depristo
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919a86e876
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Cleaned up code for by interval traversals for Jared. Initialization code refactored and made clear. by loci and by loci by interval use the same underlying code now. Everyone uses the same initialization code to set things up. It's a party in the TraversalEngine and everyone's invited...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@179 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-24 22:32:45 +00:00 |
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 |
aaron
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c047b53d6b
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added some cleanup of code, and new junit targets to the build file
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@177 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-24 21:16:12 +00:00 |
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depristo
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6df19ab793
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Support for byInterval traversals for Jared. Do not use them.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@175 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-24 20:55:34 +00:00 |
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depristo
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9f500215da
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Support for reseting the system; Cleanup later
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@174 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-24 20:52:11 +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 |
asivache
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4222016bf5
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stop printing sw matrix and other debug infoant
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@171 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-24 18:15:52 +00:00 |
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asivache
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8ea8a74fbf
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fixed bug in calculation of alignment start offset for negative offsets; toString() added
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@170 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-24 18:05:28 +00:00 |
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asivache
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9aa1ccd9b7
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fixed some bugs in calling the optimal path; parameters adjusted (?)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@169 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-24 17:27:51 +00:00 |
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kiran
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88d94d407a
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Fixed a bug in the parsing of the second end of the pair.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@168 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-24 14:34:37 +00:00 |
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asivache
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786a7845dd
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@167 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-24 14:06:44 +00:00 |
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asivache
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3d1e0bf079
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@166 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-24 14:06:24 +00:00 |
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aaron
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a3b8830855
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need more access, found out in junit testing
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@165 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-24 13:22:09 +00:00 |
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asivache
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908065125f
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computes Smith-Waterman pairwise alignment
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@164 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-24 05:36:37 +00:00 |
andrewk
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9dee9ab51c
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Added Hapmap data track (using rodGFF class for GFF file format) to toolkit as a command line option, Hapmap metrics to AlleleFrequencyMetricsWalker, and a python Geli2GFF file converter.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@163 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-24 03:58:03 +00:00 |
hanna
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f7363cf935
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Support for loading from either a jar or a class directory. Fixes troubles with IntelliJ debugging.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@162 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-24 03:56:49 +00:00 |
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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 |