752928df94
Switch to better mechanism for supplying a default.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@615 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 01:22:01 +00:00
b0cdba8bb3
Acting on Kiran's suggestion to make the doc tag in the @Argument annotation required.x
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@598 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 22:43:40 +00:00
ce470702fc
consistency with java naming conventions
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@535 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 21:44:48 +00:00
05c6679321
Enabled ReduceByInterval
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@533 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-24 21:39:44 +00:00
4eac3193f7
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.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@292 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-03 19:54:54 +00:00
6994cca988
added precision
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@246 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-01 16:21:29 +00:00
8d601a6a42
unbox
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@239 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-31 15:51:59 +00:00
234137dee8
use boolean instead of String for flag to suppress printing in map
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@236 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-31 15:14:00 +00:00
3896cc8f17
Moved avg depth of coverage functionality into the core depth of coverage
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walker. Used new command line args for walkers.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@234 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-31 05:02:33 +00:00
4a6be896b9
Provide out and err PrintStreams to the walkers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@213 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-27 15:03:32 +00:00
5f9010116a
Collapse the walker hierarchy, in preparation for in-walker output streams less hokey walker args.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@201 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-26 16:22:35 +00:00
8bdf49a01f
added slightly more useful output to Depth of Coverage walker. (now prints number of loci). Traversal engine now actually prints the reduce result (key) and no longer prints millions of locus interval updates
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@183 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-25 03:12:54 +00:00
63cd1fe201
Push core / playground lower into the tree.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@160 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-23 23:19:54 +00:00
hanna
depristo
ebanks