Commit [r2290] Maximize Restore History

moved some SAM and BAM classes into internal packages to keep them out of public API

dkatzel 2014-04-07

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added /trunk/src/org/jcvi/jillion/internal/sam/index/IndexUtil.java
added /trunk/src/org/jcvi/jillion/internal/sam/SamUtil.java
added /trunk/src/org/jcvi/jillion/internal/sam/package-info.java
added /trunk/src/org/jcvi/jillion/internal/sam/index/BamIndexer.java
added /trunk/src/org/jcvi/jillion/internal/sam/index/package-info.java
changed /trunk/src/org/jcvi/jillion/sam/SamWriterBuilder.java
changed /trunk/src/org/jcvi/jillion/sam/PresortedBamFileWriter.java
changed /trunk/src/org/jcvi/jillion/sam/BgzfOutputStream.java
changed /trunk/src/org/jcvi/jillion/sam/header/SamHeaderTagKey.java
changed /trunk/src/org/jcvi/jillion/sam/Encoding.java
changed /trunk/src/org/jcvi/jillion/sam/index/BamIndex.java
changed /trunk/src/org/jcvi/jillion/sam/index/BamIndexFileWriterBuilder.java
changed /trunk/test/org/jcvi/jillion/sam/index/TestBamIndexParser.java
changed /trunk/src/org/jcvi/jillion/sam/index/ReferenceIndexBuilder.java
changed /trunk/src/org/jcvi/jillion/sam/PresortedSamFileWriter.java
changed /trunk/src/org/jcvi/jillion/sam/BamFileParser.java
changed /trunk/src/org/jcvi/jillion/sam/ReSortSamFileWriter.java
copied /trunk/src/org/jcvi/jillion/sam/index/BaiRefIndex.java -> /trunk/src/org/jcvi/jillion/internal/sam/index/BaiRefIndex.java
copied /trunk/src/org/jcvi/jillion/sam/index/BaiBin.java -> /trunk/src/org/jcvi/jillion/internal/sam/index/BaiBin.java
copied /trunk/src/org/jcvi/jillion/sam/IndexerCallback.java -> /trunk/src/org/jcvi/jillion/internal/sam/IndexerCallback.java
/trunk/src/org/jcvi/jillion/internal/sam/index/IndexUtil.java Diff Switch to side-by-side view
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/trunk/src/org/jcvi/jillion/internal/sam/SamUtil.java Diff Switch to side-by-side view
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/trunk/src/org/jcvi/jillion/internal/sam/package-info.java Diff Switch to side-by-side view
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/trunk/src/org/jcvi/jillion/internal/sam/index/BamIndexer.java Diff Switch to side-by-side view
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/trunk/src/org/jcvi/jillion/internal/sam/index/package-info.java Diff Switch to side-by-side view
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/trunk/src/org/jcvi/jillion/sam/SamWriterBuilder.java Diff Switch to side-by-side view
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/trunk/src/org/jcvi/jillion/sam/PresortedBamFileWriter.java Diff Switch to side-by-side view
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/trunk/src/org/jcvi/jillion/sam/BgzfOutputStream.java Diff Switch to side-by-side view
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/trunk/src/org/jcvi/jillion/sam/header/SamHeaderTagKey.java Diff Switch to side-by-side view
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/trunk/src/org/jcvi/jillion/sam/Encoding.java Diff Switch to side-by-side view
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/trunk/src/org/jcvi/jillion/sam/index/BamIndex.java Diff Switch to side-by-side view
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/trunk/src/org/jcvi/jillion/sam/index/BamIndexFileWriterBuilder.java Diff Switch to side-by-side view
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/trunk/test/org/jcvi/jillion/sam/index/TestBamIndexParser.java Diff Switch to side-by-side view
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/trunk/src/org/jcvi/jillion/sam/index/ReferenceIndexBuilder.java Diff Switch to side-by-side view
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/trunk/src/org/jcvi/jillion/sam/PresortedSamFileWriter.java Diff Switch to side-by-side view
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/trunk/src/org/jcvi/jillion/sam/BamFileParser.java Diff Switch to side-by-side view
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/trunk/src/org/jcvi/jillion/sam/ReSortSamFileWriter.java Diff Switch to side-by-side view
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/trunk/src/org/jcvi/jillion/sam/index/BaiRefIndex.java to /trunk/src/org/jcvi/jillion/internal/sam/index/BaiRefIndex.java
--- a/trunk/src/org/jcvi/jillion/sam/index/BaiRefIndex.java
+++ b/trunk/src/org/jcvi/jillion/internal/sam/index/BaiRefIndex.java
@@ -1,4 +1,4 @@
-package org.jcvi.jillion.sam.index;
+package org.jcvi.jillion.internal.sam.index;
 
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -6,6 +6,8 @@
 import java.util.List;
 
 import org.jcvi.jillion.sam.VirtualFileOffset;
+import org.jcvi.jillion.sam.index.Bin;
+import org.jcvi.jillion.sam.index.ReferenceIndex;
 
 class BaiRefIndex implements ReferenceIndex {
 	private final List<Bin> bins;
/trunk/src/org/jcvi/jillion/sam/index/BaiBin.java to /trunk/src/org/jcvi/jillion/internal/sam/index/BaiBin.java
--- a/trunk/src/org/jcvi/jillion/sam/index/BaiBin.java
+++ b/trunk/src/org/jcvi/jillion/internal/sam/index/BaiBin.java
@@ -1,8 +1,11 @@
-package org.jcvi.jillion.sam.index;
+package org.jcvi.jillion.internal.sam.index;
 
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
+
+import org.jcvi.jillion.sam.index.Bin;
+import org.jcvi.jillion.sam.index.Chunk;
 
 class BaiBin implements Bin {
 
/trunk/src/org/jcvi/jillion/sam/IndexerCallback.java to /trunk/src/org/jcvi/jillion/internal/sam/IndexerCallback.java
--- a/trunk/src/org/jcvi/jillion/sam/IndexerCallback.java
+++ b/trunk/src/org/jcvi/jillion/internal/sam/IndexerCallback.java
@@ -1,5 +1,7 @@
-package org.jcvi.jillion.sam;
+package org.jcvi.jillion.internal.sam;
 
-interface IndexerCallback{
+import org.jcvi.jillion.sam.VirtualFileOffset;
+
+public interface IndexerCallback{
 	void encodedIndex(VirtualFileOffset start, VirtualFileOffset end);
 }
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