Commit [r2282] Maximize Restore History

created new ReferenceIndex interface and refactored ReferenceIndexBuilder to build a new implementation of that interface.

dkatzel 2014-03-31

added /trunk/src/org/jcvi/jillion/sam/index/ReferenceIndex.java
changed /trunk/src/org/jcvi/jillion/sam/PresortedBamFileWriter.java
changed /trunk/src/org/jcvi/jillion/sam/index/ReferenceIndexBuilder.java
changed /trunk/src/org/jcvi/jillion/sam/index/IndexUtil.java
changed /trunk/src/org/jcvi/jillion/sam/BamIndexer.java
/trunk/src/org/jcvi/jillion/sam/index/ReferenceIndex.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/index/ReferenceIndexBuilder.java Diff Switch to side-by-side view
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/trunk/src/org/jcvi/jillion/sam/index/IndexUtil.java Diff Switch to side-by-side view
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/trunk/src/org/jcvi/jillion/sam/BamIndexer.java Diff Switch to side-by-side view
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