Trim intervals loaded from interval files.

src/main/java/org/broadinstitute/hellbender/utils/GenomeLocParser.java

@@ -292,12 +292,13 @@ private void vglHelper(final String msg) {
      * Performs interval-style validation:
      *
      * contig is valid; start and stop less than the end; start <= stop, and start/stop are on the contig
-     * @param str the string to parse
+     * @param rawStr the string to parse
      *
      * @return a GenomeLoc representing the String
      *
      */
-    public GenomeLoc parseGenomeLoc(final String str) {
+    public GenomeLoc parseGenomeLoc(final String rawStr) {
+        final String str = rawStr.trim();
         try {
             if ( isUnmappedGenomeLocString(str) ) {
                 return GenomeLoc.UNMAPPED;

src/main/java/org/broadinstitute/hellbender/utils/IntervalUtils.java

@@ -403,8 +403,9 @@ else if ( glParser.isValidGenomeLoc(interval.getContig(), interval.getStart(), i
             } else {
                 try (PathLineIterator reader = new PathLineIterator(inputPath)) {
                     for (final String line : reader) {
-                        if (!line.trim().isEmpty()) {
-                            ret.add(glParser.parseGenomeLoc(line));
+                        final String trimmedLine = line.trim();
+                        if (!trimmedLine.isEmpty()) {
+                            ret.add(glParser.parseGenomeLoc(trimmedLine));
                         }
                     }
                 }

src/main/java/org/broadinstitute/hellbender/utils/io/IOUtils.java

@@ -32,6 +32,7 @@
 import java.nio.file.*;
 import java.util.Arrays;
 import java.util.HashMap;
+import java.util.List;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 import java.util.zip.GZIPInputStream;
@@ -151,6 +152,23 @@ public static File writeTempFile(String content, String prefix, String suffix, F
         }
     }
 
+    /**
+     * Writes multiple lines of content to a temp file and returns the temporary file.
+     * @param prefix prefix to use for the temp file name
+     * @param suffix extension to use for the temp file
+     * @param content List<String> Strings that will be written to the file as separate lines
+     * @return temporary File that will be deleted on exit
+     */
+    public static File writeTempFile(final List<String> content, final String prefix, final String suffix) {
+        try {
+            final File tempFile = createTempFile(prefix, suffix);
+            FileUtils.writeLines(tempFile, content);
+            return tempFile;
+        } catch (IOException e) {
+            throw new UserException.BadTempDir(e.getMessage(), e);
+        }
+    }
+
     /**
      * Returns true if the file is a special file.
      * @param file File path to check.

src/test/java/org/broadinstitute/hellbender/utils/GenomeLocParserUnitTest.java

@@ -124,6 +124,13 @@ public void testParseGoodString() {
         assertEquals(loc.getStart(), 1);
     }
 
+    @Test
+    public void testStringIsTrimmed() {
+        final String locString = "1:1-10";
+        final GenomeLoc loc = genomeLocParser.parseGenomeLoc(" " + "1:1-10" + "  ");
+        Assert.assertEquals(loc.toString(), locString);
+    }
+
     @Test
     public void testCreateGenomeLoc1() {
         GenomeLoc loc = genomeLocParser.createGenomeLoc("1", 1, 100);

src/test/java/org/broadinstitute/hellbender/utils/IntervalUtilsUnitTest.java

@@ -16,7 +16,6 @@
 import htsjdk.tribble.SimpleFeature;
 import htsjdk.variant.utils.SAMSequenceDictionaryExtractor;
 import htsjdk.variant.vcf.VCFFileReader;
-import org.apache.commons.io.FileUtils;
 import org.broadinstitute.barclay.argparser.CommandLineException;
 import org.broadinstitute.hellbender.GATKBaseTest;
 import org.broadinstitute.hellbender.exceptions.UserException;
@@ -1120,12 +1119,35 @@ public void testUnmergedIntervals(String unmergedIntervals) {
         Assert.assertEquals(merged.size(), 1);
     }
 
