dbd3d4473e
Making a copy here before changing the live copy
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2709 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-27 20:44:15 +00:00
090212c1c2
Home for retired duplicateQuals analysis utility
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2517 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-06 15:05:00 +00:00
cf3e59eb4a
back to archive
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2478 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-29 22:00:38 +00:00
295d16572e
synch; will go back to archive in a sec
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2477 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-29 22:00:03 +00:00
2de7e1a178
Move VariantAnnotator over to use a StratifiedAlignmentContext split by sample.
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The only major difference is that we are now able to get accurate allele balance ratios.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2321 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-11 05:28:28 +00:00
9da5cc25ad
More archiving (with permission from Andrey) plus a move to core.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2242 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-03 15:40:27 +00:00
67179e2412
Initial checkin of AnalyzeCovariates.java which replaces analyzeRecalQuals_1KG.py and is updated to use the new Covariates system. It creates similar plots of residual error for each covariate that was used in the calculation. There is also an option to filter out base qualities below a given threshold.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2215 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 16:47:35 +00:00
05923f7fba
Started transition to oneoffprojects.
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Moved/killed a few other walkers (with permission).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2204 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-01 21:19:02 +00:00
084337087e
Removing deprecated code and walkers for which I had the green light from repository.
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Moved piecemealannotator and secondarybases to archive.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2195 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-01 05:58:20 +00:00
2c16c18a04
Move Andrey's old indel code (plus MSG accuracy test, which depends on it) to archive.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2194 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-01 05:29:00 +00:00
ebanks
depristo
asivache
rpoplin