de6ae51f7e
Scala walkers can now be build and run like any other walker in the GATK. Added the getUrlsForClasspath to PackageUtils, the Reflections package isn't getting the manifest files from jars in the classpath, and so we weren't seeing any walkers outside of the GenomeAnalysisTK.jar.
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A couple of notes:
-Commented out BaseTransitionTableCalculator.scala because it's won't build; Chris could you fix this one (or kill it if it's not needed).
-Removed the PrintReadsScala walker; moved the code over to a ScalaCountLoci walker (which is what the code was really doing).
-Added configurations items to the ivy xml file.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1956 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-02 06:02:41 +00:00
c35a457a09
Delete duplicate jgrapht reference.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1935 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-29 17:38:01 +00:00
86573177d1
Reverting rod walkers to use underlying refwalker implementation while we work on ROD2 and reenable the system. Added some serious sparse file parsing to variant eval tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1929 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-29 01:04:37 +00:00
e3b9114664
Added jgrapht dependency.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1923 348d0f76-0448-11de-a6fe-93d51630548a
2009-10-28 14:29:17 +00:00
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
aaron
hanna
depristo