aaron
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9cfd89c54f
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a small refactoring, and some documentation cleanup
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1210 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-09 22:03:45 +00:00 |
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aaron
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d86717db93
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Refactoring of the traversal engine base class, I removed a lot of old code.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1209 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-09 21:57:00 +00:00 |
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aaron
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8b4d0412ca
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Changed the duplicate traversal over to the new style of traversal and plumbed into the genome analysis engine. Also added a CountDuplicates walker, to validate the engine.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1072 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-22 21:11:18 +00:00 |
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aaron
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bcb64d92e9
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Aaron: 1, GenomeLoc: 0. I changed our GenomeLoc class, seperating the creation of a genome loc (with the reference setup) to a parser class. GenomeLoc now just represents the actual genomic postion. The constructors are now package-protected (to enforce using the parser), but we may want to expose some constructors in the future.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1069 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-22 14:39:41 +00:00 |
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aaron
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63b5c12cbd
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Changed dataSources to datasources, to be consistant with the rest of our package names. Also, this makes me champion in the largest check-in contest.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@985 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-11 18:13:22 +00:00 |
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aaron
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109bef6c08
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We're no longer in the read-dropping business.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@901 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-04 22:37:51 +00:00 |
hanna
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5e8c08ee63
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Update to latest version of picard. Change imports in all classes dependent on picard public from import edu.mit.broad.picard... to import net.sf.picard...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@849 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-28 20:13:01 +00:00 |
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hanna
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2a5be1debe
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Cleanup in datasources.providers namespace. Make it easier for others writing traversal engines to use.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@803 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-22 19:12:00 +00:00 |
depristo
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30c63daf89
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More improvements to the duplicate quality combiner, making progress towards a clean system
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@788 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-21 22:26:57 +00:00 |
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hanna
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12ae3a22b6
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Break locus context data access providers into modular components in preparation for traverse by loci.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@689 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-13 18:51:16 +00:00 |
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hanna
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32696b13f5
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Fixed method override issue with old-style traversals.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@660 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-12 01:22:18 +00:00 |
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depristo
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5a6892900e
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fixing oddities in duplicates
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@628 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-07 18:55:45 +00:00 |
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depristo
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2204be43eb
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System for traversing duplicate reads, along with a walker to compute quality scores among duplicates and a smarter method to combine quality scores across duplicates -- v1
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@624 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-07 18:06:02 +00:00 |
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depristo
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84dae06d5a
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Initial version of ByDuplicates traversal, as well as a duplicate quality score estimator
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@576 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-30 22:16:21 +00:00 |