-cleanup

src/main/java/htsjdk/samtools/util/IntervalList.java

@@ -32,13 +32,7 @@
 
 import java.io.*;
 import java.nio.file.Path;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.Iterator;
-import java.util.LinkedHashSet;
-import java.util.List;
+import java.util.*;
 
 /**
  * Represents a list of intervals against a reference sequence that can be written to
@@ -542,10 +536,8 @@ public static IntervalList fromReader(final BufferedReader in) {
 
             // Then read in the intervals
             do {
-                Interval nullableInterval = intervalListCodec.decode(line);
-                if (nullableInterval != null) {
-                    list.intervals.add(nullableInterval);
-                }
+                final Optional<Interval> maybeInterval = Optional.ofNullable(intervalListCodec.decode(line));
+                maybeInterval.ifPresent(list.intervals::add);
             }
             while ((line = in.readLine()) != null);
 

src/main/java/htsjdk/tribble/AsciiSamFeatureCodec.java

@@ -1,21 +1,28 @@
 /*
- * Copyright (c) 2019 by The Broad Institute, Inc. and the Massachusetts Institute of Technology.
- * All Rights Reserved.
+ * Copyright (c) 2019, The Broad Institute
  *
- * This software is licensed under the terms of the GNU Lesser General Public License (LGPL), Version 2.1 which
- * is available at http://www.opensource.org/licenses/lgpl-2.1.php.
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
  *
- * THE SOFTWARE IS PROVIDED "AS IS." THE BROAD AND MIT MAKE NO REPRESENTATIONS OR WARRANTIES OF
- * ANY KIND CONCERNING THE SOFTWARE, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT
- * OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE.  IN NO EVENT SHALL THE BROAD OR MIT, OR THEIR
- * RESPECTIVE TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES, AND AFFILIATES BE LIABLE FOR ANY DAMAGES OF
- * ANY KIND, INCLUDING, WITHOUT LIMITATION, INCIDENTAL OR CONSEQUENTIAL DAMAGES, ECONOMIC
- * DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER THE BROAD OR MIT SHALL
- * BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE
- * FOREGOING.
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
  */
 
+
 package htsjdk.tribble;
 
 import htsjdk.samtools.util.*;

src/test/resources/htsjdk/tribble/interval_list/example.dict

@@ -1,3 +1,3 @@
 @SQ	SN:chr1	LN:249250621
 @SQ	SN:chr2	LN:243199373
-@SQ	SN:chr3	LN:198022430
+@SQ	SN:chr3	LN:198022430