43d1c6741c
Cleanup. Separate common packing functionality into utils class. Make base packing utility as generic as possible.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1566 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 17:54:12 +00:00
adce3bd536
My reference implementation is now generating a BWT which matches BWT-SW's.
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Note to self: never give project status in an svn log.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1550 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-08 22:11:03 +00:00
f22f590192
Successfully writing .sa files.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1549 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-08 17:34:34 +00:00
e2a79c5cd9
Checkpoint. The BWT that we generate now matches the first 16% of the BWT that BWT-SW generates. Cleaned up output streams to separate the byte packing / word packing from the data structure generation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1508 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-02 22:18:17 +00:00
d8aff9a925
Bug fixes. Was ignoring the '$' character in a few places where I shouldn't have been.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1504 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-02 16:27:31 +00:00
1ada085970
Cruddy implementation of BWT creation, for understanding and testing purposes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1501 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-02 02:16:56 +00:00
85ca68fab6
Initial version: creates a packed file from a fasta, suitable for consumption by BWT-SW. Works with E coli fasta, but will not work at this moment with multi-chr fastas.
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Will be made into a utility routine when BWA comes together.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1494 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-31 18:39:19 +00:00
hanna