Fixed max mapping quality calculation regression fault

PapenfussLab · Sep 1, 2016 · 7b1a9a1 · 7b1a9a1
1 parent 9ab5cc5
commit 7b1a9a1
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Showing 2 changed files with 24 additions and 13 deletions.
diff --git a/src/main/java/picard/analysis/directed/MapqMetricsCollector.java b/src/main/java/picard/analysis/directed/MapqMetricsCollector.java
@@ -105,20 +105,16 @@ public void addMetricsToFile(final MetricsFile<MapqMetrics,Integer> file) {
             metrics.LIBRARY            = this.library;
             metrics.READ_GROUP         = this.readGroup;
             metrics.MAPPED_READS       = (long) histogram.getCount();
-            if (!histogram.isEmpty()) {
-            	metrics.MIN_MAPQ       = (int) histogram.getMin();
+            metrics.MIN_MAPQ           = SAMRecord.UNKNOWN_MAPPING_QUALITY;
+            metrics.MAX_MAPQ           = 0;
+            for (int key : histogram.keySet()) {
+            	if (key != SAMRecord.UNKNOWN_MAPPING_QUALITY) {
+            		if (histogram.get(key).getValue() > 0) {
+            			metrics.MIN_MAPQ = Math.min(metrics.MIN_MAPQ, key);
+            			metrics.MAX_MAPQ = Math.max(metrics.MAX_MAPQ, key);
+            		}
+            	}
             }
-            int mapq = 0;
-        	for (int i = SAMRecord.UNKNOWN_MAPPING_QUALITY; i >= 0; i++) {
-        		if (histogram.containsKey(i)) {
-        			if (histogram.get(i).getValue() > 0) {
-        				mapq = (int) histogram.get(i).getValue();
-        				break;
-        			}
-        		}
-        	}
-        	metrics.MAX_MAPQ       = (int)mapq;
-
             if (histogram.get(SAMRecord.NO_MAPPING_QUALITY) != null) {
             	metrics.ZERO_MAPQ      = (long) histogram.get(SAMRecord.NO_MAPPING_QUALITY).getValue();
             }

diff --git a/src/test/java/au/edu/wehi/idsv/metrics/IdsvSamFileMetricsCollectorTest.java b/src/test/java/au/edu/wehi/idsv/metrics/IdsvSamFileMetricsCollectorTest.java
@@ -233,4 +233,19 @@ public void mapq_should_be_calculated() {
 		assertEquals(2, mq.getMetrics().get(0).MIN_MAPQ);
 		assertEquals(2, mq.getMetrics().get(0).MAX_MAPQ);
 	}
+	@Test
+	public void mapq_should_be_extrema() {
+		IdsvSamFileMetricsCollector c = new IdsvSamFileMetricsCollector(null);
+		c.acceptRecord(withMapq(1, Read(0, 1, "100M"))[0], null);
+		c.acceptRecord(withMapq(2, Read(0, 1, "101M"))[0], null);
+		c.acceptRecord(withMapq(2, Read(0, 1, "102M"))[0], null);
+		c.acceptRecord(withMapq(3, Read(0, 1, "103M"))[0], null);
+		MetricsFile<IdsvMetrics, Integer> idsv = new MetricsFile<IdsvMetrics, Integer>();
+		MetricsFile<InsertSizeMetrics, Integer> is = new MetricsFile<InsertSizeMetrics, Integer>();
+		MetricsFile<CigarDetailMetrics, Integer> sc = new MetricsFile<CigarDetailMetrics, Integer>();
+		MetricsFile<MapqMetrics, Integer> mq = new MetricsFile<MapqMetrics, Integer>();
+		c.finish(is, idsv, mq, sc);
+		assertEquals(1, mq.getMetrics().get(0).MIN_MAPQ);
+		assertEquals(3, mq.getMetrics().get(0).MAX_MAPQ);
+	}
 }