Merge pull request #512 from broadinstitute/jt_multi_allele_fix

Fix the broken AD field for multi-allelic variants

protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java

@@ -321,6 +321,18 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         executeTest("test select from multi allelic with excludeNonVariants --" + testfile, spec);
     }
 
+    @Test
+    public void testMultiAllelicAnnotationOrdering() {
+        String testfile = privateTestDir + "multi-allelic-ordering.vcf";
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T SelectVariants -R " + b37KGReference + " -o %s --no_cmdline_in_header " +
+                        "-sn SAMPLE-CC -sn SAMPLE-CT -sn SAMPLE-CA --excludeNonVariants --variant " + testfile,
+                1,
+                Arrays.asList("8fe7cdca8638461909262cb0769b2527")
+        );
+        executeTest("test multi allelic annotation ordering --" + testfile, spec);
+    }
+
     @Test()
     public void testFileWithoutInfoLineInHeader() {
         testFileWithoutInfoLineInHeader("testFileWithoutInfoLineInHeader", IllegalStateException.class);

public/repo/net/sf/picard/1.107.1683/picard-1.107.1683.pom

@@ -3,23 +3,23 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>net.sf</groupId>
     <artifactId>picard</artifactId>
-    <version>1.107.1676</version>
+    <version>1.107.1683</version>
     <name>picard</name>
     <dependencies>
         <dependency>
             <groupId>net.sf</groupId>
             <artifactId>sam</artifactId>
-            <version>1.107.1676</version>
+            <version>1.107.1683</version>
         </dependency>
         <dependency>
             <groupId>org.broadinstitute</groupId>
             <artifactId>variant</artifactId>
-            <version>1.107.1676</version>
+            <version>1.107.1683</version>
         </dependency>
         <dependency>
             <groupId>org.broad</groupId>
             <artifactId>tribble</artifactId>
-            <version>1.107.1676</version>
+            <version>1.107.1683</version>
         </dependency>
         <!-- TODO: Picard is using a custom zip with just ant's BZip2 classes. See also: http://www.kohsuke.org/bzip2 -->
         <dependency>

public/repo/net/sf/sam/1.107.1683/sam-1.107.1683.pom

@@ -3,7 +3,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>net.sf</groupId>
     <artifactId>sam</artifactId>
-    <version>1.107.1676</version>
+    <version>1.107.1683</version>
     <name>sam-jdk</name>
     <dependencies>
         <dependency>

public/repo/org/broad/tribble/1.107.1683/tribble-1.107.1683.pom

@@ -3,13 +3,13 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>org.broad</groupId>
     <artifactId>tribble</artifactId>
-    <version>1.107.1676</version>
+    <version>1.107.1683</version>
     <name>tribble</name>
     <dependencies>
         <dependency>
             <groupId>net.sf</groupId>
             <artifactId>sam</artifactId>
-            <version>1.107.1676</version>
+            <version>1.107.1683</version>
         </dependency>
     </dependencies>
 </project>

public/repo/org/broadinstitute/variant/1.107.1683/variant-1.107.1683.pom

@@ -3,18 +3,18 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>org.broadinstitute</groupId>
     <artifactId>variant</artifactId>
-    <version>1.107.1676</version>
+    <version>1.107.1683</version>
     <name>variant</name>
     <dependencies>
         <dependency>
             <groupId>org.broad</groupId>
             <artifactId>tribble</artifactId>
-            <version>1.107.1676</version>
+            <version>1.107.1683</version>
         </dependency>
         <dependency>
             <groupId>net.sf</groupId>
             <artifactId>sam</artifactId>
-            <version>1.107.1676</version>
+            <version>1.107.1683</version>
         </dependency>
         <dependency>
             <groupId>org.apache.commons</groupId>

public/sting-root/pom.xml

@@ -40,7 +40,7 @@
         <test.args>-Xmx${test.maxmemory}</test.args>
 
         <!-- Version numbers for picard sam-jdk. Usually kept in sync. -->
-        <picard.public.version>1.107.1676</picard.public.version>
+        <picard.public.version>1.107.1683</picard.public.version>
         <sam.version>${picard.public.version}</sam.version>
         <picard.version>${picard.public.version}</picard.version>
         <variant.version>${picard.public.version}</variant.version>