--include-qc-failed-reads option

src/main/java/org/broadinstitute/hellbender/tools/walkers/featuremapping/FlowFeatureMapper.java

@@ -103,6 +103,9 @@ public final class FlowFeatureMapper extends ReadWalker {
     private static final String     VCF_SMQ_RIGHT_MEAN = "X_SMQ_RIGHT_MEAN";
 
     private static final Double     LOWEST_PROB = 0.0001;
+    private static final int        VENDOR_QUALITY_CHECK_FLAG = 0x200;
+
+    private static final String     INCLUDE_QC_FAILED_READS_FULL_NAME = "include-qc-failed-reads";
 
     @Argument(fullName = StandardArgumentDefinitions.OUTPUT_LONG_NAME,
             shortName = StandardArgumentDefinitions.OUTPUT_SHORT_NAME,
@@ -131,6 +134,10 @@ public final class FlowFeatureMapper extends ReadWalker {
     @Argument(fullName=HaplotypeCallerArgumentCollection.OUTPUT_BLOCK_LOWER_BOUNDS, doc = "Output the band lower bound for each GQ block regardless of the data it represents", optional = true)
     public boolean floorBlocks = false;
 
+    @Advanced
+    @Argument(fullName=INCLUDE_QC_FAILED_READS_FULL_NAME, doc = "include reads with QC failed flag", optional = true)
+    public boolean includeQcFailedReads = false;
+
     @ArgumentCollection
     public FlowBasedArgumentCollection fbargs = new FlowBasedArgumentCollection();
 
@@ -337,6 +344,11 @@ public void apply(final GATKRead read, final ReferenceContext referenceContext,
             return;
         }
 
+        // include qc-failed reads?
+        if ( ((read.getFlags() & VENDOR_QUALITY_CHECK_FLAG) != 0) && !includeQcFailedReads ) {
+            return;
+        }
+
         // flush qeues up to this read
         flushQueue(read, referenceContext);
 

src/test/java/org/broadinstitute/hellbender/tools/walkers/featuremapping/FlowFeatureMapperIntegrationTest.java

@@ -116,4 +116,35 @@ public void testSurroundingAllQuality() throws IOException {
         }
     }
 
+    @Test
+    public void testQCFailed() throws IOException {
+
+        final File outputDir = createTempDir("testFlowFeatureMapperTest");
+        final File expectedFile = new File(testDir + "/snv_feature_mapper_qc_failed_output.vcf");
+        final File outputFile = UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS ? expectedFile : new File(outputDir + "/snv_feature_mapper_qc_failed_output.vcf");
+
+        final String[] args = new String[] {
+                "-R", largeFileTestDir + "/Homo_sapiens_assembly38.fasta.gz",
+                "-O", outputFile.getAbsolutePath(),
+                "-I", testDir + "/snv_feature_mapper_input.bam",
+                "--copy-attr", "tr",
+                "--limit-score", "100",
+                "--min-score", "0",
+                "--snv-identical-bases", "10",
+                "--debug-negatives", "false",
+                "--debug-read-name", "150451-BC94-0645901755",
+                "--include-qc-failed-reads", "true"
+        };
+
+        // run the tool
+        runCommandLine(args);  // no assert, just make sure we don't throw
+
+        // make sure we've generated the otuput file
+        Assert.assertTrue(outputFile.exists());
+
+        // walk the output and expected files, compare non-comment lines
+        if ( !UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS ) {
+            IntegrationTestSpec.assertEqualTextFiles(outputFile, expectedFile, "#");
+        }
+    }
 }