4b3578e1de
Added the base test case, fixed the rest of the test cases to follow suit. Added more verbose output to ant for junit tests.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@403 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-14 17:11:38 +00:00
32e000bbfe
Added MatchSQTagToStrand jar target.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@377 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-13 00:50:36 +00:00
49fd951d8c
Initial test suite for FastaSequenceFile2, so I can add parallelism support with abandon.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@364 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-11 21:10:42 +00:00
a2a38a4bbb
Removed RepairBadlyCombinedSamFile jar target.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@359 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-10 04:21:19 +00:00
8efedacabf
Bump sam jdk to svn rev 207.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@340 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-08 22:16:46 +00:00
decf45664a
Removed now-useless FourBaseCaller jar target (FourBaseRecaller replaces it).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@277 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-02 22:13:51 +00:00
cb6a3b7e55
Bug fix: build couldn't be forced to core. Now it can be.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@221 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-29 01:36:25 +00:00
c4f0b4cab7
Oops. Javadoc output gets a lot cleaner when I remember to add the classpath.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@220 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-29 00:29:20 +00:00
74cae62ac2
Cleaned up generation of javadoc code. Still need to fix javadoc generation to take external dependencies into account.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@219 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-29 00:03:08 +00:00
fade36a8f2
Add targets to force build to core and force build to playground.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@216 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-27 22:32:44 +00:00
1d95f06ad5
Fix path issue generating javadocs.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@202 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-26 18:51:56 +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
a55d630ef9
Added FourBaseRecaller to list of jar targets (this is just until I figure out the appropriate way to combine FourBaseCaller and FourBaseRecaller).
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@172 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-24 20:10:48 +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
411e5cf647
Added FourBaseCaller as a jar build target.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@128 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-21 17:59:13 +00:00
ffb6f8f5da
Move the basic gatk framework into the core subtree.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@95 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-18 23:39:00 +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
kiran
hanna