Rev Picard with performance enhancements.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3615 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java

@@ -2,6 +2,8 @@ package org.broadinstitute.sting.utils.sam;
 
 import net.sf.samtools.SAMFileReader;
 import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMRecordIterator;
+import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.util.CloseableIterator;
 
 import java.io.InputStream;
@@ -51,7 +53,7 @@ public class ArtificialSAMFileReader extends SAMFileReader {
      * @{inheritDoc}
      */
     @Override
-    public CloseableIterator<SAMRecord> query(final String sequence, final int start, final int end, final boolean contained) {
+    public SAMRecordIterator query(final String sequence, final int start, final int end, final boolean contained) {
         GenomeLoc region = GenomeLocParser.createGenomeLoc(sequence, start, end);
         List<SAMRecord> coveredSubset = new ArrayList<SAMRecord>();
 
@@ -62,17 +64,25 @@ public class ArtificialSAMFileReader extends SAMFileReader {
         }
 
         final Iterator<SAMRecord> iterator = coveredSubset.iterator();
-        return new CloseableIterator<SAMRecord>() {
+        return new SAMRecordIterator() {
             public boolean hasNext() { return iterator.hasNext(); }
             public SAMRecord next() { return iterator.next(); }
             public void close() {}
-            public void remove() { iterator.remove(); } 
+            public void remove() { iterator.remove(); }
+            public SAMRecordIterator assertSorted(SAMFileHeader.SortOrder sortOrder) { return this; }
         };
     }
 
     @Override
-    public CloseableIterator<SAMRecord> iterator() {
-        return StingSAMIteratorAdapter.adapt( new Reads( Collections.<File>emptyList() ), reads.iterator() );    
+    public SAMRecordIterator iterator() {
+        return new SAMRecordIterator() {
+            private final Iterator<SAMRecord> iterator = reads.iterator();
+            public boolean hasNext() { return iterator.hasNext(); }
+            public SAMRecord next() { return iterator.next(); }
+            public void close() {}
+            public void remove() { iterator.remove(); }
+            public SAMRecordIterator assertSorted(SAMFileHeader.SortOrder sortOrder) { return this; }
+        };
     }
 
     /**

java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java

@@ -121,7 +121,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
     @Test
     public void testOtherFormat() {
         HashMap<String, String> e = new HashMap<String, String>();
-        e.put( "GLF", "ddb1074b6f4a0fd1e15e4381476f1055" );
+        e.put( "GLF", "b3d463eb0b7e59604296747e1eb7103c" );
         e.put( "GELI_BINARY", "764a0fed1b3cf089230fd91f3be9c2df" );
 
         for ( Map.Entry<String, String> entry : e.entrySet() ) {

settings/repository/edu.mit.broad/picard-private-parts-1443.xml

@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="edu.mit.broad" module="picard-private-parts" revision="1432" status="integration" publication="20100616174700" />
+    <info organisation="edu.mit.broad" module="picard-private-parts" revision="1443" status="integration" publication="20100622171000" />
 </ivy-module>

settings/repository/net.sf/picard-1.22.448.xml

@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="picard" revision="1.22.448" status="release" />
-</ivy-module>

settings/repository/net.sf/picard-1.24.465.xml

@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="picard" revision="1.24.465" status="release" />
+</ivy-module>

settings/repository/net.sf/sam-1.22.448.xml

@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.22.448" status="release" />
-</ivy-module>

settings/repository/net.sf/sam-1.24.465.xml

@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="sam" revision="1.24.465" status="release" />
+</ivy-module>