Merge pull request #1441 from broadinstitute/rhl_printreads_bqsr_fail

Throw an exception if the BQSR input covariants file is not found

public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/GenomeAnalysisEngine.java

@@ -269,8 +269,13 @@ public class GenomeAnalysisEngine {
             Utils.resetRandomGenerator(System.currentTimeMillis());
 
         // if the use specified an input BQSR recalibration table then enable on the fly recalibration
-        if (args.BQSR_RECAL_FILE != null)
+        if (args.BQSR_RECAL_FILE != null) {
-            setBaseRecalibration(args);
+            if (args.BQSR_RECAL_FILE.exists()) {
+                setBaseRecalibration(args);
+            } else {
+                throw new UserException("The BQSR recalibration file, " + args.BQSR_RECAL_FILE.getAbsolutePath() + ", does not exist");
+            }
+        }
 
         // setup the runtime limits
         setupRuntimeLimits(args);

public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/readutils/PrintReadsIntegrationTest.java

@@ -135,4 +135,18 @@ public class PrintReadsIntegrationTest extends WalkerTest {
         executeTest("testPrintReadsException-"+params.args, spec);
     }
 
+    @Test
+    public void testPrintReadsNoBQSRFile() {
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T PrintReads" +
+                        " -R " + hg18Reference +
+                        " -I " + privateTestDir + "HiSeq.1mb.bam" +
+                        " -BSQR bqsrFile" +
+                        " --no_pg_tag" +
+                        " -o %s",
+                1, UserException.class);
+        executeTest("testPrintReadsNoBQSRFile-", spec);
+    }
+
 }