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Merge pull request #393 from broadinstitute/mc_qualify_updates_for_cser 

Length metric updates to QualifyMissingIntervals
This commit is contained in:
Eric Banks 2013-10-04 09:50:39 -07:00
parent 3aef87c214 63ace685c9
commit 49d489cbf8
2 changed files with 85 additions and 14 deletions
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61
protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
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@ -76,10 +76,12 @@ import java.util.List;
* <ul>
* <li>Average Base Quality</li>
* <li>Average Mapping Quality</li>
* <li>Average Depth</li>
* <li>GC Content</li>
* <li>Position in the target</li>
* <li>Coding Sequence / Intron</li>
* <li>Length of the uncovered area</li>
* <li>Position in the target (Integer.MIN_VALUE if no overlap)</li>
* <li>Length of the overlapping target (zero if no overlap)</li>
* <li>Coding Sequence / Intron (optional)</li>
* <li>Length of the uncovered interval</li>
* </ul>
*
* <h3>Input</h3>
@ -89,7 +91,7 @@ import java.util.List;
*
* <h3>Output</h3>
* <p>
* GC content calculations per interval.
* GC content, distance from the end of the target, coding sequence intersection, mapping and base quality averages and average depth per "missing" interval.
* </p>
*
* <h3>Example</h3>
@ -108,12 +110,24 @@ import java.util.List;
@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
@By(DataSource.REFERENCE)
public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics> implements NanoSchedulable {
/**
* A single GATKReport table with the qualifications on why the intervals passed by the -L argument were missing.
*/
@Output
protected PrintStream out;
/**
* List of targets used in the experiment. This file will be used to calculate the distance your missing
* intervals are to the targets (usually exons). Typically this is your hybrid selection targets file
* (e.g. Agilent exome target list)
*/
@Argument(shortName = "targets", required = true)
public String targetsFile;
/**
* List of coding sequence intervals (exons) if different from the targets file, to distinguish intervals
* that overlap the cds and intervals that don't.
*/
@Argument(shortName = "cds", required = false)
public String cdsFile = null;
@ -224,15 +238,18 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
public void onTraversalDone(List<Pair<GenomeLoc, Metrics>> results) {
for (Pair<GenomeLoc, Metrics> r : results) {
GenomeLoc interval = r.getFirst();
Metrics metrics = r.getSecond();
final GenomeLoc interval = r.getFirst();
final Metrics metrics = r.getSecond();
final List<GenomeLoc> overlappingIntervals = target.getOverlapping(interval);
simpleReport.addRow(
interval.toString(),
metrics.gccontent(),
metrics.baseQual(),
metrics.mapQual(),
metrics.depth(),
getPositionInTarget(interval),
getPositionInTarget(interval, overlappingIntervals),
getTargetSize(overlappingIntervals),
cds.overlaps(interval),
interval.size(),
interpret(metrics, interval)
@ -242,13 +259,31 @@ public final class QualifyMissingIntervals extends LocusWalker<Metrics, Metrics>
out.close();
}
private int getPositionInTarget(GenomeLoc interval) {
final List<GenomeLoc> hits = target.getOverlapping(interval);
int result = 0;
for (GenomeLoc hit : hits) {
result = interval.getStart() - hit.getStart(); // if there are multiple hits, we'll get the last one.
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() < 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() < 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() > 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
return Math.min(interval.getStart() - target.getStart(), target.getStop() - interval.getStop());
}
return result;
// if there is no overlapping interval, return int min value.
return Integer.MIN_VALUE;
}
private int getTargetSize(final List<GenomeLoc> overlappingIntervals) {
return overlappingIntervals.size() > 0 ? overlappingIntervals.get(0).size() : -1;
}
String interpret(final Metrics metrics, final GenomeLoc interval) {

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);
}
}