Fix crash on PF_READS == 0 for AlignmentSummaryMetricsCollector (#1871)

* Create a (mostly) empty metrics file instead of giving an unhelpful stacktrace if PF_READS == 0.

* Added check for the PF_READS == 0 case.

* Added a corresponding test file.

* Use a PicardException with an informative message when PF_READS == 0 and TOTAL_READS > 0.

src/main/java/picard/analysis/AlignmentSummaryMetricsCollector.java

@@ -40,6 +40,7 @@
 import htsjdk.samtools.util.CoordMath;
 import htsjdk.samtools.util.Histogram;
 import htsjdk.samtools.util.SequenceUtil;
+import picard.PicardException;
 import picard.metrics.PerUnitMetricCollector;
 import picard.metrics.SAMRecordAndReference;
 import picard.metrics.SAMRecordAndReferenceMultiLevelCollector;
@@ -261,7 +262,7 @@ public void acceptRecord(final SAMRecordAndReference samRecordAndReference) {
         @Override
         public void finish() {
             //summarize read data
-            if (metrics.TOTAL_READS > 0) {
+            if (metrics.PF_READS > 0) {
                 metrics.PCT_PF_READS = (double) metrics.PF_READS / (double) metrics.TOTAL_READS;
                 metrics.PCT_ADAPTER = adapterReads / (double) metrics.PF_READS;
                 metrics.MEAN_READ_LENGTH = readLengthHistogram.getMean();
@@ -298,6 +299,10 @@ public void finish() {
 
                     metrics.PF_HQ_MEDIAN_MISMATCHES = hqMismatchHistogram.getMedian();
                 }
+            } else {
+                if (metrics.TOTAL_READS > 0) {
+                    throw new PicardException("Input file contains no PF_READS.");
+                }
             }
         }
 

src/test/java/picard/analysis/CollectAlignmentSummaryMetricsTest.java

@@ -29,6 +29,7 @@
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
+import picard.PicardException;
 import picard.cmdline.CommandLineProgramTest;
 import picard.util.TestNGUtil;
 
@@ -771,4 +772,37 @@ public void testReadLengthHistogram(final boolean plotChart) throws IOException
             }
         }
     }
+
+    @Test(expectedExceptions = PicardException.class)
+    public void testNoPFReads() throws IOException {
+        final File input = new File(TEST_DATA_DIR, "null.sam");
+        final File outfile = getTempOutputFile("test", ".txt");
+        final String[] args = new String[]{
+                "INPUT=" + input.getAbsolutePath(),
+                "OUTPUT=" + outfile.getAbsolutePath(),
+        };
+        Assert.assertEquals(runPicardCommandLine(args), 0);
+
+        final MetricsFile<AlignmentSummaryMetrics, Comparable<?>> output = new MetricsFile<>();
+        try (FileReader reader = new FileReader(outfile)) {
+            output.read(reader);
+        }
+
+        Assert.assertEquals(output.getMetrics().size(), 1);
+        for (final AlignmentSummaryMetrics metrics : output.getMetrics()) {
+            Assert.assertEquals(metrics.MEAN_READ_LENGTH, 0.0);
+            Assert.assertEquals(metrics.TOTAL_READS, 3);
+            Assert.assertEquals(metrics.PF_READS, 0);
+            Assert.assertEquals(metrics.PF_NOISE_READS, 0);
+            Assert.assertEquals(metrics.PF_HQ_ALIGNED_READS, 0);
+            Assert.assertEquals(metrics.PF_HQ_ALIGNED_Q20_BASES, 0);
+            Assert.assertEquals(metrics.PF_HQ_MEDIAN_MISMATCHES, 0.0);
+            Assert.assertEquals(metrics.PF_READS_ALIGNED, 0);
+            Assert.assertEquals(metrics.PF_READS_IMPROPER_PAIRS, 0);
+            Assert.assertEquals(metrics.PCT_PF_READS_IMPROPER_PAIRS, 0.0);
+            Assert.assertEquals(metrics.PF_ALIGNED_BASES, 0);
+            Assert.assertEquals(metrics.PF_MISMATCH_RATE, 0.0);
+            Assert.assertEquals(metrics.BAD_CYCLES, 0);
+        }
+    }
 }

testdata/picard/sam/AlignmentSummaryMetrics/null.sam

@@ -0,0 +1,5 @@
+@HD	VN:1.6	GO:none	SO:queryname
+@RG	ID:test	SM:test_sample	LB:test_lib	PL:ILLUMINA	PU:my_platform	CN:BI	DT:2023-01-01T00:00:00-0500	DS:description
+aln1	516	*	0	0	*	*	0	0	AGCTACTG	99999999	RG:Z:test
+aln2	516	*	0	0	*	*	0	0	GTCAGTCA	99999999	RG:Z:test
+aln3	516	*	0	0	*	*	0	0	CCTTGGAA	99999999	RG:Z:test