本文整理汇总了Java中htsjdk.samtools.SamFileValidator类的典型用法代码示例。如果您正苦于以下问题：Java SamFileValidator类的具体用法？Java SamFileValidator怎么用？Java SamFileValidator使用的例子？那么, 这里精选的类代码示例或许可以为您提供帮助。
SamFileValidator类属于htsjdk.samtools包，在下文中一共展示了SamFileValidator类的4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: testCleanSam
import htsjdk.samtools.SamFileValidator; //导入依赖的package包/类
@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; //导入依赖的package包/类
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; //导入依赖的package包/类
/**
* 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");
}
}
示例4: main
import htsjdk.samtools.SamFileValidator; //导入依赖的package包/类
public static void main(String[] args) throws IOException, IllegalArgumentException, IllegalAccessException {
Params params = new Params();
JCommander jc = new JCommander(params);
try {
jc.parse(args);
} catch (Exception e) {
System.out.println("Failed to parse parameteres, detailed message below: ");
System.out.println(e.getMessage());
System.out.println();
System.out.println("See usage: -h");
System.exit(1);
}
if (args.length == 0 || params.help) {
printUsage(jc);
System.exit(1);
}
if (params.reference == null) {
System.out.println("A reference fasta file is required.");
System.exit(1);
}
if (params.cramFile == null) {
System.out.println("A CRAM input file is required. ");
System.exit(1);
}
Log.setGlobalLogLevel(Log.LogLevel.INFO);
ReferenceSequenceFile referenceSequenceFile = ReferenceSequenceFileFactory
.getReferenceSequenceFile(params.reference);
FileInputStream fis = new FileInputStream(params.cramFile);
BufferedInputStream bis = new BufferedInputStream(fis);
CRAMIterator iterator = new CRAMIterator(bis, new ReferenceSource(params.reference),
ValidationStringency.STRICT);
CramHeader cramHeader = iterator.getCramHeader();
iterator.close();
ProgressLogger progress = new ProgressLogger(log, 100000, "Validated Read");
SamFileValidator v = new SamFileValidator(new PrintWriter(System.out), 1);
final SamReader reader = SamReaderFactory.make().referenceSequence(params.reference).open(params.cramFile);
List<SAMValidationError.Type> errors = new ArrayList<SAMValidationError.Type>();
errors.add(SAMValidationError.Type.MATE_NOT_FOUND);
// errors.add(Type.MISSING_TAG_NM);
v.setErrorsToIgnore(errors);
v.validateSamFileSummary(reader, ReferenceSequenceFileFactory.getReferenceSequenceFile(params.reference));
log.info("Elapsed seconds: " + progress.getElapsedSeconds());
}