Test for /dev/stdout

broadinstitute · Feb 3, 2017 · ef13c61 · ef13c61
1 parent f005494
commit ef13c61
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Showing 2 changed files with 17 additions and 12 deletions.
diff --git a/src/main/java/picard/vcf/UpdateVcfSequenceDictionary.java b/src/main/java/picard/vcf/UpdateVcfSequenceDictionary.java
@@ -36,16 +36,13 @@
 import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder;
 import htsjdk.variant.vcf.VCFFileReader;
 import htsjdk.variant.vcf.VCFHeader;
-import picard.PicardException;
 import picard.cmdline.CommandLineProgram;
 import picard.cmdline.CommandLineProgramProperties;
 import picard.cmdline.Option;
 import picard.cmdline.StandardOptionDefinitions;
 import picard.cmdline.programgroups.VcfOrBcf;
 
 import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
 
 /**
  * Takes a VCF file and a Sequence Dictionary (from a variety of file types) and updates the Sequence Dictionary in VCF.
@@ -71,6 +68,8 @@ public class UpdateVcfSequenceDictionary extends CommandLineProgram {
 
     private final Log log = Log.getInstance(UpdateVcfSequenceDictionary.class);
 
+    static final String STD_OUT = "/dev/stdout";
+
     public static void main(final String[] args) {
         new UpdateVcfSequenceDictionary().instanceMainWithExit(args);
     }
@@ -92,10 +91,12 @@ protected int doWork() {
         if (CREATE_INDEX)
             builder.setOption(Options.INDEX_ON_THE_FLY);
 
-        try {
-            builder.setOutputStream(new FileOutputStream(OUTPUT, false));
-        } catch (final FileNotFoundException ex ) {
-            throw new PicardException("Could not open " + OUTPUT + ": " + ex.getMessage(), ex);
+        // handle stdout
+        if ( OUTPUT.getPath().equals(STD_OUT) ) {
+            builder.setOutputStream(System.out);
+        }
+        else {
+            builder.setOutputFile(OUTPUT);
         }
 
         final VariantContextWriter vcfWriter = builder.build();

diff --git a/src/test/java/picard/vcf/UpdateVcfSequenceDictionaryTest.java b/src/test/java/picard/vcf/UpdateVcfSequenceDictionaryTest.java
@@ -40,7 +40,7 @@
 public class UpdateVcfSequenceDictionaryTest {
     private static final File TEST_DATA_PATH = new File("testdata/picard/vcf/");
     private static final File OUTPUT_DATA_PATH = IOUtil.createTempDir("UpdateVcfSequenceDictionaryTest", null);
-    private static final String STD_OUT_FILE_NAME = OUTPUT_DATA_PATH + "/stdout.vcf";
+    private static final File STD_OUT_FILE = new File(OUTPUT_DATA_PATH, "stdout.vcf");
 
     @AfterClass
     public void teardown() {
@@ -52,7 +52,7 @@ public static Object[][] outputFies() {
 
         return new Object[][] {
                 {OUTPUT_DATA_PATH + "updateVcfSequenceDictionaryTest-delete-me.vcf"},
-                {STD_OUT_FILE_NAME}
+                {UpdateVcfSequenceDictionary.STD_OUT}
         };
     }
 
@@ -64,9 +64,9 @@ public void testUpdateVcfSequenceDictionary(final String outputFileName) throws
         File outputFile = new File(outputFileName);
         outputFile.deleteOnExit();
 
-        // Reassign the standard output to an ooutput stream file
-        if ( outputFileName.equals(STD_OUT_FILE_NAME) ) {
-            System.setOut(new PrintStream(STD_OUT_FILE_NAME));
+        // Stream standard output a file
+        if ( outputFileName.equals(UpdateVcfSequenceDictionary.STD_OUT) ) {
+            System.setOut(new PrintStream(STD_OUT_FILE));
         }
 
         final UpdateVcfSequenceDictionary updateVcfSequenceDictionary = new UpdateVcfSequenceDictionary();
@@ -76,6 +76,10 @@ public void testUpdateVcfSequenceDictionary(final String outputFileName) throws
 
         Assert.assertEquals(updateVcfSequenceDictionary.instanceMain(new String[0]), 0);
 
+        if ( outputFileName.equals(UpdateVcfSequenceDictionary.STD_OUT) ) {
+            outputFile = STD_OUT_FILE;
+        }
+
         IOUtil.assertFilesEqual(samSequenceDictionaryVcf, outputFile);
 
         // A little extra checking.