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 |
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 |