fixup

Author: lbergelson

src/main/java/org/broadinstitute/hellbender/tools/genomicsdb/GenomicsDBImport.java

@@ -394,7 +394,7 @@ public final class GenomicsDBImport extends GATKTool {
 
     //executor service used when vcfInitializerThreads > 1
     private ExecutorService inputPreloadExecutorService;
-    
+
     /**
      * Get the largest interval per contig that contains the intervals specified on the command line.
      * @param getIntervals intervals to be transformed

src/test/java/org/broadinstitute/hellbender/tools/spark/PileupSparkIntegrationTest.java

@@ -27,7 +27,7 @@ public Object[][] shuffleParameters() {
 
     @Test(dataProvider = "shuffle")
     public void testSimplePileup(boolean useShuffle) throws Exception {
-        final File out = createTempFile();
+        final File out = createTempDir();
         final ArgumentsBuilder args = new ArgumentsBuilder();
         args.addRaw("--input");
         args.addRaw(NA12878_20_21_WGS_bam);
@@ -47,7 +47,7 @@ public void testSimplePileup(boolean useShuffle) throws Exception {
 
     @Test(dataProvider = "shuffle")
     public void testVerbosePileup(boolean useShuffle) throws Exception {
-        final File out = createTempFile();
+        final File out = createTempDir();
         final ArgumentsBuilder args = new ArgumentsBuilder();
         args.addRaw("--input");
         args.addRaw(NA12878_20_21_WGS_bam);
@@ -68,7 +68,7 @@ public void testVerbosePileup(boolean useShuffle) throws Exception {
 
     @Test(dataProvider = "shuffle")
     public void testFeaturesPileup(boolean useShuffle) throws Exception {
-        final File out = createTempFile();
+        final File out = createTempDir();
         final ArgumentsBuilder args = new ArgumentsBuilder();
         args.addRaw("--input");
         args.addRaw(NA12878_20_21_WGS_bam);
@@ -89,7 +89,7 @@ public void testFeaturesPileup(boolean useShuffle) throws Exception {
 
     @Test(dataProvider = "shuffle")
     public void testInsertLengthPileup(boolean useShuffle) throws Exception {
-        final File out = createTempFile();
+        final File out = createTempDir();
         final ArgumentsBuilder args = new ArgumentsBuilder();
         args.addRaw("--input");
         args.addRaw(NA12878_20_21_WGS_bam);
@@ -122,7 +122,7 @@ public void testFeaturesPileupHdfs(boolean useShuffle) throws Exception {
             cluster.getFileSystem().copyFromLocalFile(new Path(dbsnp_138_b37_20_21_vcf), vcfPath);
             cluster.getFileSystem().copyFromLocalFile(new Path(dbsnp_138_b37_20_21_vcf + ".idx"), idxPath);
 
-            final File out = createTempFile();
+            final File out = createTempDir();
             final ArgumentsBuilder args = new ArgumentsBuilder();
             args.addRaw("--input");
             args.addRaw(NA12878_20_21_WGS_bam);

src/testUtils/java/org/broadinstitute/hellbender/testutils/BaseTest.java

@@ -353,6 +353,15 @@ public static File createTempDir(final String prefix){
         return IOUtils.createTempDir(prefix);
     }
 
+    /**
+     * Creates an empty temp directory which will be deleted on exit after tests are complete
+     *
+     * @return an empty directory will be deleted after the program exits
+     */
+    public static File createTempDir(){
+        return createTempDir("tmp");
+    }
+
     /**
      * Log this message so that it shows up inline during output as well as in html reports
      */