From a894a2dddbad99bf218fcff953485df8b935f568 Mon Sep 17 00:00:00 2001
From: Khalid Shakir <kshakir@broadinstitute.org>
Date: Wed, 7 May 2014 06:54:00 +0800
Subject: [PATCH] Updates to GATK classes and POMs that need updating, plus
 RodSystemValidation md5 updates. GATK classes accessing package protected
 htsjdk classes changed to new package names. POMs updated to support merging
 of sam/tribble/variant -> htsjdk and changes to picard artifact.
 RodSystemValidation outputs changed due to variant codec packages changes,
 requiring test md5 updates. Second of four commits for picard/htsjdk package
 rename.

---
 public/external-example/pom.xml               |  8 +-----
 .../java/htsjdk/samtools/GATKBAMFileSpan.java |  2 +-
 .../main/java/htsjdk/samtools/GATKBin.java    |  2 +-
 .../main/java/htsjdk/samtools/GATKChunk.java  |  2 +-
 .../htsjdk/samtools/PicardNamespaceUtils.java |  2 +-
 .../samtools/GATKBAMFileSpanUnitTest.java     |  2 +-
 .../htsjdk/samtools/GATKChunkUnitTest.java    |  2 +-
 public/gatk-package/pom.xml                   | 11 +++-----
 public/queue-package/pom.xml                  |  2 +-
 public/sting-root/pom.xml                     | 27 +++++--------------
 public/sting-utils/pom.xml                    | 14 +++-------
 11 files changed, 21 insertions(+), 53 deletions(-)

diff --git a/public/external-example/pom.xml b/public/external-example/pom.xml
index a26b7134b..87375c843 100644
--- a/public/external-example/pom.xml
+++ b/public/external-example/pom.xml
@@ -146,13 +146,7 @@
                                     </includes>
                                 </filter>
                                 <filter>
-                                    <artifact>org.broad:tribble</artifact>
-                                    <includes>
-                                        <include>**</include>
-                                    </includes>
-                                </filter>
-                                <filter>
-                                    <artifact>org.broadinstitute:variant</artifact>
+                                    <artifact>samtools:htsjdk</artifact>
                                     <includes>
                                         <include>**</include>
                                     </includes>
diff --git a/public/gatk-framework/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java b/public/gatk-framework/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java
index dc36e83c2..35388dc65 100644
--- a/public/gatk-framework/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java
+++ b/public/gatk-framework/src/main/java/htsjdk/samtools/GATKBAMFileSpan.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package net.sf.samtools;
+package htsjdk.samtools;
 
 import net.sf.picard.util.PeekableIterator;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
diff --git a/public/gatk-framework/src/main/java/htsjdk/samtools/GATKBin.java b/public/gatk-framework/src/main/java/htsjdk/samtools/GATKBin.java
index 463707252..d1e689d63 100644
--- a/public/gatk-framework/src/main/java/htsjdk/samtools/GATKBin.java
+++ b/public/gatk-framework/src/main/java/htsjdk/samtools/GATKBin.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package net.sf.samtools;
+package htsjdk.samtools;
 
 import java.util.ArrayList;
 import java.util.Collections;
diff --git a/public/gatk-framework/src/main/java/htsjdk/samtools/GATKChunk.java b/public/gatk-framework/src/main/java/htsjdk/samtools/GATKChunk.java
index db52402a4..6d695f43c 100644
--- a/public/gatk-framework/src/main/java/htsjdk/samtools/GATKChunk.java
+++ b/public/gatk-framework/src/main/java/htsjdk/samtools/GATKChunk.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package net.sf.samtools;
+package htsjdk.samtools;
 
 /**
  * A temporary solution to work around Java access rights issues:
diff --git a/public/gatk-framework/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java b/public/gatk-framework/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java
index 131793268..00f65e54c 100644
--- a/public/gatk-framework/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java
+++ b/public/gatk-framework/src/main/java/htsjdk/samtools/PicardNamespaceUtils.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package net.sf.samtools;
+package htsjdk.samtools;
 
 /**
  * Utils that insist on being in the same package as Picard.
diff --git a/public/gatk-framework/src/test/java/htsjdk/samtools/GATKBAMFileSpanUnitTest.java b/public/gatk-framework/src/test/java/htsjdk/samtools/GATKBAMFileSpanUnitTest.java
index d03c6e006..aaa20c0e5 100644
--- a/public/gatk-framework/src/test/java/htsjdk/samtools/GATKBAMFileSpanUnitTest.java
+++ b/public/gatk-framework/src/test/java/htsjdk/samtools/GATKBAMFileSpanUnitTest.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package net.sf.samtools;
+package htsjdk.samtools;
 
 import org.testng.Assert;
 import org.testng.annotations.Test;
diff --git a/public/gatk-framework/src/test/java/htsjdk/samtools/GATKChunkUnitTest.java b/public/gatk-framework/src/test/java/htsjdk/samtools/GATKChunkUnitTest.java
index 09a87d311..2b08fc4d4 100644
--- a/public/gatk-framework/src/test/java/htsjdk/samtools/GATKChunkUnitTest.java
+++ b/public/gatk-framework/src/test/java/htsjdk/samtools/GATKChunkUnitTest.java
@@ -23,7 +23,7 @@
 * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
 */
 
