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195 Commits (b08d63a6b8dc4e7b8f21c528f234d34f81ce654a)

Author SHA1 Message Date
Mark DePristo 198955f752 GATKDoc descriptions for all standard codecs, or TODO for their owners 
-- Also added vcf.gz support in the VCF codec.  This wasn't committed in the last round, because it was missed by the parallel documentation effort.
 2011-08-19 09:57:21 -04:00
David Roazen 6ee8a3a8dd Fixing the javadoc/scaladoc targets in build.xml 
Usable targets are now:

ant javadoc           (public-only)
ant javadoc.private   (public + private)
ant scaladoc          (public-only)
ant scaladoc.private  (public + private)

As documented in the comments, you need to set the ANT_OPTS environment
variable to -Xmx1G before using the scaladoc targets.

Will modify bamboo to auto-generate these and post them to the web after
successful builds.
 2011-08-11 19:24:41 -04:00
David Roazen bd5cdb8a43 The tribble dependency is now handled through ivy. Revved tribble to r18 and removed obsolete build targets in build.xml 2011-08-11 16:38:29 -04:00
Mark DePristo 4d88e72958 Merge remote-tracking branch 'remotes/khalid/rodRefactor' into rodRefactor 
Conflicts:
	public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
	public/java/test/org/broadinstitute/sting/BaseTest.java
 2011-08-07 10:32:27 -04:00
Khalid Shakir f049461120 Changed @Argument to @Input on input RodBindings. 
Changed shortname collision with longname.
Restored scala builds.
Updated HSP to use new syntax.
 2011-08-06 20:44:19 -04:00
Mark DePristo b68ed62632 Clean now removes gatkdocs 2011-08-03 18:11:22 -04:00
Mark DePristo b25140db83 Contracts and documentation for some of RefMetaDataTracker 
Continuing to fix integration tests that don't pass / run
 2011-08-03 13:34:20 -04:00
Mark DePristo a366f9a18d Updating tools to use the RodBinding<T> syntax 2011-08-02 14:05:51 -04:00
Kiran V Garimella ab69b8e4ee Merged bug fix from Stable into Unstable 2011-07-27 12:37:34 -04:00
Kiran V Garimella 6ebd83478b Fixed build.xml to reflect path changes for gsalib 2011-07-27 12:37:00 -04:00
Kiran V Garimella ada2f21976 Revert "Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable" 
This reverts commit 9c81ef835a3ac581d4eb9cf1243e30df20a46795, reversing
changes made to f23d3ad5aec1c70cc1ecc48b295258aa70d30c7d.
 2011-07-27 12:27:17 -04:00
Kiran V Garimella dc8061e7a6 Moved gsalib from private/ to public/ 2011-07-27 10:34:56 -04:00
Matt Hanna 6fd6684e86 Merged bug fix from Stable into Unstable 
Conflicts:
	build.xml
 2011-07-25 15:21:17 -04:00
Matt Hanna 6f43284053 Switch to including our entire exception tree rather than just UserException. 2011-07-25 15:19:41 -04:00
Matt Hanna af0b5883c3 In unstable, add a reference to DocumentedGATKFeature to vcf.jar, which is now 
a static dependency of UserExceptions.
 2011-07-25 14:36:12 -04:00
Matt Hanna 6c49197de6 Merged bug fix from Stable into Unstable 2011-07-25 14:32:33 -04:00
Matt Hanna a00e302321 Fix formatting issue. 2011-07-25 14:31:40 -04:00
Mark DePristo c6af4efcdc Implemented see also and version header 2011-07-24 16:10:17 -04:00
Mark DePristo 7420ed098e Semi-working version of extraDocs tag in annotation to refer to one capability being accessible in another 
Required a significant refactoring of the GATKDoclet, which now has a unified place where the ClassDoc, class, annotation, and handler are all stored together.
 2011-07-23 22:07:30 -04:00
Mark DePristo 999acacfa1 Merge branch 'master' into help 2011-07-23 20:19:33 -04:00
Mark DePristo e262f4e10b gatkdoc now generalized to use @Annotation. Multiple subsystems now use annotation to receive docs 
Index expanded to use summary() annotation field
UserExceptions, ReadFilters, GATK engine all use the system to generate docs
Doclet expanded to handle lots of new cases
 2011-07-23 20:00:35 -04:00
Khalid Shakir 1f8fc4a041 Added edu.mit.broad.picard to Queue packaged jar. 
Added hack to workaround EDU.oswego namespace and staging on mac case-insensitive filesystems.
 2011-07-23 14:40:29 -04:00
Mark DePristo f0be7348be Generalized handler to allow it to be used with any arbitrary class structure. 
DocumentedGATKFeature now includes a field for the group name.
Build.xml works with public / private now.
 2011-07-22 14:07:40 -04:00
Mark DePristo e892489696 V2 of the document system. 
Now uses GATKDoc class to organize documentation for arguments.
Arguments now listed by feature (required, optional, hidden, etc) and link to detailed information about the argument in the html
Lots of code moving between Class and ClassDoc objects.  Should be refactored into a single static utility class.
 2011-07-21 15:20:34 -04:00
Mark DePristo 6fa17d86ae Completely hacked together version of a FreeMarker + javadoc + custom doclet walker documentation generator 2011-07-21 00:18:07 -04:00
Mauricio Carneiro 0cac5e9ebe Merged bug fix from Stable into Unstable 2011-07-15 19:38:20 -04:00
Mauricio Carneiro 1e4798d5d0 Added targets to build.xml to re-run only tests that have failed (integration, unit, performance or pipeline tests). 
This is very useful and easy. After running any test (for example ant integrationtest) and seeing failures, you can rerun ONLY THE TESTS THAT FAILED by using one of the following commands:

