- implementing the spec change in

src/main/java/htsjdk/samtools/SAMSequenceRecord.java

@@ -57,10 +57,10 @@ public class SAMSequenceRecord extends AbstractSAMHeaderRecord implements Clonea
 
 
     /**
-     * This is not a valid sequence name, because it is reserved in the MRNM field of SAM text format
+     * This is not a valid sequence name, because it is reserved in the RNEXT field of SAM text format
      * to mean "same reference as RNAME field."
      */
-    public static final String RESERVED_MRNM_SEQUENCE_NAME = "=";
+    public static final String RESERVED_RNEXT_SEQUENCE_NAME = "=";
 
     /**
      * The standard tags are stored in text header without type information, because the type of these tags is known.
@@ -70,10 +70,12 @@ public class SAMSequenceRecord extends AbstractSAMHeaderRecord implements Clonea
                                                 SPECIES_TAG));
 
     // Split on any whitespace
-    private static final Pattern SEQUENCE_NAME_SPLITTER = Pattern.compile("\\s");
+    private static final Pattern SEQUENCE_NAME_SPLITTER = Pattern.compile("[\\s]");
     // These are the chars matched by \\s.
     private static final char[] WHITESPACE_CHARS = {' ', '\t', '\n', '\013', '\f', '\r'}; // \013 is vertical tab
 
+    private static Pattern LEGAL_RNAME_PATTERN = Pattern.compile("[0-9A-Za-z!#$%&+./:;?@^_|~-][0-9A-Za-z!#$%&*+./:;=?@^_|~-]*");
+
     /**
      * @deprecated Use {@link #SAMSequenceRecord(String, int)} instead.
      * sequenceLength is required for the object to be considered valid.
@@ -85,8 +87,8 @@ public SAMSequenceRecord(final String name) {
 
     public SAMSequenceRecord(final String name, final int sequenceLength) {
         if (name != null) {
-            if (SEQUENCE_NAME_SPLITTER.matcher(name).find()) {
-                throw new SAMException("Sequence name contains invalid character: " + name);
+            if (!LEGAL_RNAME_PATTERN.matcher(name).useAnchoringBounds(true).matches()) {
+                throw new SAMException(String.format("Sequence name '%s' doesn't match regex: '%s' ", name, LEGAL_RNAME_PATTERN));
             }
             validateSequenceName(name);
             mSequenceName = name.intern();
@@ -204,8 +206,8 @@ public static String truncateSequenceName(final String sequenceName) {
      * Throw an exception if the sequence name is not valid.
      */
     public static void validateSequenceName(final String name) {
-        if (RESERVED_MRNM_SEQUENCE_NAME.equals(name)) {
-            throw new SAMException("'" + RESERVED_MRNM_SEQUENCE_NAME + "' is not a valid sequence name");
+        if (RESERVED_RNEXT_SEQUENCE_NAME.equals(name)) {
+            throw new SAMException("'" + RESERVED_RNEXT_SEQUENCE_NAME + "' is not a valid sequence name");
         }
     }
 

src/test/java/htsjdk/samtools/SAMSequenceRecordTest.java

@@ -85,11 +85,32 @@ public void testIsSameSequence(final SAMSequenceRecord rec1 , final SAMSequenceR
     }
 
     @Test
-    public void testSetAndCheckDescription(){
+    public void testSetAndCheckDescription() {
         final SAMSequenceRecord record = new SAMSequenceRecord("Test", 1000);
         Assert.assertNull(record.getDescription());
         final String description = "A description.";
         record.setDescription(description);
         Assert.assertEquals(record.getDescription(), description);
     }
+
+    @DataProvider
+    public Object[][] illegalSequenceNames(){
+        return new Object[][]{
+                {"space "},
+                {"comma,"},
+                {"lbrace["},
+                {"rbrace]"},
+                {"slash\\"},
+                {"smaller<"},
+                {"bigger<"},
+                {"lparen("},
+                {"rparen)"},
+                {"lbracket{"},
+                {"rbracket}"}};
+    }
+
+    @Test(dataProvider = "illegalSequenceNames", expectedExceptions = SAMException.class)
+    public void testIllegalSequenceNames(final String sequenceName){
+        new SAMSequenceRecord(sequenceName,100);
+    }
 }

src/test/java/htsjdk/samtools/SequenceNameTruncationAndValidationTest.java

@@ -43,7 +43,7 @@ public class SequenceNameTruncationAndValidationTest extends HtsjdkTest {
     @Test(expectedExceptions = {SAMException.class}, dataProvider = "badSequenceNames")
     public void testSequenceRecordThrowsWhenInvalid(final String sequenceName) {
         new SAMSequenceRecord(sequenceName, 123);
-        Assert.fail("Should not reach here.");
+        Assert.fail("Should not reach here. Sequence " + sequenceName + " should have failed.");
     }
 
     @DataProvider(name = "badSequenceNames")
@@ -53,7 +53,13 @@ public Object[][] badSequenceNames() {
                 {"\t"},
                 {"\n"},
                 {"="},
-                {"Hi, Mom!"}
+                {"Hi: Mom!"},
+                {"=Hi:Mom!"},
+                {"Hi:'Mom!"},
+                {"Hi:\"Mom!"},
+                {"Hi:)Mom!"},
+                {"Hi:(Mom!"},
+                {"Hi,@Mom!"}
         };
     }
 
@@ -65,7 +71,8 @@ public void testSequenceRecordPositiveTest(final String sequenceName) {
     @DataProvider(name = "goodSequenceNames")
     public Object[][] goodSequenceNames() {
         return new Object[][]{
-                {"Hi,@Mom!"}
+                {"Hi:@Mom!"},
+                {"Hi:=Mom!"}
         };
     }