hanna
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de1c282e62
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Reference-ordered data relies on bugs in the old command-line argument system to work. Update the ROD system to from -B track1 type1 file1 track2 type2 file2 to -B track1,type1,file1 -B track2,type2,file2.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@640 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-08 15:28:19 +00:00 |
depristo
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17b3d5b554
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New ROD accessing system, including a generalized interface for binding ROD on the command line that doesn't require you to chance GenomeAnalysisTK.java
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@355 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-09 22:04:59 +00:00 |
asivache
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0d25e71953
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a declaration is made generic
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@295 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-04 21:55:02 +00:00 |
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depristo
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4eac3193f7
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Added RefMetaDataTracker system as a replacement for the List<RefenenceOrderedData> going into walkers. This system allows you to more easily get a tracker for processing using the lookup(name, default) system. See Pileup for an example.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@292 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-03 19:54:54 +00:00 |
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depristo
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edc44807af
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rod's now have names. Use getName() to access it. Next step is better interface to accessing rods
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@286 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-03 16:41:33 +00:00 |
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depristo
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d952790258
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GFF now parses attributes correctly and efficiently. Slightly better interface to Utils.join
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@253 348d0f76-0448-11de-a6fe-93d51630548a
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2009-04-01 22:54:38 +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 |