kiran
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e48078b476
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Updated to reflect change to BasecallingReadModel constructor.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@760 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-20 15:43:26 +00:00 |
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kiran
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505f588768
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Forgot to say that the mate is unmapped too. This is necessary to prevent SAM-JDK from yelling at me about an invalid SAM file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@759 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-20 15:38:51 +00:00 |
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kiran
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6c5fbb988b
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Now basecalls an entire read (both ends of the pair, barcode... everything) at once. After, RawRead and FourProbRead can be asked to return a specified subset (corresponding to the ranges specified for each end of the read.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@754 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-20 00:09:20 +00:00 |
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kiran
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e293d65ede
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Refactored to allow the user to specify the range of cycles they wish to call. Simply specify a single range (i.e. '0-75') or two ranges ('0-75,76-151'). This allows single and paired-end read processing to coexist happily. Also implements annotation of an aligned bam file (which should hopefully fit in under two gigs now, but I'm waiting on a bug fix or a clarification from the Picard team.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@753 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-20 00:07:24 +00:00 |
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kiran
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08c9f4d86b
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Renamed to BasecallingTrainer.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@752 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-20 00:03:46 +00:00 |
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kiran
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7c615c8fb0
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Some changes to the system for annotating a pre-aligned bam file. Doesn't fit within 2gigs.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@746 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-18 17:42:08 +00:00 |
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kiran
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28bf7ec8ad
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Aesthetic cleanup.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@735 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-17 04:09:23 +00:00 |
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kiran
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a0464633fd
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Whoops. Changed denominator from reads to bases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@734 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-17 03:42:25 +00:00 |
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kiran
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5d60efc498
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Factored out some simple stats accumulation.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@733 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-17 03:37:57 +00:00 |
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kiran
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6f1559bd77
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Cleaned up a bit. Added some documentation.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@728 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-15 21:22:24 +00:00 |
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kiran
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dae77bf14a
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Fixed a typo in a comment.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@723 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-15 20:07:31 +00:00 |
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kiran
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bfc40f54f0
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Nicer output when training off of perfect reads. Not that that works yet...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@722 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-15 20:07:08 +00:00 |
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kiran
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36db44620b
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Improved output. Can optionally limit the number reads actually called.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@720 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-15 00:07:57 +00:00 |
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kiran
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5858f20902
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Documentation.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@712 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-14 18:58:43 +00:00 |
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kiran
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3761c0900b
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Added Bustard vs. Four-prob percent bases consistent output.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@710 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-14 18:01:41 +00:00 |
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kiran
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959cf09d4b
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Removed some debugging print statements.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@707 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-14 17:12:42 +00:00 |
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kiran
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2f42a643a8
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A new, much simpler (and now, complete) driver program for four-base probs. Serves as a model for anyone who wants to write their own driver program that trains and calls with data from a different source than the raw Illumina data.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@706 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-14 16:58:22 +00:00 |
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kiran
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5824dea0c1
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Trains and calls a read at a time rather than a base at a time (which, given it's name, it should have done in the first place)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@705 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-14 16:57:00 +00:00 |
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kiran
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e4770885fd
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The four-probs for all bases in a single read. Some utility functions for generating the primary and secondary base strings, as well as generating the SQ tag byte array in a manner that's consistent with the Bustard base calls (meaning the primary Bustard call and the secondary Four-Prob call are not permitted to be the same).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@704 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-14 16:55:49 +00:00 |
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kiran
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fdd123fe16
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A parser the raw Illumina data. Allows one to arbitrarily jump from one tile to another.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@703 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-14 16:53:07 +00:00 |
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kiran
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6d98234555
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Holds raw intensities, sequence, and quality scores.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@701 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-14 16:52:03 +00:00 |
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kiran
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241de0b235
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A class that implements multiple training strategies and presents the training data in a common form.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@700 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-14 16:51:29 +00:00 |
depristo
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5b47c5ab6c
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fixing kiran's busted build
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@686 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-12 21:29:04 +00:00 |
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kiran
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4f2c8bf0a3
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Fixed an import statement that broke when all the files were moved to this directory.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@685 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-12 20:43:16 +00:00 |
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kiran
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cedc4c9ccb
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Refactored into oblivion.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@684 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-12 20:33:07 +00:00 |
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kiran
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688358190c
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Moved secondary base stuff out of playground for the purpose of making it a core utility. Modified package names and imports such that things would build properly.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@680 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-12 20:24:18 +00:00 |