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BWT.java
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Proof-of-concept perfect read aligner, implemented as described in sec 2.4 of BWA paper. Has successfully aligned a handful of reads. Requires significant cleanup and refactoring.
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2009-09-14 21:54:56 +00:00 |
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BWTReader.java
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Data structure for counts, to isolate the user from wonky 'sometimes counts are cumulative, other times base-by-base' gotchas.
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2009-09-11 20:53:24 +00:00 |
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BWTWriter.java
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Data structure for counts, to isolate the user from wonky 'sometimes counts are cumulative, other times base-by-base' gotchas.
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2009-09-11 20:53:24 +00:00 |
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Base.java
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Data structure for counts, to isolate the user from wonky 'sometimes counts are cumulative, other times base-by-base' gotchas.
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2009-09-11 20:53:24 +00:00 |
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BasePackedInputStream.java
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Start to build BWT abstractions, so we can present a reasonable facsimile of the BWT to the user no matter how it's represented on disk.
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2009-09-11 18:23:15 +00:00 |
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BasePackedOutputStream.java
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Start to build BWT abstractions, so we can present a reasonable facsimile of the BWT to the user no matter how it's represented on disk.
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2009-09-11 18:23:15 +00:00 |
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Counts.java
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Data structure for counts, to isolate the user from wonky 'sometimes counts are cumulative, other times base-by-base' gotchas.
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2009-09-11 20:53:24 +00:00 |
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CreateBWTFromReference.java
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Data structure for counts, to isolate the user from wonky 'sometimes counts are cumulative, other times base-by-base' gotchas.
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2009-09-11 20:53:24 +00:00 |
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CreatePACFromReference.java
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Start to build BWT abstractions, so we can present a reasonable facsimile of the BWT to the user no matter how it's represented on disk.
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2009-09-11 18:23:15 +00:00 |
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IntPackedInputStream.java
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Higher-level readers and writers for BWTs and suffix arrays.
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2009-09-09 22:45:32 +00:00 |
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IntPackedOutputStream.java
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Higher-level readers and writers for BWTs and suffix arrays.
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2009-09-09 22:45:32 +00:00 |
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PackUtils.java
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Start to build BWT abstractions, so we can present a reasonable facsimile of the BWT to the user no matter how it's represented on disk.
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2009-09-11 18:23:15 +00:00 |
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PerfectAlignerTestHarness.java
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Proof-of-concept perfect read aligner, implemented as described in sec 2.4 of BWA paper. Has successfully aligned a handful of reads. Requires significant cleanup and refactoring.
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2009-09-14 21:54:56 +00:00 |
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SuffixArray.java
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Data structure for counts, to isolate the user from wonky 'sometimes counts are cumulative, other times base-by-base' gotchas.
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2009-09-11 20:53:24 +00:00 |
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SuffixArrayReader.java
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Data structure for counts, to isolate the user from wonky 'sometimes counts are cumulative, other times base-by-base' gotchas.
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2009-09-11 20:53:24 +00:00 |
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SuffixArrayWriter.java
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Data structure for counts, to isolate the user from wonky 'sometimes counts are cumulative, other times base-by-base' gotchas.
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2009-09-11 20:53:24 +00:00 |
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