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

@@ -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>

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;

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;

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:

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.

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;

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;

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>

public/queue-package/pom.xml

@@ -44,7 +44,7 @@
         </dependency>
         <!-- Picard -->
         <dependency>
-            <groupId>net.sf</groupId>
+            <groupId>picard</groupId>
             <artifactId>picard</artifactId>
         </dependency>
         <!-- JavaMail -->

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>

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>