230c1ad161
moved a bunch of files over to the logging system. In some cases I ballparked the severity level of an error, so if you see something wrong feel free to make changes.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@211 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-27 14:02:55 +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
f7097c8ee7
Cleanup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@205 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-26 21:24:12 +00:00
728f932ecf
Fix exclusive options.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@204 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-26 20:59:32 +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
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
2808fd4bbd
Better support for required mutually exclusive options.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@199 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-26 03:22:30 +00:00
08ece8df79
Bug fixes and support for mutually exclusive options. Still a bit rough, but will
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be easier to clean up after a walker refactoring.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@198 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-26 03:11:56 +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
c18f8fbf5f
Documentation and cleanup of xReadLines.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@190 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-25 15:36:21 +00:00
d11bb0fc64
Added xReadLines class to utils. It is a iterator<string> and iterable<string> so you can easily read all lines from a file. It's been used to simplify the code to process intervals, and will be used to add merging data support to the system...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@187 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-25 15:17:38 +00:00
ff98e28abf
High-performance interval list implement -- uses StringBuilder to avoid n^2 calculation. Can handle millions of locations quickly now
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@182 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-25 02:17:48 +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
c047b53d6b
added some cleanup of code, and new junit targets to the build file
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@177 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-24 21:16:12 +00:00
6df19ab793
Support for byInterval traversals for Jared. Do not use them.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@175 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-24 20:55:34 +00:00
a3b8830855
need more access, found out in junit testing
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@165 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-24 13:22:09 +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
aaron
hanna
depristo