAMContentsIfCRAM(sam);
try (final SamReader samReader = getReader(sam, validationStringency, reference)) {
final SamFileValidator validator = new SamFileValidator(new PrintWriter(System.out), 8000);
validator.setIgnoreWarnings(true);
validator.setVerbose(true, 1000);
validator.setErrorsToIgnore(Arrays.asList(SAMValidationError.Type.MISSING_READ_GROUP));
final boolean validated = validator.validateSamFileVerbose(samReader, null);
Assert.assertTrue(validated, "SAM file validation failed");
}
}