ant failed-integration
ant failed-pipeline
ant failed-test
ant failed-performance

obviously matching whatever tests you were running and got failures on.

This should run only the failed tests, and you can keep using this command until you have fixed everything.

(Thanks to David Roazen for major help with ANT)
 2011-07-15 19:34:14 -04:00
Mark DePristo f313e14e4e Now deletes the dump directory on ant clean 
Moving diffengine tests from private to public
 2011-07-12 08:50:58 -04:00
David Roazen 68e19edf59 Merged bug fix from Stable into Unstable, and resolved merge conflicts. 
Conflicts:
	build.xml
	settings/ivysettings.xml
 2011-07-08 15:50:31 -04:00
David Roazen a3c9d9c3ff Fixing Contracts for Java, and enabling contracts by default for unit/integration tests. 
The NullPointerException we were seeing when trying to run with contracts enabled was being caused
by an outdated version of the asm library.

To run tests without contracts and disable their compilation, pass in "-Duse.contracts=false" to ant.

Also did some minor unrelated cleanup in build.xml
 2011-07-08 15:34:39 -04:00
Mark DePristo 8add2a3866 Merge branch 'master' into diffengine 2011-07-08 09:15:54 -04:00
Khalid Shakir 515553c801 Merged bug fix from Stable into Unstable 2011-07-06 11:34:13 -04:00
Khalid Shakir c93d0b37a8 Fixed namespace of the pipeline classes. 2011-07-06 11:32:46 -04:00
Khalid Shakir 7b699f8b17 Switched GridEngine from looking from environment variable to using embedded jar. 2011-07-05 21:59:00 -04:00
Mark A. DePristo 080875d5da Refactored DiffNode/DiffElement/DiffValue class structure. DiffElement is now a pair of Name -> Value, where value is either a DiffValue or its subclass DiffNode. Code cleaned up, more tests added. DiffEngine is now working, with tests. DiffObjectWalker can now take two VCFs and itemize the difference between the two files correctly and concisely. 2011-07-05 16:13:39 -04:00
David Roazen 4b17f34640 Fixes to the packaging system to work with the new directory structure. 
Also added a few R scripts to the list of files to include in the resources
directory of the binary distribution, at Ryan's request.
 2011-06-30 18:27:17 -04:00
Matt Hanna 9a22d78e48 Fix up gsalib target to work with new public/private directory structure. 2011-06-29 14:48:10 -04:00
David Roazen 7e243fae6e Bug fixes for build.xml related to the public/private restructuring. 2011-06-28 12:55:18 -04:00
David Roazen 139c6b84a1 Modified build.xml and the help extractor doclet to use the output of "git 
describe" as an absolute version number (if the repository has at least one
tag), using the raw SHA-1 hash value as a fallback version number in the case
where there are no tags.
 2011-06-28 08:37:05 -04:00
David Roazen 3c9497788e Reorganized the codebase beneath top-level public and private directories, 
removing the playground and oneoffprojects directories in the process. Updated
build.xml accordingly.
 2011-06-28 06:55:19 -04:00
