Commit [r2298] Maximize Restore History

IOUtil improvements to improve performance for SAM and CAS file parsing.

dkatzel 2014-04-18

changed /trunk/src/org/jcvi/jillion/assembly/clc/cas/CasUtil.java
changed /trunk/src/org/jcvi/jillion/core/io/IOUtil.java
changed /trunk/src/org/jcvi/jillion/internal/sam/SamUtil.java
changed /trunk/src/org/jcvi/jillion/sam/BamFileParser.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/PresortedBamFileWriter.java
changed /trunk/src/org/jcvi/jillion/sam/ReSortSamFileWriter.java
changed /trunk/src/org/jcvi/jillion/sam/SamRecord.java
changed /trunk/src/org/jcvi/jillion/sam/cigar/Cigar.java
changed /trunk/test/org/jcvi/jillion/assembly/clc/cas/TestCasUtil.java
changed /trunk/test/org/jcvi/jillion/sam/cigar/TestCigar.java
/trunk/src/org/jcvi/jillion/assembly/clc/cas/CasUtil.java Diff Switch to side-by-side view
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/trunk/src/org/jcvi/jillion/core/io/IOUtil.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/sam/BamFileParser.java Diff Switch to side-by-side view
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/trunk/src/org/jcvi/jillion/sam/BgzfInputStream.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/PresortedBamFileWriter.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/SamRecord.java Diff Switch to side-by-side view
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/trunk/src/org/jcvi/jillion/sam/cigar/Cigar.java Diff Switch to side-by-side view
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/trunk/test/org/jcvi/jillion/assembly/clc/cas/TestCasUtil.java Diff Switch to side-by-side view
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/trunk/test/org/jcvi/jillion/sam/cigar/TestCigar.java Diff Switch to side-by-side view
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