Very simple integration tests for basic VCF streaming functionality.

Rather than try to fork the integration test process to get a pipe source
and sink, creates a new named pipe by Runtime.exec()ing the 'mkfifo' shell
command.  We'll see whether this proves to be a reliable method for testing
streaming.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5028 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/commandline/ParsingEngine.java

@@ -556,7 +556,7 @@ class TooManyValuesForArgumentException extends ArgumentException {
     private static String formatArguments( Collection<ArgumentMatch> arguments ) {
         StringBuilder sb = new StringBuilder();
         for( ArgumentMatch argument: arguments )
-            sb.append( String.format("%nArgument '%s' has to many values: %s.", argument.label, Arrays.deepToString(argument.values().toArray())) );
+            sb.append( String.format("%nArgument '%s' has too many values: %s.", argument.label, Arrays.deepToString(argument.values().toArray())) );
         return sb.toString();
     }
 }

java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VCFStreamingIntegrationTest.java

@@ -0,0 +1,108 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.walkers.variantutils;
+
+import org.broadinstitute.sting.WalkerTest;
+import org.testng.annotations.Test;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.Collections;
+
+/**
+ * Test the generic VCF streaming workflow with a few basic VCF routines.
+ */
+public class VCFStreamingIntegrationTest extends WalkerTest {
+    @Test
+    public void testSimpleVCFStreaming() throws IOException {
+        // Create a FIFO.  This seems to be the only way to create an interprocess FIFO in Java (java.nio.Pipe is intraprocess only).
+        File tmpFifo = File.createTempFile("vcfstreaming","");
+        tmpFifo.deleteOnExit();
+        Runtime.getRuntime().exec(new String[] {"mkfifo",tmpFifo.getAbsolutePath()});
+
+
+        // Copy VCF data from the test file into the FIFO.
+        String testFile = validationDataLocation + "yri.trio.gatk.ug.head.vcf";
+        FileInputStream inputStream = new FileInputStream(testFile);
+        FileOutputStream outputStream = new FileOutputStream(tmpFifo);
+        outputStream.getChannel().transferFrom(inputStream.getChannel(),0,inputStream.getChannel().size());
+        outputStream.close();
+        inputStream.close();
+
+        WalkerTestSpec spec = new WalkerTestSpec(
+            "-T SelectVariants " +
+                    "-R " + b36KGReference +
+                    "-B:variant,vcf " + tmpFifo.getAbsolutePath() +
+                    " -rit STREAM --NO_HEADER " + 
+                    "-o %s",
+            1,
+            Arrays.asList("2cae3d16f9ed00b07d87e9c49272d877")
+        );
+
+        executeTest("testSimpleVCFStreaming", spec);
+
+    }
+
+    @Test
+    public void testVCFStreamingChain() throws IOException {
+        // Create a FIFO.  This seems to be the only way to create an interprocess FIFO in Java (java.nio.Pipe is intraprocess only).
+        File tmpFifo = File.createTempFile("vcfstreaming","");
+        tmpFifo.deleteOnExit();
+        Runtime.getRuntime().exec(new String[] {"mkfifo",tmpFifo.getAbsolutePath()});
+
+        String testFile = validationDataLocation + "yri.trio.gatk.ug.head.vcf";
+
+        // Output select to FIFO
+        WalkerTestSpec selectTestSpec = new WalkerTestSpec(
+            "-T SelectVariants " +
+            "-R " + b36KGReference + " " +
+            "-B:variant,vcf " + testFile + " " +
+            "--NO_HEADER " +
+            "-select 'QD > 2.0' " +
+            "-o " + tmpFifo.getAbsolutePath(),
+            0,
+            Collections.<String>emptyList()
+        );
+        executeTest("testVCFStreamingChain", selectTestSpec);
+
+        // Eval compare the full set to the subselection.
+        selectTestSpec = new WalkerTestSpec(
+            "-T VariantEval " +
+            "-R " + b36KGReference + " " +
+            "-B:eval,vcf " + testFile + " " +
+            "-B:comp,vcf " + tmpFifo.getAbsolutePath() + " " +
+            "-E CompOverlap -noStandard " +
+            "-rit STREAM " +
+            "-reportType CSV -o %s",
+            1,
+            Arrays.asList("f7df3ac0777b1a45aa7a58228a290600")
+        );
+        executeTest("testVCFStreamingChain", selectTestSpec);
+
+    }
+}