f41965a73e
Fixed incompatiblity in variable name between my script and the new elements merged into my script.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2235 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 23:40:50 +00:00
357abc9e89
Update build.xml to make it oneoffprojects-aware, and do some misc formatting cleanup and moves.
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Here goes nothing.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2234 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 23:27:45 +00:00
c524b8e84b
add VCFTool.jar
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2221 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 19:04:38 +00:00
67179e2412
Initial checkin of AnalyzeCovariates.java which replaces analyzeRecalQuals_1KG.py and is updated to use the new Covariates system. It creates similar plots of residual error for each covariate that was used in the calculation. There is also an option to filter out base qualities below a given threshold.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2215 348d0f76-0448-11de-a6fe-93d51630548a
2009-12-02 16:47:35 +00:00
b7097a8db9
Build aligner as separate jar file.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2044 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-13 22:29:29 +00:00
8eff1cc436
Extract and include only the Tim Fennell-approved parts of picard private.
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Hopefully this is a temporary solution and these classes will be migrated
into picard-public.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2041 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-13 19:42:33 +00:00
21b1ece45d
removed some extra debugging commands from the build.xml
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1972 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-04 06:28:12 +00:00
c313abf0be
Restore a jar packaging change that got clobbered.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1962 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-03 00:15:45 +00:00
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
b95165e39c
Make alignment (temporarily) part of main GenomeAnalysisTK.jar. Add some extra logging errors on failure.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1953 348d0f76-0448-11de-a6fe-93d51630548a
2009-11-01 00:33:18 +00:00
5a64a80ab5
changes to the variation class, updates to SSG, updated tests based on changes to the SSGenotypeCall, and added the ability to run a single integration test from using the build script.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1577 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-10 04:31:33 +00:00
d9588e6083
bug fixes to LIBS and LIBH following ultra-aggressive regression testing across 454, solid, and solexa
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1558 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 15:36:12 +00:00
0df6a9da5c
-Seperating out normal (unit) tests and integration tests. From now on if your test are more of an integration test (i.e. you're testing a walker and all the subunits it relies on) please name the test "______IntegrationTest.java" instead of "______Test.java".
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-Bamboo will now run the integration tests once a day, and the normal units tests on each check-in.
-Also added a bunch of unit tests for VariantEval walker
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1555 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-09 15:01:40 +00:00
515fc7c476
overaggressively removed the STD outputs, back in for tests
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1514 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-03 15:07:45 +00:00
7d0a13d711
added options for building with xml output to files
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1513 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-03 15:00:27 +00:00
6c604af86c
Nicer building of scala programs
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1476 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-29 16:41:56 +00:00
ab9458d06d
support for scala walkers
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1468 348d0f76-0448-11de-a6fe-93d51630548a
2009-08-28 00:15:01 +00:00
f3e63f00bc
Exclude secondary base caller code from playground jar. Still TODO: figure
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out how do deal with the playground jar.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1344 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-30 21:02:46 +00:00
f7168bd7cf
added the abilty to build the jar's to a different location, like the following:
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ant -Ddist=altDist
or
ant -Ddist=/where/you/want/jars
Also changed the test build to depend on playground build instead of core, right now tests fail if you only build the core.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1299 348d0f76-0448-11de-a6fe-93d51630548a
2009-07-23 04:06:58 +00:00
af7a759ba4
Convert the somatic coverage tool to output from the packaging tool rather than from the dist target.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1050 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-18 21:29:30 +00:00
e2ccea4883
Cleanup. Move output of packaging to dist directory. Don't always create resources directory. Make jar take on the package name.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1023 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-16 22:47:23 +00:00
29df74ae23
Plumbed packaging support into build.xml and added package for GATK.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1012 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-15 19:41:16 +00:00
94b0e46d12
checked in a sample xml file used to store the defaults for the SomaticCoverage tool, and added it to the SomaticCoverage.jar in build.sml. Also added a inputStream marshalling method to the GATKArgumentCollection.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@979 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 20:46:16 +00:00
3a340ca887
adding the SomaticCoverage.jar to the list of generated jars, at least for now.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@977 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-10 20:05:54 +00:00
57e5f22987
We now only build the files that have changed. It should speed up compile time as our source tree grows.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@726 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-15 20:48:01 +00:00
d14cab0be7
Added IterableLocusContextQueue and test. Cleaned up tests, adding BaseTest where it didn't exist. Enhanced test runner to run only classes ending in ...Test.java, so that utility classes can sit alongside the tests but won't be run by JUnit.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@693 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-13 21:32:05 +00:00
688358190c
Moved secondary base stuff out of playground for the purpose of making it a core utility. Modified package names and imports such that things would build properly.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@680 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-12 20:24:18 +00:00
ff1b92acc4
Switch over to the GenomeAnalysisEngine/CommandLineGATK system from the GenomeAnalysisTK code.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@655 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-11 22:05:58 +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
89344ccc0f
Not sure why junit is so excited about running inner classes with no @Tests.
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Omit inner classes from the fileset of tests to run.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@595 348d0f76-0448-11de-a6fe-93d51630548a
2009-05-05 21:56:34 +00:00
b6a7ebd3c4
You can now test a single JUnit test from the command line, by specifying the test with the command line parameter -Dsingle=myTestName.
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example:
ant test -Dsingle=TraverseReadsTest
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@559 348d0f76-0448-11de-a6fe-93d51630548a
2009-04-29 13:30:47 +00:00
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
hanna
jmaguire
rpoplin
aaron
depristo
kiran