Update to the latest rev of the picard sharding patch. Includes updates reflecting

the imminent move of IlluminaUtil into picard public.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3493 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TileCovariate.java

@@ -26,7 +26,7 @@ package org.broadinstitute.sting.gatk.walkers.recalibration;
 
 import org.broadinstitute.sting.utils.StingException;
 import net.sf.samtools.SAMRecord;
-import edu.mit.broad.picard.illumina.parser.IlluminaUtil;
+import net.sf.picard.util.IlluminaUtil;
 
 /**
  * @author alecw@broadinstitute.org

packages/PicardPrivate.xml

@@ -7,7 +7,6 @@
       <class name="edu.mit.broad.picard.genotype.geli.GeliFileWriter" />
       <class name="edu.mit.broad.picard.genotype.geli.GenotypeLikelihoods" />
       <class name="edu.mit.broad.picard.util.BasicTextFileParser" />
-      <class name="edu.mit.broad.picard.illumina.parser.IlluminaUtil" />
       <class name="edu.mit.broad.picard.util.PasteParser" />
       <class name="edu.mit.broad.picard.variation.KnownVariantCodecV2" />
       <class name="edu.mit.broad.picard.variation.KnownVariantCodec" />
@@ -21,6 +20,7 @@
       <class name="edu.mit.broad.picard.variation.KnownVariant" />
       <class name="edu.mit.broad.picard.variation.DbSnpFileReader" />
       <class name="edu.mit.broad.picard.variation.DbSnpFileGenerator" />
+      <class name="net.sf.picard.util.IlluminaUtil" />
     </dependencies>
   </executable>
 </package>

settings/repository/edu.mit.broad/picard-private-parts-1409-sharding.xml

@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="edu.mit.broad" module="picard-private-parts" revision="1377-sharding" status="integration" publication="20100507172500" />
+    <info organisation="edu.mit.broad" module="picard-private-parts" revision="1409-sharding" status="integration" publication="20100606141600" />
 </ivy-module>

settings/repository/net.sf/picard-1.19.395-sharding.xml

@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="picard" revision="1.19.395-sharding" status="release" />
-</ivy-module>

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

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

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

@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.19.395-sharding" status="release" />
+    <info organisation="net.sf" module="sam" revision="1.19.430-sharding" status="release" />
 </ivy-module>