5eac510b2f
Refactor the code I gave Eric yesterday to output command line arguments.
...
Convert it from a completely wonky solution to a slightly less wonky solution
that will work in more cases.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2310 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-10 18:57:54 +00:00
10be5a5de9
Move some files around to reflect our growing help infrastructure.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2280 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-07 19:23:12 +00:00
62c484b57a
Fixes for GSA-201, where enumerated types in command line arguments had to be defined as all uppercase for the system to work.
...
Also a little playground walker that changes the sort order flag of a BAM file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1805 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-09 18:11:32 +00:00
70e1aef550
Better integrate the @ArgumentCollection into the command-line argument parser. Walkers can now specify their own @ArgumentCollections. Also cleaned up a bit of the CommandLineProgram template method pattern to minimize duplicate code.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1746 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-29 22:23:19 +00:00
ccdb4a0313
General-purpose management of output streams.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1454 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-23 00:56:02 +00:00
21091b9839
Fix for invalid format error when outputting BAM files.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1438 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-19 19:42:39 +00:00
7a13647c35
Support for specifying SAMFileReaders and SAMFileWriters as @Arguments directly. *Very*
...
rough initial implementation, but should provide enough support so that people can stop
creating SAMFileWriters in reduceInit.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1332 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-29 16:11:45 +00:00
2024fb3e32
Better division of responsibilities between sources and type descriptors.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1314 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-24 22:15:57 +00:00
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.
...
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
6e4fd8db4a
Better formatting of available walkers, and only output them along with help. Cleanup JVMUtils.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1290 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-21 22:23:28 +00:00
5c321f9630
Oops! Accidentally deactivated the ArgumentFactory, needed by the CleanedReadInjector, while refactoring last night.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1223 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-13 16:41:55 +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.
...
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
da4d26b1ea
Enum support for command-line argument system, and some cleanup for hacks to the CleanedReadInjector that were required because Enum support was missing.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1199 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-08 20:26:16 +00:00
5d7393d7cb
Temporary fix for Eric's problems with SOLiD reads: make sure the command-line argument system takes the --validation-strictness command-line argument into account when creating SAMFileReaders.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1183 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-07 15:18:05 +00:00
5859948e80
Fixed bugs in CleanedReadInjector arising from integration testing.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@999 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-12 17:37:33 +00:00
fa93661133
Eric wins the prize for pointing out that doubles weren't valid command-line arguments. Made all primitive types parseable as command-line arguments.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@884 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-02 22:41:10 +00:00
dc748d9c9c
Integrate more feedback on command-line argument system. Focus on help
...
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
01a3cb27c7
@Required / @Allows flags for main arguments.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@751 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-19 23:26:17 +00:00
40dbc21df7
Moved ParseException to it's own file and made it public.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@750 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-19 14:42:44 +00:00
e6ce80c8e3
Fix for GSA-44...don't throw exception when user specifies -h.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@742 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-18 00:42:00 +00:00
7161b8f927
Disable support for short name values directly abutting their arguments.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@740 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-17 16:09:32 +00:00
ee02b61068
added support for the argument collections code
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@648 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-09 07:07:33 +00:00
7f8850a8a2
Argument validation.
...
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
a3d8febbf2
Error message cleanup.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@630 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 19:31:32 +00:00
c241d386a7
Beefed up command-line usage string.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@629 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 19:08:19 +00:00
4f85062004
Cleanup parsing method to make it less generic.
...
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.
...
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
1fe8155111
Some critical fixes for cases where argument values directly abut argument names
...
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.
...
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
98716138e9
Cleanup: add support for non-public fields. Track matches as state of parsing engine as well as definitions.
...
Made fields of command-line argument system non-public by default.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@606 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 19:38:05 +00:00
ef211f96b1
Remove old Apache CLI-based arg system.
...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@604 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 18:37:51 +00:00
521aa40baa
Bring new command-line argument parsing system live.
...
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.
...
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
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.
...
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
...
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.
...
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
aaron
kiran