hanna
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08c4fb86e3
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Derive examples from real data.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1213 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-10 04:21:37 +00:00 |
aaron
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9d659199f3
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bam and fasta files generated with the artificial tools. These will be included in the GATK distro.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1151 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-01 22:49:31 +00:00 |
depristo
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9e26550b0d
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Apprach v2. Added python analysis script, so java no longer must be used to analyses quality score data. About to refactor out lots of unneeded code
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1063 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-20 16:00:23 +00:00 |
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depristo
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8ac40e8e2d
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Updated version of the recalibration tool
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1060 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-19 17:45:47 +00:00 |
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depristo
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7834b969b4
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Better interface to the tabular ROD, now makes writing files easier. Also has corresponding test files
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@719 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-14 23:20:11 +00:00 |
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depristo
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8e9e2f4502
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Revised ROD system. Split the system in Basic type and interface. Enabled more control over rod accessing, including an initialize() function to fetch headers and other options from the file. Added general tabular rod, which has a named columns and supports a map<String,String> interface. Comes with shiny new Junit system for RODs. Also, added simple python script for accessing picard data.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@716 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-14 21:06:28 +00:00 |
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depristo
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30218ee31a
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Better validation scripts and data
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@562 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-29 17:40:07 +00:00 |
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depristo
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40a2b3eeb3
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Basic logistic regression support for calibrating qualities; mostly for Andrew to experiment with
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@529 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-24 19:09:50 +00:00 |
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depristo
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e842b543c9
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Better validation scripts
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@458 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-16 23:18:00 +00:00 |
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depristo
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f47f640df6
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Better debugging output and testing
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@455 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-16 21:54:56 +00:00 |
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depristo
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6c9d110eb9
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better description
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@440 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-15 22:06:36 +00:00 |
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depristo
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2eabcfedb7
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Fixed potential bug with next() operation returning empty contexts when a read contains a large deletion. We can now use the look ahead safely...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@439 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-15 21:41:30 +00:00 |
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hanna
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25ddc0f5ea
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Skeleton of new directory structure.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@34 348d0f76-0448-11de-a6fe-93d51630548a
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2009-03-11 20:05:05 +00:00 |