Examples with SamReaderFactory htsjdk.samtools.SamReaderFactory used on opensource projects

Example 6 with SamReaderFactory

use of htsjdk.samtools.SamReaderFactory in project gatk by broadinstitute.

the class CompareSAMs method doWork.

@Override
protected Object doWork() {
    IOUtil.assertFileIsReadable(samFiles.get(0));
    IOUtil.assertFileIsReadable(samFiles.get(1));
    SamReaderFactory factory = SamReaderFactory.makeDefault().validationStringency(VALIDATION_STRINGENCY);
    SamReader sam1 = factory.referenceSequence(REFERENCE_SEQUENCE).open(samFiles.get(0));
    SamReader sam2 = factory.referenceSequence(REFERENCE_SEQUENCE).open(samFiles.get(1));
    SamComparison comparison = new SamComparison(sam1, sam2);
    comparison.printReport();
    if (comparison.areEqual()) {
        System.out.println("Files match.");
    } else {
        System.out.println("Files differ.");
    }
    CloserUtil.close(sam1);
    CloserUtil.close(sam2);
    return comparison.areEqual();
}

Example 7 with SamReaderFactory

use of htsjdk.samtools.SamReaderFactory in project gatk by broadinstitute.

the class GATKToolUnitTest method testReadsHeader.

@Test
public void testReadsHeader() throws Exception {
    final GATKTool tool = new TestGATKToolWithReads();
    final CommandLineParser clp = new CommandLineArgumentParser(tool);
    final File bamFile = new File(publicTestDir + "org/broadinstitute/hellbender/engine/reads_data_source_test1.bam");
    final String[] args = { "-I", bamFile.getCanonicalPath() };
    clp.parseArguments(System.out, args);
    tool.onStartup();
    final SAMFileHeader headerForReads = tool.getHeaderForReads();
    final SamReaderFactory factory = //read the file directly and compare headers
    SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
    try (SamReader samReader = factory.open(bamFile)) {
        final SAMFileHeader samFileHeader = samReader.getFileHeader();
        Assert.assertEquals(headerForReads, samFileHeader);
    }
    tool.doWork();
    tool.onShutdown();
}

Example 8 with SamReaderFactory

use of htsjdk.samtools.SamReaderFactory in project gatk by broadinstitute.

the class PrintReadsSparkIntegrationTest method testReadFilters.

@Test(dataProvider = "readFilterTestData", groups = "spark")
public void testReadFilters(final String input, final String reference, final String extOut, final List<String> inputArgs, final int expectedCount) throws IOException {
    final File outFile = createTempFile("testReadFilter", extOut);
    final ArgumentsBuilder args = new ArgumentsBuilder();
    args.add("-I");
    args.add(new File(TEST_DATA_DIR, input).getAbsolutePath());
    args.add("-O");
    args.add(outFile.getAbsolutePath());
    if (reference != null) {
        args.add("-R");
        args.add(new File(TEST_DATA_DIR, reference).getAbsolutePath());
    }
    for (final String filter : inputArgs) {
        args.add(filter);
    }
    runCommandLine(args);
    SamReaderFactory factory = SamReaderFactory.makeDefault();
    if (reference != null) {
        factory = factory.referenceSequence(new File(TEST_DATA_DIR, reference));
    }
    int count = 0;
    try (final SamReader reader = factory.open(outFile)) {
        Iterator<SAMRecord> it = reader.iterator();
        while (it.hasNext()) {
            SAMRecord rec = it.next();
            count++;
        }
    }
    Assert.assertEquals(count, expectedCount);
}