521aa40baa
Bring new command-line argument parsing system live.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@603 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 18:16:11 +00:00
4ac9e72739
Migrate default and GATK arguments over to new attribute system in preparation for conversion.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@600 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 23:57:48 +00:00
ce57fed2fb
Hack to work around an Apache CLI bug, where core arguments couldn't be commingled with walker arguments. These arguments can commingle now. Everybody into the pool.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@252 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-01 20:56:42 +00:00
935a4d81c9
fixed the problem where you could specify a logging level that didn't exist
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@208 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-27 04:29:27 +00:00
53fe9acf65
Make command-line arguments available in walker constructor, provide back door from
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walker into GATK itself, do some cleanup of output messages, and add some bug fixes.
Command-line arguments in walkers are now feature-complete, but still a bit messy.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@203 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-26 20:45:27 +00:00
4b7bfb284a
Support for more complex command-line types: arrays, untyped collections, typed collections, interfaces to typed and untyped collections.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@194 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-25 20:11:31 +00:00
9e2a373184
Prototype, buggy implementation of walker command-line arguments. Doesn't
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(yet) deal elegantly with even simple cases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@180 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-25 00:12:00 +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
aaron