Examples of validateSamFileVerbose()

Examples of htsjdk.samtools.SamFileValidator.validateSamFileVerbose()

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            }
            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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Examples of htsjdk.samtools.SamFileValidator.validateSamFileVerbose()

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            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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Examples of htsjdk.samtools.SamFileValidator.validateSamFileVerbose()

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        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");
    }

    @DataProvider(name = "testCleanSamDataProvider")
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