kiran
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99579a1ef8
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Math correction.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@310 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-07 02:18:13 +00:00 |
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kiran
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9be978e006
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Intermediate commit (debugging info).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@309 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-07 01:20:15 +00:00 |
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kiran
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5a5c6d1276
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Added some debugging stuff (writes model parameters to one file per cycle).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@304 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-06 22:00:58 +00:00 |
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kiran
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f12d40dde8
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Simplified SAMRecord construction and emission.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@296 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-05 04:48:31 +00:00 |
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kiran
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ef06924f73
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JavaDocs!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@290 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-03 19:19:17 +00:00 |
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kiran
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5019971290
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Now outputs four-base SAM record (read name prefixed with KIR) and bustard SAM record (prefixed with BUS) for easy debugging.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@285 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-03 15:48:51 +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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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 |