depristo
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58105636c8
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getBoundRods() convenience method
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1595 348d0f76-0448-11de-a6fe-93d51630548a
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2009-09-12 19:07:57 +00:00 |
aaron
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b4adb5133a
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GLF rod as a AllelicVariant object.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1282 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-21 00:55:52 +00:00 |
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depristo
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819862e04e
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major restructuring of generalized variant analysis framework. Now trivally easy to add additional analyses. Easy partitioning of all analyses by features, such as singleton status. Now has transition/transversional bias, counting, dbSNP coverage, HWE violation, selecting of variants by presence/absense in dbs. Also restructured the ROD system to make it easier to add tracks. Also, added the interval track -- if you provide an interval list, then the system autoatmically makese this available to you as a bound rod -- you can always find out where you are in the interval at every site. Python scripts improved to handle more merging, etc, into population snps.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@918 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-05 23:34:37 +00:00 |
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depristo
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ce6a0f522b
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First incarnation of the population-based SNP analysis tool. Also bug fixes throughout the GATK
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@845 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-27 22:02:24 +00:00 |
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depristo
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17b3d5b554
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New ROD accessing system, including a generalized interface for binding ROD on the command line that doesn't require you to chance GenomeAnalysisTK.java
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@355 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-09 22:04:59 +00:00 |
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depristo
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4eac3193f7
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Added RefMetaDataTracker system as a replacement for the List<RefenenceOrderedData> going into walkers. This system allows you to more easily get a tracker for processing using the lookup(name, default) system. See Pileup for an example.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@292 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-03 19:54:54 +00:00 |