2db86b7829
Move the cleaned read injector test from playground to core. Remove CovariateCounterTest's dependency on the CleanedReadInjector. Start doing a bit of cleanup on the CLP's FieldParsers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1312 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-24 19:44:04 +00:00
b61f9af4d7
Cleaning up, preparing to incorporate a better fix for Eric's problems with validation stringency in BAM files opened directly from the walkers.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1222 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-13 01:42:13 +00:00
dc748d9c9c
Integrate more feedback on command-line argument system. Focus on help
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formatter: separate required from optional but otherwise keep ordering
the same, reorder GATK arguments by usage.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@764 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 19:01:25 +00:00
d152c2b911
New GATKArgumentCollection caused a subtle bug with argument grouping and the help system. Fixed.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@738 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-17 14:54:25 +00:00
7f8850a8a2
Argument validation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@631 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 20:28:56 +00:00
4f85062004
Cleanup parsing method to make it less generic.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@619 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 16:21:17 +00:00
4177560543
Mutually exclusive options.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@616 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 13:27:48 +00:00
9c0b81e946
Default flags to 'not required'.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@612 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 22:09:49 +00:00
1fe8155111
Some critical fixes for cases where argument values directly abut argument names
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and for arguments with missing short names.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@610 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 21:47:34 +00:00
62e7e46754
Miscellaneous cleanup. Better display of help output. Better exception subtyping. More thought-out access routines.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@608 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 21:16:01 +00:00
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
bfd6dfe36c
Added real-world tests and tests for conditional validation.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@601 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 13:38:46 +00:00
2ee9374975
Check for proper error output in case of boolean args with parameter specified.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@599 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 23:08:48 +00:00
ec0261275b
Lots of command line argument validation. Catches all common validation problems, including missing required arguments, invalid arguments, and several types of misplaced argument value errors.
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Still pending:
- Help system.
- Mutually exclusive arguments.
- Design includes too many classes per file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@597 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 22:08:00 +00:00
6550fe6f97
Another pass of command-line arguments. Revised parser supports all types
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of arguments that the existing parser supports, but does a poor job with
validation.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@591 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-04 22:41:23 +00:00
4f2ccda56a
Interface skeleton for a new command line argument parser. Nowhere near the point of being a drop-in replacement for apache cli yet.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@588 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-04 00:11:42 +00:00
hanna