+    @Test
+    public void testIntervalFileIntervalsAreTrimmed() throws IOException {
+        final GenomeLoc expectedGenomeLoc = hg19GenomeLocParser.createGenomeLoc("1", 1, 10);
+        final File gatkIntervalFile = IOUtils.writeTempFile(
+                Arrays.asList(
+                    String.format(
+                       // add some spaces around the start/end to test that it gets trimmed down to something valid
+                        " %s:%d-%d ",
+                        expectedGenomeLoc.getContig(),
+                        expectedGenomeLoc.getStart(),
+                        expectedGenomeLoc.getEnd())),
+                "testIntervalFileIntervalsAreTrimmed", ".intervals.list");
+
+        final List<String> intervalArgs = new ArrayList<>(1);
+        intervalArgs.add(gatkIntervalFile.getAbsolutePath());
+
+        final GenomeLocSortedSet locs = IntervalUtils.loadIntervals(
+                intervalArgs, IntervalSetRule.UNION, IntervalMergingRule.ALL, 0, hg19GenomeLocParser);
+        Assert.assertEquals(locs.size(), 1);
+        Assert.assertEquals(locs.toList().get(0), expectedGenomeLoc);
+    }
+
     @Test(expectedExceptions=UserException.MalformedGenomeLoc.class, dataProvider="invalidIntervalTestData")
     public void testInvalidGATKFileIntervalHandling(GenomeLocParser genomeLocParser,
                                                     String contig, int intervalStart, int intervalEnd ) throws Exception {
 
-        File gatkIntervalFile = createTempFile("testInvalidGATKFileIntervalHandling", ".intervals",
-                String.format("%s:%d-%d", contig, intervalStart, intervalEnd));
+        File gatkIntervalFile = IOUtils.writeTempFile(
+                Arrays.asList(String.format("%s:%d-%d", contig, intervalStart, intervalEnd)),
+                "testInvalidGATKFileIntervalHandling", ".intervals");
 
         List<String> intervalArgs = new ArrayList<>(1);
         intervalArgs.add(gatkIntervalFile.getAbsolutePath());
@@ -1220,12 +1242,6 @@ public Object[][] negativeOneLengthIntervalDataProvider() throws Exception {
         };
     }
 
-    private File createTempFile( String tempFilePrefix, String tempFileExtension, String... lines ) throws Exception {
-        File tempFile = GATKBaseTest.createTempFile(tempFilePrefix, tempFileExtension);
-        FileUtils.writeLines(tempFile, Arrays.asList(lines));
-        return tempFile;
-    }
-
     @DataProvider(name = "sortAndMergeIntervals")
     public Object[][] getSortAndMergeIntervals() {
         return new Object[][] {

src/test/java/org/broadinstitute/hellbender/utils/io/IOUtilsUnitTest.java

@@ -28,6 +28,7 @@
 import java.nio.file.attribute.BasicFileAttributes;
 import java.util.*;
 import java.util.stream.Collectors;
+import java.util.stream.Stream;
 
 public final class IOUtilsUnitTest extends GATKBaseTest {
 
@@ -594,6 +595,26 @@ public void testCreateTempFileInDirectory() {
                 "file was not written to temp file: " + tempFile + " in dir: " + tempDir);
     }
 
+    @Test
+    public void testCreateTempFileWithContent() throws IOException {
+        final String prefix = "prefix";
+        final String suffix = ".txt";
+        final List<String> inputStrings = Arrays.asList("first line", "second line");
+
+        final File tempFile = IOUtils.writeTempFile(inputStrings,prefix, suffix);
+
+        Assert.assertTrue(tempFile.exists(), "file was not written to temp file: " + tempFile);
+        Assert.assertTrue(tempFile.getName().startsWith("prefix"));
+        Assert.assertTrue(tempFile.getName().endsWith(".txt"));
+
+        final List<String> actualStrings = new ArrayList<>();
+        try (Stream<String> lines = Files.lines( tempFile.toPath())) {
+            lines.forEach(actualStrings::add);
+        }
+
+        Assert.assertEquals(actualStrings, inputStrings);
+    }
+
     @DataProvider
     public Object[][] tmpPathDirs() throws Exception {
         return new Object[][] {