-package net.sf.samtools;
+package htsjdk.samtools;
 
 import org.testng.Assert;
 import org.testng.annotations.Test;
diff --git a/public/gatk-package/pom.xml b/public/gatk-package/pom.xml
index 9e06dce73..a8500815c 100644
--- a/public/gatk-package/pom.xml
+++ b/public/gatk-package/pom.xml
@@ -28,15 +28,10 @@
             <artifactId>gatk-framework</artifactId>
             <version>${project.version}</version>
         </dependency>
-        <!-- Tribble codecs -->
+        <!-- Tribble codecs & the variant package (VCF, BCF, and VariantContext) -->
         <dependency>
-            <groupId>org.broad</groupId>
-            <artifactId>tribble</artifactId>
-        </dependency>
-        <!-- The variant package (VCF, BCF, and VariantContext) -->
-        <dependency>
-            <groupId>org.broadinstitute</groupId>
-            <artifactId>variant</artifactId>
+            <groupId>samtools</groupId>
+            <artifactId>htsjdk</artifactId>
         </dependency>
         <!-- Workaround - depend on the logger impl required by JEXL -->
         <dependency>
diff --git a/public/queue-package/pom.xml b/public/queue-package/pom.xml
index cb75a6891..3a266236c 100644
--- a/public/queue-package/pom.xml
+++ b/public/queue-package/pom.xml
@@ -44,7 +44,7 @@
         </dependency>
         <!-- Picard -->
         <dependency>
-            <groupId>net.sf</groupId>
+            <groupId>picard</groupId>
             <artifactId>picard</artifactId>
         </dependency>
         <!-- JavaMail -->
diff --git a/public/sting-root/pom.xml b/public/sting-root/pom.xml
index fe807da50..38078312f 100644
--- a/public/sting-root/pom.xml
+++ b/public/sting-root/pom.xml
@@ -42,12 +42,9 @@
         <java.gc.heapFreeLimit>10</java.gc.heapFreeLimit>
         <test.args>-Xmx${test.maxmemory} -XX:+UseParallelOldGC -XX:ParallelGCThreads=${java.gc.threads} -XX:GCTimeLimit=${java.gc.timeLimit} -XX:GCHeapFreeLimit=${java.gc.heapFreeLimit}</test.args>
 
-        <!-- Version numbers for picard sam-jdk. Usually kept in sync. -->
-        <picard.public.version>1.111.1920</picard.public.version>
-        <sam.version>${picard.public.version}</sam.version>
-        <picard.version>${picard.public.version}</picard.version>
-        <variant.version>${picard.public.version}</variant.version>
-        <tribble.version>${picard.public.version}</tribble.version>
+        <!-- Version numbers for picard and htsjdk -->
+        <htsjdk.version>1.112.1452</htsjdk.version>
+        <picard.version>1.112.1452</picard.version>
     </properties>
 
     <!-- Dependency configuration (versions, etc.) -->
@@ -69,9 +66,9 @@
                 <version>1.0-r139</version>
             </dependency>
             <dependency>
-                <groupId>net.sf</groupId>
-                <artifactId>sam</artifactId>
-                <version>${sam.version}</version>
+                <groupId>samtools</groupId>
+                <artifactId>htsjdk</artifactId>
+                <version>${htsjdk.version}</version>
                 <exclusions>
                     <exclusion>
                         <groupId>org.testng</groupId>
@@ -80,20 +77,10 @@
                 </exclusions>
             </dependency>
             <dependency>
-                <groupId>net.sf</groupId>
+                <groupId>picard</groupId>
                 <artifactId>picard</artifactId>
                 <version>${picard.version}</version>
             </dependency>
-            <dependency>
-                <groupId>org.broad</groupId>
-                <artifactId>tribble</artifactId>
-                <version>${tribble.version}</version>
-            </dependency>
-            <dependency>
-                <groupId>org.broadinstitute</groupId>
-                <artifactId>variant</artifactId>
-                <version>${variant.version}</version>
-            </dependency>
             <dependency>
                 <groupId>log4j</groupId>
                 <artifactId>log4j</artifactId>
diff --git a/public/sting-utils/pom.xml b/public/sting-utils/pom.xml
index fddd43946..ab4b7e1b7 100644
--- a/public/sting-utils/pom.xml
+++ b/public/sting-utils/pom.xml
@@ -21,21 +21,13 @@
 
     <dependencies>
         <dependency>
-            <groupId>net.sf</groupId>
-            <artifactId>sam</artifactId>
+            <groupId>samtools</groupId>
+            <artifactId>htsjdk</artifactId>
         </dependency>
         <dependency>
-            <groupId>net.sf</groupId>
+            <groupId>picard</groupId>
             <artifactId>picard</artifactId>
         </dependency>
-        <dependency>
-            <groupId>org.broad</groupId>
-            <artifactId>tribble</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.broadinstitute</groupId>
-            <artifactId>variant</artifactId>
-        </dependency>
         <dependency>
             <groupId>log4j</groupId>
             <artifactId>log4j</artifactId>