Learn how easy it is to sync an existing GitHub or Google Code repo to a SourceForge project! See Demo

Close

Commit [r2246] Maximize Restore History

Added new BGZFInputStream implementation based on OpenJDK GzipInputStream to be able to get access to private fields. more work on BAM indexing. Now closer to Picard. Should be valid index even though not yet byte for byte compatible.

dkatzel 2014-03-12

added /trunk/src/org/jcvi/jillion/sam/BgzfInputStream2.java
added /trunk/src/org/jcvi/jillion/sam/IndexerCallback.java
removed /trunk/src/org/jcvi/jillion/sam/BamWriterPrototype.java
changed /trunk/src/org/jcvi/jillion/sam/BgzfInputStream.java
changed /trunk/src/org/jcvi/jillion/sam/BgzfOutputStream.java
changed /trunk/src/org/jcvi/jillion/sam/index/BamIndexer.java
changed /trunk/src/org/jcvi/jillion/sam/index/ReferenceIndex.java
changed /trunk/src/org/jcvi/jillion/sam/SamVisitor.java
changed /trunk/src/org/jcvi/jillion/sam/transform/SamTransformationService.java
changed /trunk/src/org/jcvi/jillion/sam/BamFileParser.java
changed /trunk/src/org/jcvi/jillion/sam/ReSortSamFileWriter.java
changed /trunk/src/org/jcvi/jillion/sam/index/IndexUtil.java
changed /trunk/src/org/jcvi/jillion/sam/index/Bin.java
changed /trunk/src/org/jcvi/jillion/sam/index/Chunk.java
changed /trunk/src/org/jcvi/jillion/sam/index/BamIndexWriterPrototype.java
changed /trunk/src/org/jcvi/jillion/sam/transform/SamGappedReferenceBuilderVisitor.java
copied /trunk/src/org/jcvi/jillion/sam/index/VirtualFileOffset.java -> /trunk/src/org/jcvi/jillion/sam/VirtualFileOffset.java
/trunk/src/org/jcvi/jillion/sam/BgzfInputStream2.java Diff Switch to side-by-side view
Loading...
/trunk/src/org/jcvi/jillion/sam/IndexerCallback.java Diff Switch to side-by-side view
Loading...
/trunk/src/org/jcvi/jillion/sam/BgzfInputStream.java Diff Switch to side-by-side view
Loading...
/trunk/src/org/jcvi/jillion/sam/BgzfOutputStream.java Diff Switch to side-by-side view
Loading...
/trunk/src/org/jcvi/jillion/sam/index/BamIndexer.java Diff Switch to side-by-side view
Loading...
/trunk/src/org/jcvi/jillion/sam/index/ReferenceIndex.java Diff Switch to side-by-side view
Loading...
/trunk/src/org/jcvi/jillion/sam/SamVisitor.java Diff Switch to side-by-side view
Loading...
/trunk/src/org/jcvi/jillion/sam/transform/SamTransformationService.java Diff Switch to side-by-side view
Loading...
/trunk/src/org/jcvi/jillion/sam/BamFileParser.java Diff Switch to side-by-side view
Loading...
/trunk/src/org/jcvi/jillion/sam/ReSortSamFileWriter.java Diff Switch to side-by-side view
Loading...
/trunk/src/org/jcvi/jillion/sam/index/IndexUtil.java Diff Switch to side-by-side view
Loading...
/trunk/src/org/jcvi/jillion/sam/index/Bin.java Diff Switch to side-by-side view
Loading...
/trunk/src/org/jcvi/jillion/sam/index/Chunk.java Diff Switch to side-by-side view
Loading...
/trunk/src/org/jcvi/jillion/sam/index/BamIndexWriterPrototype.java Diff Switch to side-by-side view
Loading...
/trunk/src/org/jcvi/jillion/sam/transform/SamGappedReferenceBuilderVisitor.java Diff Switch to side-by-side view
Loading...
/trunk/src/org/jcvi/jillion/sam/index/VirtualFileOffset.java to /trunk/src/org/jcvi/jillion/sam/VirtualFileOffset.java
--- a/trunk/src/org/jcvi/jillion/sam/index/VirtualFileOffset.java
+++ b/trunk/src/org/jcvi/jillion/sam/VirtualFileOffset.java
@@ -1,4 +1,4 @@
-package org.jcvi.jillion.sam.index;
+package org.jcvi.jillion.sam;
 
 
 public class VirtualFileOffset implements Comparable<VirtualFileOffset>{
@@ -26,7 +26,7 @@
 		return new VirtualFileOffset(encodedValue);
 	}
 	
-	private VirtualFileOffset(long encodedValue) {
+	public VirtualFileOffset(long encodedValue) {
 		this.encodedValue = encodedValue;
 	}