Package htsjdk.samtools

Class SAMTestUtil

java.lang.Object

htsjdk.samtools.SAMTestUtil

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.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	SAMTestUtil.SanityCheckFailedException	Indicates that a required sanity-check condition was not met.

Constructor Summary

Constructors

Constructor	Description
SAMTestUtil()

Method Summary

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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

SAMTestUtil

public SAMTestUtil()

Method Details

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

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 null

SAMTestUtil.SanityCheckFailedException - if errors