Fix regular expression (and add tests failing previously)

Author: magicDGS

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

@@ -85,7 +85,7 @@ public class SAMSequenceRecord extends AbstractSAMHeaderRecord implements Clonea
     private static char[] WHITESPACE_CHARS = {' ', '\t', '\n', '\013', '\f', '\r'}; // \013 is vertical tab
 
     // alternative sequence name regexp
-    private static final Pattern ALTERNATIVE_SEQUENCE_NAME_REGEXP = Pattern.compile("[0-9A-Za-z][0-9A-Za-z*+.@-]*");
+    private static final Pattern ALTERNATIVE_SEQUENCE_NAME_REGEXP = Pattern.compile("[0-9A-Za-z][0-9A-Za-z*+.@_|-]*");
     private static final String ALTERNATIVE_SEQUENCE_NAME_SEPARATOR = ",";
 
     /** a (private) empty constructor is required for JAXB.XML-serialisation */

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

@@ -109,6 +109,32 @@ public void testAlternativeSequences() {
         Assert.assertEquals("@SQ\tSN:1\tLN:100\tAN:chr1,chr01,01,CM000663", chr1.getSAMString());
     }
 
+    @DataProvider
+    public Object[][] validAlternativeSequences() {
+        return new Object[][] {
+                // only characters
+                {"a"},
+                {"alias"},
+                // valid symbols after first character ('*', '+', '.', '@', '_', '|', '-')
+                {"my*contig"},
+                {"my+contig"},
+                {"my.contig"},
+                {"my@contig"},
+                {"my_contig"},
+                {"my|contig"},
+                {"my-contig"}
+        };
+    }
+
+    @Test(dataProvider = "validAlternativeSequences")
+    public void testValidAlternativeSequences(final String altName) {
+        final SAMSequenceRecord contig = new SAMSequenceRecord("contig", 100);
+        // should not throw
+        contig.setAlternativeSequenceName(Collections.singleton(altName));
+        Assert.assertTrue(contig.hasAlternativeSequenceNames());
+        Assert.assertEquals(contig.getAlternativeSequenceNames(), Collections.singleton(altName));
+    }
+
     @DataProvider
     public Object[][] invalidAlternativeSequences() {
         return new Object[][] {