initial VariantEvalWalker test. More to be added soon...

Also fixed the case where MD5 sums had leading zero's clipped off

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1551 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java

@@ -52,6 +52,9 @@ public class VariantEvalWalker extends RefWalker<Integer, Integer> {
     @Argument(fullName="extensiveSubsets", shortName = "A", doc="If provided, output will be calculated over a lot of subsets, by default we only operate over all variants", required=false)
     public boolean extensiveSubsets = false;
 
+    @Argument(fullName="supressDateInformation", doc="This flag indicates that we want to suppress the date information from the output, so that if can be diff'ed against previous evals.", required=false)
+    public boolean supressDateInformation = false;
+
     String analysisFilenameBase = null;
 
     final String knownSNPDBName = "dbSNP";
@@ -253,8 +256,8 @@ public class VariantEvalWalker extends RefWalker<Integer, Integer> {
             //stream.printf("%s Analysis set       %s%n", analysisSetName, , analysisSetName);
             stream.printf("%sAnalysis name      %s%n", header, analysis.getName());
             stream.printf("%sAnalysis params    %s%n", header, Utils.join(" ", analysis.getParams()));
-            stream.printf("%sAnalysis class     %s%n", header, analysis);
+            stream.printf("%sAnalysis class     %s%n", header, analysis.getClass().getName());
-            stream.printf("%sAnalysis time      %s%n", header, now);
+            if (!supressDateInformation) stream.printf("%sAnalysis time      %s%n", header, now);
             for ( String line : analysis.done()) {
                 stream.printf("%s%s%n", header, line);
             }

java/test/org/broadinstitute/sting/WalkerTest.java

@@ -1,22 +1,20 @@
 package org.broadinstitute.sting;
 
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.Pair;
-import org.broadinstitute.sting.utils.cmdLine.ArgumentException;
-import org.junit.Test;
-import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.CommandLineExecutable;
-
-import java.io.*;
-import java.util.Arrays;
-import java.util.List;
-import java.util.ArrayList;
-import java.security.MessageDigest;
-import java.math.BigInteger;
-
 import junit.framework.Assert;
+import org.broadinstitute.sting.gatk.CommandLineExecutable;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
+import org.broadinstitute.sting.utils.Pair;
+import org.broadinstitute.sting.utils.Utils;
+import org.junit.Test;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.math.BigInteger;
+import java.security.MessageDigest;
+import java.util.ArrayList;
+import java.util.List;
 
 public class WalkerTest extends BaseTest {
     public String assertMatchingMD5(final String name, final File resultsFile, final String expectedMD5 ) {
@@ -25,13 +23,13 @@ public class WalkerTest extends BaseTest {
             byte[] thedigest = MessageDigest.getInstance("MD5").digest(bytesOfMessage);
             BigInteger bigInt = new BigInteger(1, thedigest);
             String filemd5sum = bigInt.toString(16);
-
+            while (filemd5sum.length() < 32) filemd5sum = "0" + filemd5sum; // pad to length 32
             if ( parameterize() || expectedMD5.equals("") ) {
                 logger.warn(String.format("PARAMETERIZATION[%s]: file %s has md5 = %s, stated expectation is %s, equal? = %b",
                         name, resultsFile, filemd5sum, expectedMD5, filemd5sum.equals(expectedMD5)));
             } else {
                 logger.warn(String.format("Checking MD5 for %s [calculated=%s, expected=%s]", resultsFile, filemd5sum, expectedMD5));
-                Assert.assertEquals(name + "Mismatching MD5s", expectedMD5, filemd5sum);
+                Assert.assertEquals(name + " Mismatching MD5s", expectedMD5, filemd5sum);
                 logger.warn(String.format("  => %s PASSED", name));
             }
 

java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerTest.java

@@ -0,0 +1,43 @@
+package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
+
+import org.broadinstitute.sting.WalkerTest;
+import org.junit.Test;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * @author aaron
+ *         <p/>
+ *         Class VariantEvalWalkerTest
+ *         <p/>
+ *         test out the variant eval walker under a bunch of different runtime conditions.
+ */
+public class VariantEvalWalkerTest extends WalkerTest {
+
+    @Test
+    public void emptyTest() {
+
+    }
+
+    @Test
+    public void testEvalVariantROD() {
+        List <String> md5 = new ArrayList<String>();
+        md5.add("094c0adb8e4ae4de424f26482fd43152");
+
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-R /broad/1KG/reference/human_b36_both.fasta" +
+                        " --rodBind eval,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.variants.geli.calls" +
+                        " -T VariantEval" +
+                        " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" +
+                        " -L 1:10,000,000-11,000,000" +
+                        " --outerr %s" +
+                        " --supressDateInformation",
+                1, // just one output file
+                md5);
+        List<File> result = executeTest("testEvalVariantROD", spec).getFirst();
+
+    }
+}
+