Add fromPath to IntervalList.

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

@@ -778,9 +778,14 @@ public static File createTempDir(final String prefix, final String suffix) {
 
     /** Checks that a file exists and is readable, and then returns a buffered reader for it. */
     public static BufferedReader openFileForBufferedReading(final File file) {
-        return new BufferedReader(new InputStreamReader(openFileForReading(file)), Defaults.NON_ZERO_BUFFER_SIZE);
+        return openFileForBufferedReading(file.toPath());
 	}
 
+    /** Checks that a path exists and is readable, and then returns a buffered reader for it. */
+    public static BufferedReader openFileForBufferedReading(final Path path) {
+        return new BufferedReader(new InputStreamReader(openFileForReading(path)), Defaults.NON_ZERO_BUFFER_SIZE);
+    }
+
     /** Takes a string and replaces any characters that are not safe for filenames with an underscore */
     public static String makeFileNameSafe(final String str) {
         return str.trim().replaceAll("[\\s!\"#$%&'()*/:;<=>?@\\[\\]\\\\^`{|}~]", "_");

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

@@ -34,6 +34,7 @@
 import java.io.File;
 import java.io.IOException;
 import java.io.Serializable;
+import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
@@ -397,12 +398,21 @@ public static IntervalList copyOf(final IntervalList list){
      * @return an IntervalList object that contains the headers and intervals from the file
      */
     public static IntervalList fromFile(final File file) {
-        final BufferedReader reader= IOUtil.openFileForBufferedReading(file);
+        return fromPath(file.toPath());
+    }
+
+    /**
+     * Parses an interval list from a path.
+     * @param path the path containing the intervals
+     * @return an IntervalList object that contains the headers and intervals from the path
+     */
+    public static IntervalList fromPath(final Path path) {
+        final BufferedReader reader = IOUtil.openFileForBufferedReading(path);
         final IntervalList list = fromReader(reader);
         try {
             reader.close();
         } catch (final IOException e) {
-            throw new SAMException(String.format("Failed to close file %s after reading",file));
+            throw new SAMException(String.format("Failed to close file %s after reading", path.toUri().toString()));
         }
 
         return list;

src/test/java/htsjdk/samtools/util/IntervalListTest.java

@@ -25,14 +25,17 @@
 package htsjdk.samtools.util;
 
 import htsjdk.samtools.SAMFileHeader;
+import htsjdk.samtools.SAMSequenceDictionary;
 import htsjdk.samtools.SAMSequenceRecord;
+import htsjdk.samtools.SamFileHeaderMerger;
 import htsjdk.variant.vcf.VCFFileReader;
 import org.testng.Assert;
 import org.testng.annotations.BeforeTest;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
 import java.io.File;
+import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
@@ -75,6 +78,15 @@ public IntervalListTest() {
         list3.add(new Interval("3", 50, 470));
     }
 
+    @Test
+    public void testIntervalListFrom() {
+        final String testPath = "src/test/resources/htsjdk/samtools/intervallist/IntervalListFromVCFTestComp.interval_list";
+        final IntervalList fromFileList = IntervalList.fromFile(new File(testPath));
+        final IntervalList fromPathList = IntervalList.fromPath(Paths.get(testPath));
+        fromFileList.getHeader().getSequenceDictionary().assertSameDictionary(fromPathList.getHeader().getSequenceDictionary());
+        Assert.assertEquals(CollectionUtil.makeCollection(fromFileList.iterator()), CollectionUtil.makeCollection(fromPathList.iterator()));
+    }
+
     @DataProvider(name = "intersectData")
     public Object[][] intersectData() {
         final IntervalList intersect123 = new IntervalList(fileHeader);