From be6a549e7b4553190df865044d456aaac4842ff0 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 24 Nov 2009 02:34:48 +0000
Subject: [PATCH] Added the capability to allow expressions in an integration
 test command (i.e. -filter 'foo') by escaping them in the command.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2132 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../org/broadinstitute/sting/utils/Utils.java |  8 +++++++
 .../org/broadinstitute/sting/WalkerTest.java  | 22 ++++++++++++++++++-
 2 files changed, 29 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/utils/Utils.java b/java/src/org/broadinstitute/sting/utils/Utils.java
index 36fa44539..e41aa817d 100755
--- a/java/src/org/broadinstitute/sting/utils/Utils.java
+++ b/java/src/org/broadinstitute/sting/utils/Utils.java
@@ -541,6 +541,14 @@ public class Utils {
         return new Pair<Double, Integer>(max, index);
     }
 
+    public static String[] concatArrays(String[] A, String[] B) {
+       String[] C = new String[A.length + B.length];
+       System.arraycopy(A, 0, C, 0, A.length);
+       System.arraycopy(B, 0, C, A.length, B.length);
+       return C;
+    }
+
+
     /** Returns indices of all occurrences of the specified symbol in the string */
     public static int[] indexOfAll(String s, int ch) {
         int[] pos = new int[64];
diff --git a/java/test/org/broadinstitute/sting/WalkerTest.java b/java/test/org/broadinstitute/sting/WalkerTest.java
index e508e4953..bc53720d9 100755
--- a/java/test/org/broadinstitute/sting/WalkerTest.java
+++ b/java/test/org/broadinstitute/sting/WalkerTest.java
@@ -126,13 +126,33 @@ public class WalkerTest extends BaseTest {
         System.out.println(String.format("Executing test %s with GATK arguments: %s", name, args));
 
         CommandLineGATK instance = new CommandLineGATK();
-        CommandLineExecutable.start(instance, args.split(" "));
+        String[] command;
+
+        // special case for ' and " so we can allow expressions
+        if ( args.indexOf('\'') != -1 )
+            command = escapeExpressions(args, "'");
+        else if ( args.indexOf('\"') != -1 )
+            command = escapeExpressions(args, "\"");
+        else
+            command = args.split(" ");
+
+        CommandLineExecutable.start(instance, command);
 
         if ( CommandLineExecutable.result != 0 ) {
             throw new RuntimeException("Error running the GATK with arguments: " + args);
         }
 
         return new Pair<List<File>, List<String>>(tmpFiles, assertMatchingMD5s(name, tmpFiles, spec.md5s));
+    }    
+
+    private static String[] escapeExpressions(String args, String delimiter) {
+        String[] command = {};
+        String[] split = args.split(delimiter);
+        for (int i = 0; i < split.length - 1; i+=2) {
+            command = Utils.concatArrays(command, split[i].trim().split(" "));
+            command = Utils.concatArrays(command, new String[] { split[i+1] } );
+        }
+        return Utils.concatArrays(command, split[split.length-1].trim().split(" "));
     }
 
     @Test