Count the number of warnings and errors during SAM file validation

src/main/java/htsjdk/samtools/SamFileValidator.java

@@ -96,6 +96,8 @@
     private boolean bisulfiteSequenced;
     private IndexValidationStringency indexValidationStringency;
     private boolean sequenceDictionaryEmptyAndNoWarningEmitted;
+    private int numWarnings;
+    private int numErrors;
 
     private final int maxTempFiles;
 
@@ -111,6 +113,8 @@ public SamFileValidator(final PrintWriter out, final int maxTempFiles) {
         this.ignoreWarnings = false;
         this.bisulfiteSequenced = false;
         this.sequenceDictionaryEmptyAndNoWarningEmitted = false;
+        this.numWarnings = 0;
+        this.numErrors = 0;
     }
 
     Histogram<Type> getErrorsByType() {
@@ -566,11 +570,41 @@ private void validateHeader(final SAMFileHeader fileHeader) {
         }
     }
 
+    /**
+     * Number of warnings during SAM file validation
+     *
+     * @return number of warnings
+     */
+    public int getNumWarnings() {
+        return this.numWarnings;
+    }
+
+    /**
+     * Number of errors during SAM file validation
+     *
+     * @return number of errors
+     */
+    public int getNumErrors() {
+        return this.numErrors;
+    }
+
     private void addError(final SAMValidationError error) {
         // Just ignore an error if it's of a type we're not interested in
         if (this.errorsToIgnore.contains(error.getType())) return;
 
-        if (this.ignoreWarnings && error.getType().severity == SAMValidationError.Severity.WARNING) return;
+        switch (error.getType().severity) {
+            case WARNING:
+                if ( this.ignoreWarnings ) {
+                    return;
+                }
+                this.numWarnings++;
+                break;
+            case ERROR:
+                this.numErrors++;
+                break;
+            default:
+                throw new SAMException("Unknown SAM validation error severity: " + error.getType().severity);
+        }
 
         this.errorsByType.increment(error.getType());
         if (verbose) {

src/test/java/htsjdk/samtools/ValidateSamFileTest.java

@@ -119,7 +119,9 @@ public void testVerbose() throws IOException {
         validator.validateSamFileVerbose(samBuilder.getSamReader(), null);
 
         final int lineCount = results.toString().split("\n").length;
-        Assert.assertEquals(lineCount, 11);
+        Assert.assertEquals(lineCount, 11); // 1 extra message added to indicate maximum number of errors
+        Assert.assertEquals(validator.getNumErrors(), 6);
+        Assert.assertEquals(validator.getNumWarnings(), 4);
     }
 
     @Test
@@ -522,16 +524,18 @@ public void tagCorrectlyProcessTest(byte[] bytesFromFile,
     @DataProvider(name = "validateBamFileTerminationData")
     public Object[][] validateBamFileTerminationData() throws IOException {
         return new Object[][]{
-                {getBrokenFile(TERMINATION_GZIP_BLOCK_SIZE), SAMValidationError.Type.BAM_FILE_MISSING_TERMINATOR_BLOCK},
-                {getBrokenFile(RANDOM_NUMBER_TRUNC_BYTE), SAMValidationError.Type.TRUNCATED_FILE}
+                {getBrokenFile(TERMINATION_GZIP_BLOCK_SIZE), SAMValidationError.Type.BAM_FILE_MISSING_TERMINATOR_BLOCK, 1, 0},
+                {getBrokenFile(RANDOM_NUMBER_TRUNC_BYTE), SAMValidationError.Type.TRUNCATED_FILE, 0, 1}
         };
     }
 
     @Test(dataProvider = "validateBamFileTerminationData")
-    public void validateBamFileTerminationTest(File file, SAMValidationError.Type errorType) throws IOException {
+    public void validateBamFileTerminationTest(final File file, final SAMValidationError.Type errorType, final int numWarnings, final int numErrors) throws IOException {
         final SamFileValidator samFileValidator = new SamFileValidator(new PrintWriter(System.out), 8000);
         samFileValidator.validateBamFileTermination(file);
         Assert.assertEquals(samFileValidator.getErrorsByType().get(errorType).getValue(), 1.0);
+        Assert.assertEquals(samFileValidator.getNumWarnings(), numWarnings);
+        Assert.assertEquals(samFileValidator.getNumErrors(), numErrors);
     }
 
     private Histogram<String> executeValidation(final SamReader samReader, final ReferenceSequenceFile reference,