Package htsjdk.samtools
Class SAMTestUtil
- java.lang.Object
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- htsjdk.samtools.SAMTestUtil
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public class SAMTestUtil extends Object
Misc methods for SAM-related unit tests. These are in the src tree rather than the tests tree so that they will be included in sam.jar, and therefore can be used by tests outside of htsjdk.samtools.
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
SAMTestUtil.SanityCheckFailedException
Indicates that a required sanity-check condition was not met.
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Constructor Summary
Constructors Constructor Description SAMTestUtil()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
assertPairValid(SAMRecord firstEnd, SAMRecord secondEnd)
Basic sanity check for a pair of SAMRecords.static void
assertReadValid(SAMRecord read)
Basic sanity check for a SAMRecord.
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Method Detail
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assertPairValid
public void assertPairValid(SAMRecord firstEnd, SAMRecord secondEnd) throws SAMTestUtil.SanityCheckFailedException
Basic sanity check for a pair of SAMRecords.- Throws:
SAMTestUtil.SanityCheckFailedException
- if the sanity check failed
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assertReadValid
public static void assertReadValid(SAMRecord read) throws SAMTestUtil.SanityCheckFailedException
Basic sanity check for a SAMRecord. Print errors to screen.- Parameters:
read
- SAM record- Throws:
IllegalArgumentException
- if read is nullSAMTestUtil.SanityCheckFailedException
- if errors
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