30babbf5b9
Restructured AlleleFrequencyMetricsWalker to correctly report Hapmap concordance numbers for genotyping and added reporting for Hapmap reference/variant calling. Also, tiny bugfix in interval code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@181 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-25 01:12:05 +00:00
9e2a373184
Prototype, buggy implementation of walker command-line arguments. Doesn't
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(yet) deal elegantly with even simple cases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@180 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-25 00:12:00 +00:00
919a86e876
Cleaned up code for by interval traversals for Jared. Initialization code refactored and made clear. by loci and by loci by interval use the same underlying code now. Everyone uses the same initialization code to set things up. It's a party in the TraversalEngine and everyone's invited...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@179 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-24 22:32:45 +00:00
6df19ab793
Support for byInterval traversals for Jared. Do not use them.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@175 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-24 20:55:34 +00:00
9f500215da
Support for reseting the system; Cleanup later
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@174 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-24 20:52:11 +00:00
9dee9ab51c
Added Hapmap data track (using rodGFF class for GFF file format) to toolkit as a command line option, Hapmap metrics to AlleleFrequencyMetricsWalker, and a python Geli2GFF file converter.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@163 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-24 03:58:03 +00:00
f7363cf935
Support for loading from either a jar or a class directory. Fixes troubles with IntelliJ debugging.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@162 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-24 03:56:49 +00:00
63cd1fe201
Push core / playground lower into the tree.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@160 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-23 23:19:54 +00:00
andrewk
hanna
depristo