From 721e8cb67981f253442b0768ff55fceefa588c99 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 18 Nov 2010 18:54:59 +0000
Subject: [PATCH] VariantsToTable now supports wildcard captures.  -F PREFIX*
 now captures all fields that begin with PREFIX, output as a comma-separated
 list of unique values.  Added integration test for VariantsToTable since I
 find it so useful.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4706 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/variantutils/VariantsToTable.java | 18 ++++++-
 .../VariantToTableIntegrationTest.java        | 48 +++++++++++++++++++
 2 files changed, 65 insertions(+), 1 deletion(-)
 create mode 100644 java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantToTableIntegrationTest.java

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
index 40678ec58..26079d94b 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
@@ -119,7 +119,6 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
             for ( VariantContext vc : vcs) {
                 if ( (! ignoreMultiAllelic || vc.isBiallelic()) && ( showFiltered || vc.isNotFiltered() ) ) {
                     List<String> vals = extractFields(vc, fieldsToTake);
-
                     out.println(Utils.join("\t", vals));
                 }
             }
@@ -134,6 +133,10 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
         }
     }
 
+    private static final boolean isWildCard(String s) {
+        return s.endsWith("*");
+    }
+
     public static List<String> extractFields(VariantContext vc, List<String> fields) {
         List<String> vals = new ArrayList<String>();
 
@@ -144,6 +147,19 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
                 val = getters.get(field).get(vc);
             } else if ( vc.hasAttribute(field) ) {
                 val = vc.getAttributeAsString(field);
+            } else if ( isWildCard(field) ) {
+                Set<String> wildVals = new HashSet<String>();
+                for ( Map.Entry<String,Object> elt : vc.getAttributes().entrySet()) {
+                    if ( elt.getKey().startsWith(field.substring(0, field.length() - 1)) ) {
+                        wildVals.add(elt.getValue().toString());
+                    }
+                }
+
+                if ( wildVals.size() > 0 ) {
+                    List<String> toVal = new ArrayList<String>(wildVals);
+                    Collections.sort(toVal);
+                    val = Utils.join(",", toVal);
+                }
             }
 
             vals.add(val);
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantToTableIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantToTableIntegrationTest.java
new file mode 100644
index 000000000..a1efbf4a4
--- /dev/null
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/VariantToTableIntegrationTest.java
@@ -0,0 +1,48 @@
+/*
+ * Copyright (c) 2010, 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.broadinstitute.sting.utils.exceptions.UserException;
+import org.testng.annotations.Test;
+import org.testng.annotations.DataProvider;
+
+import java.util.*;
+import java.io.File;
+
+public class VariantToTableIntegrationTest extends WalkerTest {
+    @Test(enabled = true)
+    public void testComplexVariantsToTable() {
+        // functional class is a wild card operator
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-R " + hg18Reference +
+                        " -B:eval,vcf " + validationDataLocation + "/soap_gatk_annotated.vcf" +
+                        " -T VariantsToTable" +
+                        " -F CHROM,POS,ID,REF,ALT,QUAL,FILTER,TRANSITION,DP,SB,set,RankSumP,refseq.functionalClass*" +
+                        " -L chr1 -o %s",
+                Arrays.asList("b2a3712c1bfad8f1383ffada8b5017ba"));
+        executeTest("testComplexVariantsToTable", spec).getFirst();
+    }
+}
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