Bumping version of Picard for firehose compatibility.

Integration tests were validated against svn rev 1861, before the wonder
twins committed their changes.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1864 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -70,7 +70,8 @@ public class IndexedFastaSequenceFile implements ReferenceSequenceFile {
 
         try {
             final SAMTextHeaderCodec codec = new SAMTextHeaderCodec();
-            final SAMFileHeader header = codec.decode(new AsciiLineReader(new FileInputStream(dictionary)), dictionary);
+            final SAMFileHeader header = codec.decode(new AsciiLineReader(new FileInputStream(dictionary)),
+                                                      dictionary.toString());
             if (header.getSequenceDictionary() != null && header.getSequenceDictionary().size() > 0) {
                 this.sequenceDictionary = header.getSequenceDictionary();
             }

settings/repository/edu.mit.broad/picard-private-1084.xml

@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="edu.mit.broad" module="picard-private" revision="1060" status="integration" publication="20090930104500" />
+    <info organisation="edu.mit.broad" module="picard-private" revision="1084" status="integration" publication="20091016142400" />
 </ivy-module>

settings/repository/net.sf/picard-1.04.xml

@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="picard" revision="1.04" status="release" />
-</ivy-module>

settings/repository/net.sf/picard-1.05.140.xml

@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="picard" revision="1.05.140" status="release" />
+</ivy-module>

settings/repository/net.sf/sam-1.04.xml

@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.04" status="release" />
-</ivy-module>

settings/repository/net.sf/sam-1.05.140.xml

@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="sam" revision="1.05.140" status="release" />
+</ivy-module>