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add unit tests

This commit is contained in:
Mauricio Carneiro 2013-09-10 10:59:27 -04:00
parent 839b918f58
commit 63ace685c9
2 changed files with 47 additions and 14 deletions
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23
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
View File

@ -259,27 +259,24 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
out.close();
}
private int getPositionInTarget(final GenomeLoc interval, final List<GenomeLoc> hits) {
if (hits.size() > 0) {
final GenomeLoc hit = hits.get(0);
protected static int getPositionInTarget(final GenomeLoc interval, final List<GenomeLoc> targets) {
if (targets.size() > 0) {
final GenomeLoc target = targets.get(0);
// interval is larger on both ends than the target -- return the maximum distance to either side as a negative number. (min of 2 negative numbers)
if (interval.getStart() < hit.getStart() && interval.getStop() > hit.getStop())
return Math.min(interval.getStart() - hit.getStart(),
interval.getStop() - hit.getStop());
if (interval.getStart() < target.getStart() && interval.getStop() > target.getStop())
return Math.min(target.getStart() - interval.getStart(), target.getStop() - interval.getStop());
// interval is a left overlap -- return a negative number representing the distance between the two starts
else if (interval.getStart() < hit.getStart())
return hit.getStart() - interval.getStart();
else if (interval.getStart() < target.getStart())
return interval.getStart() - target.getStart();
// interval is a right overlap -- return a negative number representing the distance between the two stops
else if (interval.getStop() > hit.getStop())
return hit.getStop() - interval.getStop();
else if (interval.getStop() > target.getStop())
return target.getStop() - interval.getStop();
// interval is fully contained -- return the smallest distance to the edge of the target (left or right) as a positive number
else
return Math.min(Math.abs(hit.getStart() - interval.getStart()),
Math.abs(hit.getStop() - interval.getStop()));
return Math.min(interval.getStart() - target.getStart(), target.getStop() - interval.getStop());
}
// if there is no overlapping interval, return int min value.
return Integer.MIN_VALUE;

38
protected/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervalsUnitTest.java
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@ -46,6 +46,8 @@
package org.broadinstitute.sting.gatk.walkers.diagnostics.missing;
import it.unimi.dsi.fastutil.objects.ObjectArrayList;
import java.util.List;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.UnvalidatingGenomeLoc;
@ -57,7 +59,6 @@ import org.testng.annotations.Test;
* User: carneiro
* Date: 9/20/13
* Time: 3:59 PM
* To change this template use File | Settings | File Templates.
*/
public class QualifyMissingIntervalsUnitTest extends BaseTest {
@Test(enabled = true)
@ -92,4 +93,39 @@ public class QualifyMissingIntervalsUnitTest extends BaseTest {
for (Metrics m : array)
Assert.assertEquals(tool.interpret(m, smallInterval), QualifyMissingIntervals.Interpretation.SMALL_INTERVAL.toString());
}
@Test(enabled = true)
void testGetPositionInTarget () {
final UnvalidatingGenomeLoc target = new UnvalidatingGenomeLoc("a", 0, 30, 50);
final List<GenomeLoc> targets = new ObjectArrayList<>(1);
targets.add(target);
// left overlap
UnvalidatingGenomeLoc interval = new UnvalidatingGenomeLoc("a", 0, 10, 50);
Assert.assertEquals(QualifyMissingIntervals.getPositionInTarget(interval, targets), -20);
// right overlap
interval = new UnvalidatingGenomeLoc("a", 0, 40, 60);
Assert.assertEquals(QualifyMissingIntervals.getPositionInTarget(interval, targets), -10);
// interval > target with short right tail
interval = new UnvalidatingGenomeLoc("a", 0, 10, 60);
Assert.assertEquals(QualifyMissingIntervals.getPositionInTarget(interval, targets), -10);
// interval > target with short left tail
interval = new UnvalidatingGenomeLoc("a", 0, 10, 80);
Assert.assertEquals(QualifyMissingIntervals.getPositionInTarget(interval, targets), -30);
// interval < target with short right tail
interval = new UnvalidatingGenomeLoc("a", 0, 32, 40);
Assert.assertEquals(QualifyMissingIntervals.getPositionInTarget(interval, targets), 2);
// interval < target with short left tail
interval = new UnvalidatingGenomeLoc("a", 0, 40, 42);
Assert.assertEquals(QualifyMissingIntervals.getPositionInTarget(interval, targets), 8);
// no overlap
interval = new UnvalidatingGenomeLoc("a", 0, 40, 42);
Assert.assertEquals(QualifyMissingIntervals.getPositionInTarget(interval, new ObjectArrayList<GenomeLoc>()), Integer.MIN_VALUE);
}
}