hanna
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ec2e8d5726
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Fixes for getting ValidatingPileup running in parallel.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@807 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-22 21:20:24 +00:00 |
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hanna
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01a3cb27c7
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@Required / @Allows flags for main arguments.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@751 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-19 23:26:17 +00:00 |
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hanna
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752928df94
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Switch to better mechanism for supplying a default.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@615 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-07 01:22:01 +00:00 |
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hanna
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b0cdba8bb3
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Acting on Kiran's suggestion to make the doc tag in the @Argument annotation required.x
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@598 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-05 22:43:40 +00:00 |
depristo
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50ae1763f7
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Support for -continue_after_errors flag in the validating pileup walker in case you want to see errors as they arise, rather than aborting greedily
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@461 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-17 03:13:11 +00:00 |
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depristo
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24722a442e
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Slight code cleanup
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@421 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-14 22:21:36 +00:00 |
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depristo
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72a3d84ed2
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General purpose pileup code -- you can use these features to obtain detailed pileup data from reads and offsets. Useful for all pileup based walkers. Expanded support for rodSAMPileup to enable the new ValidatingPileupWalker, which takes a samtools pileup output and checks that GATK gives identical output as samtools on a per base and per qual pileup. It's going to be a very useful validation tool.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@418 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-14 22:13:10 +00:00 |