ebanks c2ec2891d1 Other people besides Mark also wanted VariantContext moved to the GATK, so I listened. I am moving VariantContext and all codecs that rely on it (VCF, SoapSNP, HapMap, and CGvar) to the GATK - including relevant unit tests and data files. Additionally, Matt has modified build.xml to generate the necessary jar files so that people can use our VCF codec with Tribble. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6077 348d0f76-0448-11de-a6fe-93d51630548a
 2011-06-24 16:56:04 +00:00
depristo e87c40d89c Fix for CoFoJa exception by upgrading to latest version 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5971 348d0f76-0448-11de-a6fe-93d51630548a
 2011-06-09 17:49:15 +00:00
hanna 6c4f2f1b36 Temporarily disable contracts during integrationtest, take 2. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5968 348d0f76-0448-11de-a6fe-93d51630548a
 2011-06-09 16:36:31 +00:00
hanna 44b98bed8c Killed sonatype repository; it's failed me too many times at this point. 
Temporarily disabled contracts in integrationtests until we can find the cause
of the new error that's cropping up for Ryan.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5967 348d0f76-0448-11de-a6fe-93d51630548a
 2011-06-09 16:07:02 +00:00
depristo 311dfa0998 Now builds examples, as I expected. GATKPaperGenotyper lives again. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5953 348d0f76-0448-11de-a6fe-93d51630548a
 2011-06-07 00:13:44 +00:00
kshakir 77cae39c8e Step towards tribble precompiled jar, support in build.xml for source with fallback to the checked in jar. 
Current tribble-129M.jar in SVN does not work with current version of GATK code.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5897 348d0f76-0448-11de-a6fe-93d51630548a
 2011-05-27 21:04:27 +00:00
depristo a02ab4028b Build for tests now includes path to contracts 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5840 348d0f76-0448-11de-a6fe-93d51630548a
 2011-05-22 19:44:49 +00:00
depristo 0095aa2627 Contracts for java now enabled by default in GATK build. The contract checking is automatically enabled when running tests and integrationtests. If you want to run the GATK with Contract checking enabled, add -javaagent:lib/cofoja.jar to your jvm args 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5826 348d0f76-0448-11de-a6fe-93d51630548a
 2011-05-20 02:53:42 +00:00
depristo 218354e338 Contracts for Java (http://code.google.com/p/cofoja/) infrastructure enabled. No piece of code actually uses this, so it's possible to remove easily. Does not build by default (you must modify build.xml). Really an intermediate commit so I can play around with the system in my java classes and revert safely. Very much looking forward to DVCS 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5815 348d0f76-0448-11de-a6fe-93d51630548a
 2011-05-18 18:05:59 +00:00
kshakir ec443e89cf Added pass-throughs for -Djava.io.tmpdir to javac and testng. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5791 348d0f76-0448-11de-a6fe-93d51630548a
 2011-05-11 20:56:35 +00:00