fromer
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004f5295ea
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Moved scripts to phasing/scripts sub-directory
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5612 348d0f76-0448-11de-a6fe-93d51630548a
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2011-04-11 15:25:39 +00:00 |
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fromer
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822b4d66ce
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FOR KIRAN: Adding R scripts and functions that perform theoretical calculations of phasing
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5611 348d0f76-0448-11de-a6fe-93d51630548a
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2011-04-11 14:18:30 +00:00 |
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fromer
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cc909602c7
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Vectorize() pDirectlyPhaseHetPairAtDistanceUsingDepth; deal with minor precision issues
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4890 348d0f76-0448-11de-a6fe-93d51630548a
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2010-12-21 17:18:26 +00:00 |
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fromer
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a829284d84
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Return analyzed window sizes as well
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4884 348d0f76-0448-11de-a6fe-93d51630548a
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2010-12-20 17:00:17 +00:00 |
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fromer
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6310a524d9
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Do not abort integration (over het-het distances) on errors, but warn about them
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4855 348d0f76-0448-11de-a6fe-93d51630548a
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2010-12-16 17:20:25 +00:00 |
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fromer
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b1f0df0047
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Handle case where read lengths are longer than fragment size
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4852 348d0f76-0448-11de-a6fe-93d51630548a
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2010-12-16 02:19:55 +00:00 |
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fromer
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a5e1854b3a
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Forgot to pass correct parameters to calcPhasingProbsForWindowDistances()
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4851 348d0f76-0448-11de-a6fe-93d51630548a
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2010-12-16 01:58:06 +00:00 |
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fromer
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2b0dc8625c
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Updated RBP theoretical model as per Mark's insights regarding the correct understanding of insert sizes being calculated post-hoc from the distance between read lengths. The correct way to think of it is: 1) There's a fragment of length F. 2) Each of it's two ends are read for L bases. 3) The insert size = i = F - 2 * L, after the fragment's assumed identity is determined by mapping the read mates to a reference sequence. Therefore, the external user-defined distribution is on the FRAGMENT SIZES
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4850 348d0f76-0448-11de-a6fe-93d51630548a
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2010-12-16 01:45:20 +00:00 |
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fromer
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aea481ae01
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Trivial bug fix
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4848 348d0f76-0448-11de-a6fe-93d51630548a
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2010-12-15 18:29:15 +00:00 |
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fromer
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c167c6f9eb
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Calculate the phasing probabilities for particular intra-het distances
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4838 348d0f76-0448-11de-a6fe-93d51630548a
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2010-12-14 18:44:59 +00:00 |
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fromer
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4dbdf7a13d
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Added ability to sample from intra-het distance distribution
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4836 348d0f76-0448-11de-a6fe-93d51630548a
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2010-12-14 18:09:03 +00:00 |
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fromer
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4403b9d276
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Added probability bound on phasing paths, which slightly speeds up calculations. It seems that a real speed-up can only be achieved by considering fewer paths by doing some form of caching of sub-problems (e.g., dynamic programming or matrix multiplication, as Mark suggested)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4832 348d0f76-0448-11de-a6fe-93d51630548a
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2010-12-13 23:53:56 +00:00 |
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fromer
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2bf4fc94f0
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Try to use more sampling to get a "correct" estimate of multivariate integral
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4815 348d0f76-0448-11de-a6fe-93d51630548a
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2010-12-10 02:58:46 +00:00 |
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fromer
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c64bf80b57
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Added theoretical model of read-backed phasing (RBP)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4814 348d0f76-0448-11de-a6fe-93d51630548a
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2010-12-10 01:46:09 +00:00 |