enable -L to read Feature Files from Paths (#4854)

* expand -L support for Feature Files to work with Paths
* previously interval files could be read from Paths, but not feature
files like vcf and bed
* fixes #4852

src/main/java/org/broadinstitute/hellbender/engine/FeatureManager.java

@@ -493,8 +493,8 @@ private <T extends Feature> FeatureDataSource<T> lookupDataSource( final Feature
      * @param file file to check
      * @return True if the file exists and contains Features (ie., we have a FeatureCodec that can decode it), otherwise false
      */
-    public static boolean isFeatureFile( final File file ) {
-        return file.exists() && ! getCandidateCodecsForFile(file.toPath()).isEmpty();
+    public static boolean isFeatureFile( final Path file ) {
+        return Files.exists(file) && ! getCandidateCodecsForFile(file).isEmpty();
     }
 
     /**

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

@@ -270,7 +270,7 @@ public static List<GenomeLoc> parseIntervalArguments(final GenomeLocParser parse
                     "interval or an interval file instead.");
         }
         // If it's a Feature-containing file, convert it to a list of intervals
-        else if ( FeatureManager.isFeatureFile(new File(arg)) ) {
+        else if ( FeatureManager.isFeatureFile(IOUtils.getPath(arg)) ) {
             rawIntervals.addAll(featureFileToIntervals(parser, arg));
         }
         // If it's an interval file, add its contents to the raw interval list
@@ -307,12 +307,11 @@ else if ( new File(arg).exists() ) {
      * Converts a Feature-containing file to a list of intervals
      *
      * @param parser GenomeLocParser for creating intervals
-     * @param featureFileName file containing Features to convert to intervals
+     * @param featureFile file containing Features to convert to intervals
      * @return a List of intervals corresponding to the locations of the Features in the provided file
      * @throws UserException.CouldNotReadInputFile if the provided file is not in a supported Feature file format
      */
-    public static List<GenomeLoc> featureFileToIntervals( final GenomeLocParser parser, final String featureFileName ) {
-        final File featureFile = new File(featureFileName);
+    public static List<GenomeLoc> featureFileToIntervals( final GenomeLocParser parser, final String featureFile ) {
 
         try ( final FeatureDataSource<? extends Feature> dataSource = new FeatureDataSource<>(featureFile) ) {
             final List<GenomeLoc> featureIntervals = new ArrayList<>();

src/test/java/org/broadinstitute/hellbender/engine/FeatureManagerUnitTest.java

@@ -89,7 +89,7 @@ public Object[][] getIsFeatureFileTestData() {
 
     @Test(dataProvider = "IsFeatureFileTestData")
     public void testIsFeatureFile( final File file, final boolean expectedIsFeatureFile ) {
-        Assert.assertEquals(FeatureManager.isFeatureFile(file), expectedIsFeatureFile, "isFeatureFile() returned incorrect result for file " + file.getAbsolutePath());
+        Assert.assertEquals(FeatureManager.isFeatureFile(file.toPath()), expectedIsFeatureFile, "isFeatureFile() returned incorrect result for file " + file.getAbsolutePath());
     }
 
     @CommandLineProgramProperties(summary = "", oneLineSummary = "", programGroup = TestProgramGroup.class)

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

@@ -3,6 +3,8 @@
 import com.google.common.collect.ImmutableMap;
 import com.google.common.collect.Lists;
 import com.google.common.collect.Sets;
+import com.google.common.jimfs.Configuration;
+import com.google.common.jimfs.Jimfs;
 import htsjdk.samtools.QueryInterval;
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMSequenceDictionary;
@@ -28,6 +30,9 @@
 import java.io.File;
 import java.io.FileWriter;
 import java.io.IOException;
+import java.nio.file.FileSystem;
+import java.nio.file.Files;
+import java.nio.file.Path;
 import java.util.*;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
@@ -1245,10 +1250,21 @@ public Object[][] loadIntervalsFromFeatureFileData() {
 
     @Test(dataProvider = "loadIntervalsFromFeatureFileData")
     public void testLoadIntervalsFromFeatureFile( final File featureFile, final List<GenomeLoc> expectedIntervals ) {
-        final GenomeLocSortedSet actualIntervals = IntervalUtils.loadIntervals(Arrays.asList(featureFile.getAbsolutePath()), IntervalSetRule.UNION, IntervalMergingRule.ALL, 0, hg19GenomeLocParser);
+        final GenomeLocSortedSet actualIntervals = IntervalUtils.loadIntervals(Collections.singletonList(featureFile.getAbsolutePath()), IntervalSetRule.UNION, IntervalMergingRule.ALL, 0, hg19GenomeLocParser);
         Assert.assertEquals(actualIntervals, expectedIntervals, "Wrong intervals loaded from Feature file " + featureFile.getAbsolutePath());
     }
 
+    @Test(dataProvider = "loadIntervalsFromFeatureFileData")
+    public void testLoadIntervalsFromFeatureFileInJimfs( final File featureFile, final List<GenomeLoc> expectedIntervals ) throws IOException {
+        try(final FileSystem fs = Jimfs.newFileSystem(Configuration.unix())){
+            final Path jimfsRootPath = fs.getRootDirectories().iterator().next();
+            final Path jimfsCopy = Files.copy(featureFile.toPath(), jimfsRootPath.resolve(featureFile.getName()));
+            final String jimfsPathString = jimfsCopy.toAbsolutePath().toUri().toString();
+            final GenomeLocSortedSet actualIntervals = IntervalUtils.loadIntervals(Collections.singletonList(jimfsPathString), IntervalSetRule.UNION, IntervalMergingRule.ALL, 0, hg19GenomeLocParser);
+            Assert.assertEquals(actualIntervals, expectedIntervals, "Wrong intervals loaded from Feature file " + jimfsPathString);
+        }
+    }
+
     // Note: because the file does not exist and all characters are allowed in contig names,
     // we will not know that this is supposed to be interpreted as a file.
     // So we'll blow up with MalformedGenomeLoc and not anything related to files