Rev picard, sam-jdk, and tribble

This is a necessary prerequisite for the org.broadinstitute.variant migration.

-Picard and sam-jdk go from version 1.67.1197 to 1.84.1337

-Picard-private goes from version 2375 to 2662

-Tribble goes from version 119 to 1.84.1337

-RADICALLY trimmed down the list of classes we extract from Picard-private
 (jar goes from 326993 bytes to 6445 bytes!)

public/java/src/org/broadinstitute/sting/gatk/datasources/reads/BlockLoader.java

@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.gatk.datasources.reads;
 
-import org.broad.tribble.util.BlockCompressedStreamConstants;
+import net.sf.samtools.util.BlockCompressedStreamConstants;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.FileInputStream;

public/java/src/org/broadinstitute/sting/gatk/datasources/reads/GATKBAMIndex.java

@@ -25,8 +25,8 @@
 
 package org.broadinstitute.sting.gatk.datasources.reads;
 
-import org.broad.tribble.util.SeekableBufferedStream;
-import org.broad.tribble.util.SeekableFileStream;
+import net.sf.samtools.seekablestream.SeekableBufferedStream;
+import net.sf.samtools.seekablestream.SeekableFileStream;
 
 import net.sf.samtools.*;
 

public/java/src/org/broadinstitute/variant/vcf/AbstractVCFCodec.java

@@ -30,7 +30,7 @@ import org.broad.tribble.Feature;
 import org.broad.tribble.NameAwareCodec;
 import org.broad.tribble.TribbleException;
 import org.broad.tribble.readers.LineReader;
-import org.broad.tribble.util.BlockCompressedInputStream;
+import net.sf.samtools.util.BlockCompressedInputStream;
 import org.broad.tribble.util.ParsingUtils;
 import org.broadinstitute.variant.utils.GeneralUtils;
 import org.broadinstitute.variant.variantcontext.*;

public/packages/PicardPrivate.xml

@@ -2,26 +2,9 @@
 <package name="picard-private-parts">
   <executable name="picard-private-parts">
     <dependencies>
-      <class name="edu.mit.broad.picard.genotype.DiploidGenotype" />
-      <class name="edu.mit.broad.picard.genotype.geli.GeliFileReader" />
-      <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.PasteParser" />
       <class name="edu.mit.broad.picard.util.PicardAggregationFsUtil" />
-      <class name="edu.mit.broad.picard.util.PicardFileSystemUtil" />
-      <class name="edu.mit.broad.picard.variation.KnownVariantCodecV2" />
-      <class name="edu.mit.broad.picard.variation.KnownVariantCodec" />
-      <class name="edu.mit.broad.picard.variation.KnownVariantFileHeader" />
-      <class name="edu.mit.broad.picard.variation.VariantType" />
-      <class name="edu.mit.broad.picard.variation.ObsoleteKnownVariantCodecV1" />
-      <class name="edu.mit.broad.picard.variation.AbstractKnownVariantCodec" />
-      <class name="edu.mit.broad.picard.variation.KnownVariantIterator" />
-      <class name="edu.mit.broad.picard.variation.KnownVariantCodecFactory" />
-      <class name="edu.mit.broad.picard.variation.KnownVariant" />
-      <class name="net.sf.picard.util.IlluminaUtil" />
       <class name="edu.mit.broad.picard.genotype.fingerprint.v2.FingerprintingSummaryMetrics" />
       <class name="edu.mit.broad.picard.genotype.concordance.DbSnpMatchMetrics" />
     </dependencies>
-
   </executable>
 </package>

settings/repository/edu.mit.broad/picard-private-parts-2662.xml

@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="edu.mit.broad" module="picard-private-parts" revision="2375" status="integration" publication="20120502094400" />
+    <info organisation="edu.mit.broad" module="picard-private-parts" revision="2662" status="integration" publication="" />
 </ivy-module>

settings/repository/net.sf/picard-1.67.1197.xml

@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="picard" revision="1.67.1197" status="release" />
-</ivy-module>

settings/repository/net.sf/picard-1.84.1337.xml

@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="picard" revision="1.84.1337" status="release" />
+</ivy-module>

settings/repository/net.sf/sam-1.67.1197.xml

@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.67.1197" status="release" />
-</ivy-module>

settings/repository/net.sf/sam-1.84.1337.xml

@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="sam" revision="1.84.1337" status="release" />
+</ivy-module>

settings/repository/org.broad/tribble-1.84.1337.xml

@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="org.broad" module="tribble" revision="1.84.1337" status="integration" />
+</ivy-module>

settings/repository/org.broad/tribble-119.xml

@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="org.broad" module="tribble" revision="119" status="integration" />
-</ivy-module>