htsjdk.samtools.SAMTestUtil Maven / Gradle / Ivy
/*
* The MIT License
*
* Copyright (c) 2009 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package htsjdk.samtools;
import java.util.List;
/**
* 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.
*/
public class SAMTestUtil {
/**
* Indicates that a required sanity-check condition was not met.
*/
public static class SanityCheckFailedException extends RuntimeException {
public SanityCheckFailedException(String message) {
super(message);
}
}
/**
* Basic sanity check for a pair of SAMRecords.
* @throws SanityCheckFailedException if the sanity check failed
*/
public void assertPairValid(final SAMRecord firstEnd, final SAMRecord secondEnd) throws SanityCheckFailedException {
assertEquals(firstEnd.getReadName(), secondEnd.getReadName());
assertTrue(firstEnd.getFirstOfPairFlag());
assertTrue(secondEnd.getSecondOfPairFlag());
assertFalse(secondEnd.getFirstOfPairFlag());
assertFalse(firstEnd.getSecondOfPairFlag());
if (!firstEnd.getReadUnmappedFlag() && !secondEnd.getReadUnmappedFlag()) {
assertNotSame(firstEnd.getReadNegativeStrandFlag(),
secondEnd.getReadNegativeStrandFlag());
}
}
/**
* Basic sanity check for a SAMRecord. Print errors to screen.
* @param read SAM record
* @throws IllegalArgumentException if read is null
* @throws SanityCheckFailedException if errors
*/
public static void assertReadValid(final SAMRecord read) throws SanityCheckFailedException {
if (read == null) {
throw new IllegalArgumentException("SAMRecord is null");
}
final List errors = read.isValid(false);
if ( errors != null) {
errors.forEach(v -> System.out.println(v.toString()));
}
assertTrue(errors.isEmpty());
}
private static void assertEquals(T a, T b) {
if (a == null) {
if (b != null) {
throw new SanityCheckFailedException("\"" + a + "\" does not equal \"" + b + "\"");
}
} else if (!a.equals(b)) {
throw new SanityCheckFailedException("\"" + a + "\" does not equal \"" + b + "\"");
}
}
private static void assertNotSame(T a, T b) {
if (a != b) {
throw new SanityCheckFailedException("\"" + a + "\" and \"" + b + "\" are not the same object");
}
}
private static void assertTrue(boolean condition) {
if (!condition) {
throw new SanityCheckFailedException("The condition is false");
}
}
private static void assertFalse(boolean condition) {
if (condition) {
throw new SanityCheckFailedException("The condition is true");
}
}
}