From f196cb16b24a8e86710c1be5da6f4cf81d4eb90e Mon Sep 17 00:00:00 2001
From: Ron Levine <rlevine@broadinstitute.org>
Date: Sat, 28 Jan 2017 09:17:14 -0500
Subject: [PATCH] UpdateVcfSequenceDictionary handles stdout

---
 .../vcf/UpdateVcfSequenceDictionary.java      | 13 ++++-
 .../vcf/UpdateVcfSequenceDictionaryTest.java  | 47 ++++++++++++++++---
 2 files changed, 52 insertions(+), 8 deletions(-)

diff --git a/src/main/java/picard/vcf/UpdateVcfSequenceDictionary.java b/src/main/java/picard/vcf/UpdateVcfSequenceDictionary.java
index b68f96c9f2..06e77ded19 100644
--- a/src/main/java/picard/vcf/UpdateVcfSequenceDictionary.java
+++ b/src/main/java/picard/vcf/UpdateVcfSequenceDictionary.java
@@ -36,6 +36,7 @@
 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;
@@ -43,6 +44,8 @@
 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.
@@ -56,7 +59,7 @@
         programGroup = VcfOrBcf.class
 )
 public class UpdateVcfSequenceDictionary extends CommandLineProgram {
-     @Option(shortName = StandardOptionDefinitions.INPUT_SHORT_NAME, doc = "Input VCF")
+    @Option(shortName = StandardOptionDefinitions.INPUT_SHORT_NAME, doc = "Input VCF")
     public File INPUT;
 
     @Option(shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME, doc = "Output VCF to be written.")
@@ -89,7 +92,13 @@ protected int doWork() {
         if (CREATE_INDEX)
             builder.setOption(Options.INDEX_ON_THE_FLY);
 
-        final VariantContextWriter vcfWriter = builder.setOutputFile(OUTPUT).build();
+        try {
+            builder.setOutputStream(new FileOutputStream(OUTPUT));
+        } catch (final FileNotFoundException ex ) {
+            throw new PicardException("Could not open " + OUTPUT.getAbsolutePath() + ": " + ex.getMessage(), ex);
+        }
+
+        final VariantContextWriter vcfWriter = builder.build();
         fileHeader.setSequenceDictionary(samSequenceDictionary);
         vcfWriter.writeHeader(fileHeader);
 
diff --git a/src/test/java/picard/vcf/UpdateVcfSequenceDictionaryTest.java b/src/test/java/picard/vcf/UpdateVcfSequenceDictionaryTest.java
index 3f8f4d9bb9..d26d459708 100644
--- a/src/test/java/picard/vcf/UpdateVcfSequenceDictionaryTest.java
+++ b/src/test/java/picard/vcf/UpdateVcfSequenceDictionaryTest.java
@@ -28,8 +28,13 @@
 import org.testng.Assert;
 import org.testng.annotations.AfterClass;
 import org.testng.annotations.Test;
+import org.testng.annotations.DataProvider;
 
 import java.io.File;
+import java.io.FileDescriptor;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.lang.reflect.Field;
 
 /**
  * @author George Grant
@@ -37,28 +42,58 @@
 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 File STD_OUT_FILE = new File(OUTPUT_DATA_PATH, "stdout.vcf");
+    private static final String STD_OUT_NAME = "/dev/stdout";
 
     @AfterClass
     public void teardown() {
         IOUtil.deleteDirectoryTree(OUTPUT_DATA_PATH);
     }
 
-    @Test
-    public void testUpdateVcfSequenceDictionary() {
-        final File input = new File(TEST_DATA_PATH, "vcfFormatTest.vcf");
+    @DataProvider(name = "OutputFiles")
+    public static Object[][] outputFies() {
+
+        return new Object[][] {
+                {OUTPUT_DATA_PATH + "updateVcfSequenceDictionaryTest-delete-me.vcf"},
+                {STD_OUT_NAME}
+        };
+    }
+
+    @Test(dataProvider = "OutputFiles")
+    public void testUpdateVcfSequenceDictionary(final String outputFileName) throws IOException, NoSuchFieldException, IllegalAccessException {
+        File input = new File(TEST_DATA_PATH, "vcfFormatTest.vcf");
         // vcfFormatTest.bad_dict.vcf is a vcf with two (2) ##contig lines deleted
         final File samSequenceDictionaryVcf = new File(TEST_DATA_PATH, "vcfFormatTest.bad_dict.vcf");
-        final File outputFile = new File(OUTPUT_DATA_PATH, "updateVcfSequenceDictionaryTest-delete-me.vcf");
-
+        File outputFile = new File(outputFileName);
         outputFile.deleteOnExit();
 
         final UpdateVcfSequenceDictionary updateVcfSequenceDictionary = new UpdateVcfSequenceDictionary();
+
+        if (outputFileName.equals(STD_OUT_NAME)) {
+
+            final FileOutputStream stream = new FileOutputStream(STD_OUT_FILE);
+
+            // Ugliness required to write to a stream given as a string on the commandline.
+            // Since the actual fd number is private inside FileDescriptor, needs reflection
+            // in order to pull it out.
+
+            final Field fdField = FileDescriptor.class.getDeclaredField("fd");
+            fdField.setAccessible(true);
+            updateVcfSequenceDictionary.OUTPUT = new File("/dev/fd/" + fdField.getInt(stream.getFD()));
+
+        } else {
+            final FileOutputStream stream = null;
+            updateVcfSequenceDictionary.OUTPUT = outputFile;
+        }
         updateVcfSequenceDictionary.INPUT = input;
         updateVcfSequenceDictionary.SEQUENCE_DICTIONARY = samSequenceDictionaryVcf;
-        updateVcfSequenceDictionary.OUTPUT = outputFile;
 
         Assert.assertEquals(updateVcfSequenceDictionary.instanceMain(new String[0]), 0);
 
+        if (outputFileName.equals(STD_OUT_NAME)) {
+            outputFile = STD_OUT_FILE;
+        }
+
         IOUtil.assertFilesEqual(samSequenceDictionaryVcf, outputFile);
 
         // A little extra checking.