Modified VariantContextWriterBuilder to automatically set output type… (

#495)

Modified VariantContextWriterBuilder to automatically set output type to VCF_STREAM when the output file exists but is not a symlink, regular file or directory.

src/main/java/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilder.java

@@ -157,7 +157,7 @@ public VariantContextWriterBuilder setReferenceDictionary(final SAMSequenceDicti
     public VariantContextWriterBuilder setOutputFile(final File outFile) {
         this.outFile = outFile;
         this.outStream = null;
-        determineOutputTypeFromFilename();
+        this.outType = determineOutputTypeFromFile(outFile);
         return this;
     }
 
@@ -169,10 +169,7 @@ public VariantContextWriterBuilder setOutputFile(final File outFile) {
      * @return this <code>VariantContextWriterBuilder</code>
      */
     public VariantContextWriterBuilder setOutputFile(final String outFile) {
-        this.outFile = new File(outFile);
-        this.outStream = null;
-        determineOutputTypeFromFilename();
-        return this;
+        return setOutputFile(new File(outFile));
     }
 
     /**
@@ -465,28 +462,43 @@ else if (STREAM_TYPES.contains(this.outType))
         return writer;
      }
 
-    private void determineOutputTypeFromFilename() {
-        if (isBCF(this.outFile)) {
-            this.outType = OutputType.BCF;
-        } else if (isCompressedVCF(this.outFile)) {
-            this.outType = OutputType.BLOCK_COMPRESSED_VCF;
-        } else if (isVCF(this.outFile)) {
-            this.outType = OutputType.VCF;
+    /**
+     * Attempts to determine the type of file/data to write based on the File path being
+     * written to. Will attempt to determine using the logical filename; if that fails it will
+     * attempt to resolve any symlinks and try again.  If that fails, and the output file exists
+     * but is neither a file or directory then VCF_STREAM is returned.
+     */
+    protected static OutputType determineOutputTypeFromFile(final File f) {
+        if (isBCF(f)) {
+            return OutputType.BCF;
+        } else if (isCompressedVCF(f)) {
+            return OutputType.BLOCK_COMPRESSED_VCF;
+        } else if (isVCF(f)) {
+            return OutputType.VCF;
         }
         else {
-            this.outType = OutputType.UNSPECIFIED;
+            // See if we have a special file (device, named pipe, etc.)
+            final File canonical = new File(IOUtil.getFullCanonicalPath(f));
+            if (!canonical.equals(f)) {
+                return determineOutputTypeFromFile(canonical);
+            }
+            else if (f.exists() && !f.isFile() && !f.isDirectory()) {
+                return OutputType.VCF_STREAM;
+            } else {
+                return OutputType.UNSPECIFIED;
+            }
         }
     }
 
-    private boolean isVCF(final File outFile) {
+    private static boolean isVCF(final File outFile) {
         return outFile != null && outFile.getName().endsWith(".vcf");
     }
 
-    private boolean isBCF(final File outFile) {
+    private static boolean isBCF(final File outFile) {
         return outFile != null && outFile.getName().endsWith(".bcf");
     }
 
-    private boolean isCompressedVCF(final File outFile) {
+    private static boolean isCompressedVCF(final File outFile) {
         if (outFile == null)
             return false;
 

src/test/java/htsjdk/variant/variantcontext/writer/VariantContextWriterBuilderUnitTest.java

@@ -28,20 +28,19 @@
 import htsjdk.samtools.Defaults;
 import htsjdk.samtools.SAMSequenceDictionary;
 import htsjdk.samtools.util.BlockCompressedOutputStream;
+import htsjdk.samtools.util.RuntimeIOException;
 import htsjdk.tribble.AbstractFeatureReader;
 import htsjdk.tribble.Tribble;
 import htsjdk.tribble.util.TabixUtils;
 import htsjdk.variant.VariantBaseTest;
-import htsjdk.variant.variantcontext.writer.Options;
+import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder.OutputType;
 import org.testng.Assert;
 import org.testng.annotations.BeforeSuite;
 import org.testng.annotations.Test;
 
-import java.io.BufferedOutputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.File;
-import java.io.IOException;
-import java.io.OutputStream;
+import java.io.*;
+import java.nio.file.Files;
+import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -122,6 +121,29 @@ public void testSetOutputFile() throws IOException {
         Assert.assertTrue(writer instanceof BCF2Writer, "testSetOutputFile BCF File");
     }
 
+    @Test
+    public void testDetermineOutputType() {
+        Assert.assertEquals(OutputType.VCF, VariantContextWriterBuilder.determineOutputTypeFromFile(this.vcf));
+        Assert.assertEquals(OutputType.BCF, VariantContextWriterBuilder.determineOutputTypeFromFile(this.bcf));
+        Assert.assertEquals(OutputType.VCF_STREAM, VariantContextWriterBuilder.determineOutputTypeFromFile(new File("/dev/stdout")));
+        for (final File f: this.blockCompressedVCFs) {
+            Assert.assertEquals(OutputType.BLOCK_COMPRESSED_VCF, VariantContextWriterBuilder.determineOutputTypeFromFile(f));
+        }
+
+        // Test symlinking
+        try {
+            final Path link = Files.createTempFile("foo.", ".tmp");
+            Files.deleteIfExists(link);
+            Files.createSymbolicLink(link, this.vcf.toPath());
+            link.toFile().deleteOnExit();
+            Assert.assertEquals(OutputType.VCF, VariantContextWriterBuilder.determineOutputTypeFromFile(link.toFile()));
+            link.toFile().delete();
+        }
+        catch (final IOException ioe) {
+            throw new RuntimeIOException(ioe);
+        }
+    }
+
     @Test
     public void testSetOutputFileType() {
         final VariantContextWriterBuilder builder = new VariantContextWriterBuilder()
@@ -374,4 +396,4 @@ public void testModifyOption() {
             Assert.assertFalse(builder.isOptionSet(option)); // has been unset
         }
     }
-}
+}