b43925c01e
Switched to Reflections ( http://code.google.com/p/reflections/ ) project for
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inspecting the source tree and loading walkers, rather than trying to roll
our own by hand.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1286 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-21 18:32:22 +00:00
ed7fac1c90
Add bcel and cleanup.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1032 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-17 19:28:04 +00:00
5e8c08ee63
Update to latest version of picard. Change imports in all classes dependent on picard public from import edu.mit.broad.picard... to import net.sf.picard...
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@849 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-28 20:13:01 +00:00
aa17c4a468
Farewell, functionalj. You promised much, but you could not deliver.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@847 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-28 01:35:49 +00:00
df8490a0cf
Remove unused dependency on commons logging.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@829 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-27 14:12:26 +00:00
1a3ca97d29
remove the ivy command for dependency on BCEL, we're not using it right now.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@775 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-21 19:35:53 +00:00
c34eaa6962
add javassist, which is a less lower level version of bcel.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@755 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-20 05:11:03 +00:00
21536df308
Change the sample XML marshalling code over to simple XML, and take out the castor lines in the ivy.xml
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@633 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-08 00:08:25 +00:00
5d9536d2b4
Added simple xml to replace castor (at least for now)
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@632 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-07 23:57:18 +00:00
ef211f96b1
Remove old Apache CLI-based arg system.
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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
98f4920739
Added BCEL and some basic instrumenation code to the test library.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@602 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-06 17:18:23 +00:00
abe2d25f10
Added castor dependency.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@321 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-07 22:27:39 +00:00
067ae09cd0
Bump picard and samtools to latest.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@207 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-27 02:26:28 +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
046cecb067
Switched our code over to the new command line style (gnu style args), added the initial logger code, and added apache commons CLI to the IVY script.
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There will be a slow conversion of all the System.out and System.err in other files to the logger style output.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@145 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-22 21:06:22 +00:00
1fcf4c0cbf
Update picard to work with new samtools.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@123 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-20 21:51:26 +00:00
7bc45b68aa
Added dependences on two libraries: the Colt package, which is a collection of high performance computing libraries from CERN; and Log4j, which will be our new logging platform.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@100 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-19 16:16:31 +00:00
1096bbd4d9
Moved build.xml, ivy.xml and settings to root of Sting repository.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@88 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-18 19:13:19 +00:00
hanna
aaron