Rev the latest version of Picard.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3575 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFile.java

@@ -82,6 +82,14 @@ public class IndexedFastaSequenceFile implements ReferenceSequenceFile {
         sanityCheckDictionaryAgainstIndex();
     }
 
+    /**
+     * Always returns true for this implementation.
+     * @return True.
+     */
+    public boolean isIndexed() {
+        return true;
+    }
+
     /**
      * Loads a dictionary, if available.
      * @param fastaFile File to check for a match.

java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusViewTemplate.java

@@ -278,10 +278,20 @@ public abstract class LocusViewTemplate extends BaseTest {
                 return dictionary;
             }
 
+            public boolean isIndexed() { return false; }
+
             public ReferenceSequence nextSequence() {
                 throw new UnsupportedOperationException("Fake implementation doesn't support a getter");
             }
 
+            public ReferenceSequence getSequence( String contig ) {
+                throw new UnsupportedOperationException("Fake implementation doesn't support a getter");
+            }
+
+            public ReferenceSequence getSubsequenceAt( String contig, long start, long stop ) {
+                throw new UnsupportedOperationException("Fake implementation doesn't support a getter");
+            }
+
             public void reset() {
                 return;
             }

settings/repository/edu.mit.broad/picard-private-parts-1432.xml

@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="edu.mit.broad" module="picard-private-parts" revision="1409-sharding" status="integration" publication="20100606141600" />
+    <info organisation="edu.mit.broad" module="picard-private-parts" revision="1432" status="integration" publication="20100616174700" />
 </ivy-module>

settings/repository/net.sf/picard-1.19.430-sharding.xml

@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="picard" revision="1.19.430-sharding" status="release" />
-</ivy-module>

settings/repository/net.sf/picard-1.22.448.xml

@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="picard" revision="1.22.448" status="release" />
+</ivy-module>

settings/repository/net.sf/sam-1.19.430-sharding.xml

@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.19.430-sharding" status="release" />
-</ivy-module>

settings/repository/net.sf/sam-1.22.448.xml

@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="sam" revision="1.22.448" status="release" />
+</ivy-module>