kiran
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7949e377e4
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Intermediate commit. Refactored some simple base manipulation stuff into BaseUtils.java. Generalized some likelihood computation logic to make future possible EM-ing easier.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@424 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-15 04:18:07 +00:00 |
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kiran
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c51f51f255
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Make sure we always write at least 1000 points per base in each cycle's scatterplot. Print the disagreement rate between Bustard and FourBaseRecaller.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@375 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-13 00:49:41 +00:00 |
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kiran
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35fc002d5d
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Debugging information is now written in such a way to make it easier to import into R.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@372 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-12 19:45:33 +00:00 |
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kiran
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6ee4fe5a20
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Fixed a Bustard/Firecrest file synchronization bug.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@371 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-12 19:44:07 +00:00 |
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kiran
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817278be46
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If a SAMRecord is on the negative strand, reverse complement the SQ tag.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@370 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-12 19:42:24 +00:00 |
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kiran
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2b59110dca
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CombineSamAndFourProbs is better.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@358 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-10 04:19:53 +00:00 |
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kiran
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56aa98ad30
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Ignore null values.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@357 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-10 04:18:20 +00:00 |
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kiran
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f5cc2d8b0b
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Commented out import of IlluminaParser.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@354 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-09 21:30:29 +00:00 |
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kiran
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9bc763a835
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A better (aka 'working') tool for combining four-base probs with an aligned sam file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@350 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-09 20:51:37 +00:00 |
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kiran
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b7a2e82b46
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Can optionally process raw or corrected intensities.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@349 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-09 20:50:11 +00:00 |
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kiran
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6db9a00a0b
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SAMFileWriter doesn't appear to flush the buffer when its destructor is called. You have to call the close() method. Also, choose a random base for Ns in the forward and reverse strands so that samtools doesn't pitch a fit.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@338 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-08 21:48:24 +00:00 |
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kiran
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eb2f0ebd62
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If the first base of a read is 'N', and the alignment cigar says every base matches, samtools calls shennanigans. Now I just output an A, but the real way to do this is to modify the cigar string accordingly.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@337 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-08 19:58:18 +00:00 |
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kiran
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62ac7366ed
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A quick hack to ensure that the sequence, qualities, and secondary qualities are in accordance with the strand flag.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@331 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-08 15:57:28 +00:00 |
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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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15151ac125
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Corrected the use of the prior.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@284 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-03 15:47:47 +00:00 |
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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 |