kiran
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02c0afdb85
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Added the ability to specify the sorted, unaligned bam and/or the sorted, aligned bam such that broken computations can be restarted.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@805 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-22 19:33:34 +00:00 |
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kiran
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287bb52e81
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Refreshes the mount points that we'll be using (so that the program will play nicely with LSF).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@783 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-21 20:36:12 +00:00 |
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kiran
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5f67914b08
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Added loads of documentation.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@777 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-21 19:40:47 +00:00 |
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kiran
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747521c849
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Fixed the simplest of typos.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@761 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-20 16:00:30 +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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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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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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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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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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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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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 |