Package htsjdk.samtools

Examples of htsjdk.samtools.SamFileValidator

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    }


    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));
            SAMFileReader samReader = new SAMFileReader(getOutput());
            samReader.setValidationStringency(ValidationStringency.LENIENT);
            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);
                }
            }
            samReader.close();

            // Run validation on the output file
            samReader = new SAMFileReader(getOutput());
            final boolean validated = validator.validateSamFileVerbose(samReader, null);
            samReader.close();
            Assert.assertTrue(validated, "ValidateSamFile failed");
        } finally {
            TestUtil.recursiveDelete(getOutputDir());
        }
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            if (VALIDATE_INDEX){
                samReader.enableIndexCaching(true);
            }
            samReader.enableCrcChecking(true);

            final SamFileValidator validator = new SamFileValidator(out, MAX_OPEN_TEMP_FILES);
            validator.setErrorsToIgnore(IGNORE);

            if (IGNORE_WARNINGS) {
                validator.setIgnoreWarnings(IGNORE_WARNINGS);
            }
            if (MODE == Mode.SUMMARY) {
                validator.setVerbose(false, 0);
            } else {
                validator.setVerbose(true, MAX_OUTPUT);
            }
            if (IS_BISULFITE_SEQUENCED) {
                validator.setBisulfiteSequenced(IS_BISULFITE_SEQUENCED);
            }
            if (VALIDATE_INDEX){
                validator.setValidateIndex(VALIDATE_INDEX);
            }
            if (IOUtil.isRegularPath(INPUT)) {
                // Do not check termination if reading from a stream
                validator.validateBamFileTermination(INPUT);
            }

            result = false;

            switch (MODE) {
                case SUMMARY:
                    result = validator.validateSamFileSummary(samReader, reference);
                    break;
                case VERBOSE:
                    result = validator.validateSamFileVerbose(samReader, reference);
                    break;
            }
            out.flush();
        } finally {
            SAMFileReader.setDefaultValidationStringency(originalStringency);
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                "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));
        SAMFileReader samReader = new SAMFileReader(cleanedFile);
        samReader.setValidationStringency(ValidationStringency.LENIENT);
        final SAMRecord rec = samReader.iterator().next();
        samReader.close();
        Assert.assertEquals(rec.getCigarString(), expectedCigar);
        samReader = new SAMFileReader(cleanedFile);
        final boolean validated = validator.validateSamFileVerbose(samReader, null);
        samReader.close();
        Assert.assertTrue(validated, "ValidateSamFile failed");
    }
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Related Classes of htsjdk.samtools.SamFileValidator

  • picard.sam.CleanSamTest
  • picard.sam.testers.CleanSamTester
  • picard.sam.ValidateSamFile
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