kiran
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7d889c0661
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Refactored into oblivon.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@276 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-02 22:12:15 +00:00 |
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kiran
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dffc879240
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Should now be appropriately using Bustard data to call bases (there are some mathematical subtleties that arise when no longer using ICs as initialization data. Also writes some more relevant fields in the SAM records. WAAAAAY simpler than old version. Like, super way.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@275 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-02 22:10:13 +00:00 |
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kiran
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59334b0270
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A convenience class for manipulation base probability distributions.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@274 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-02 22:08:31 +00:00 |
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kiran
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399d9b8c1e
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A class that represents the model parameters for all of the Gaussian models for all cycles.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@273 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-02 22:08:10 +00:00 |
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kiran
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f0f94b6c72
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A class that represents the model parameters for all of the Gaussian models at a given cycle. Handles the accumulation of parameter initialization data and provides for efficient computation of base probability distribution.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@272 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-02 22:07:47 +00:00 |
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kiran
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607731da91
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Fixed a harmless (but annoying) bug wherein the read name for the SAMRecords increases by two on every iteration rather than one.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@189 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-25 15:20:29 +00:00 |
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kiran
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28c1330b4b
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Fixed a bug wherein the loop variable for the second end of the pair was actually looping over the entire raw read (first and second ends combined).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@178 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-24 21:59:25 +00:00 |
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kiran
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499c422de6
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A version of the four-base caller that computes the probability distribution over base call space by initializing off the Bustard calls rather than the ICs.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@173 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-24 20:11:39 +00:00 |
hanna
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63cd1fe201
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Push core / playground lower into the tree.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@160 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-23 23:19:54 +00:00 |