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142 Commits (81f8e05bfadc3033e962a7b3d25b847f0bce58dc)

Author SHA1 Message Date
Mark DePristo 2039ce6102 Default values now displayed in arguments 
DiffEngine fixed so that newInstance() would work.  Pretty quickly encountered a situation where newInstance() failed.  Debug output now written when this occurs in the log.
Logger now used instead of standard out, with INFO the default level.
 2011-07-24 22:56:55 -04:00
Mark DePristo 7b84347047 Main index is sorted by the template now. 2011-07-24 18:19:40 -04:00
Mark DePristo 83996f7951 Enumerated types are working. 2011-07-24 18:14:21 -04:00
Mark DePristo 3c34e9fa65 Cleanup emuns and tables 2011-07-24 17:45:58 -04:00
Mark DePristo c620d96c96 Inline enum documentation is working 2011-07-24 17:22:14 -04:00
Mark DePristo 793e7d3d1d Improved header and argument details 
Argument detail structure cleaned up. Only relevant pieces of information are shown now, and in a cleaner layout.
Misc. cleanup in the code.
 2011-07-24 16:36:25 -04:00
Mark DePristo c6af4efcdc Implemented see also and version header 2011-07-24 16:10:17 -04:00
Mark DePristo b8db0510e0 Sytle sheet and common functions 2011-07-24 15:43:23 -04:00
Mark DePristo 5e0fe2d0f9 Support for style.css via refactored common.html included in all files 2011-07-24 15:42:39 -04:00
Mark DePristo d0ab6bf7a9 Now links to sub and superclass documentation, where possible. 2011-07-24 09:56:17 -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 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
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 453954182e Generalized the documentation system to use a class-specific annotation and processor. 
Need to generalize and bug fix the system.  But at a high level it's working now.
 2011-07-22 13:18:33 -04:00
Mark DePristo e922ebc29d Missed this template for walker index. 2011-07-22 09:13:33 -04:00
Mark DePristo 81d0cab27e Walker index html now emited. 2011-07-21 16:01:54 -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
David Roazen baae381acb Revert "Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable" 
This reverts commit 039a6bb01f345322ce2be50ae3634308bb24e77e, reversing
changes made to b9c9973d1c638dfc9f8c19b5eb845e99844f9d29.
 2011-07-19 18:38:53 -04:00
Matt Hanna 00b650a35d Get rid of accidental commit of emacs backup '~' file. 2011-07-17 20:52:46 -04:00
Matt Hanna 567ed66085 Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-07-17 20:44:43 -04:00
Matt Hanna 0a0363aef2 Revving Picard to get a parser that works with the latest metrics file formats 
we're starting to see.
 2011-07-17 20:43:35 -04:00
Mark DePristo 35ec82a467 Oops, need this 2011-07-17 13:08:08 -04:00
Mark DePristo 4db2b13e9e Rev tribble. 
Just added more documentation for diffEngine and pointer to new wiki:

http://www.broadinstitute.org/gsa/wiki/index.php/DiffEngine
 2011-07-17 13:05:04 -04:00
Mark DePristo a5bfcb1ed9 V15 is broken. Going up to v16 in a second. 2011-07-17 10:25:34 -04:00
Mark DePristo 2b55d5b7c0 Test tribble library where equals() ignores time stamps. 2011-07-16 16:45:55 -04:00
David Roazen 07b875c779 Renaming the updated tribble jar file to match the svn revision number. 2011-07-16 09:57:46 -04:00
Mark DePristo 5e7bc862a3 Rev tribble to include new equal() method that prints out details of why two indices are not the same. 2011-07-16 08:51:21 -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
Khalid Shakir 7b699f8b17 Switched GridEngine from looking from environment variable to using embedded jar. 2011-07-05 21:59:00 -04:00
David Roazen 643458d7db Updated the tribble jar -- this should fix most of the integration test 
failures we've been seeing.

Note that with tribble's new svn repository the revision numbers have reset,
hence "revision 3"
 2011-06-29 01:11:03 -04:00
droazen 171e20a111 Updated the tribble jar to revision 351 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6068 348d0f76-0448-11de-a6fe-93d51630548a
 2011-06-22 22:55:57 +00:00
droazen ab1de3bfda Updated the tribble jar to revision 350 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6065 348d0f76-0448-11de-a6fe-93d51630548a
 2011-06-22 22:55:46 +00:00
droazen 95614ce3d6 Updated the tribble jar to revision 345 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6033 348d0f76-0448-11de-a6fe-93d51630548a
 2011-06-22 22:53:25 +00:00
droazen 32a991c4d3 Updated the tribble jar to revision 343 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6031 348d0f76-0448-11de-a6fe-93d51630548a
 2011-06-22 22:53:17 +00:00
hanna 14d7ee073b Rev Picard to get new PF_INDEL_RATE metric. Rev preQC generator script 
to incorporate PF_INDEL_RATE.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5998 348d0f76-0448-11de-a6fe-93d51630548a
 2011-06-14 17:43:43 +00:00
hanna cde2b409a7 Oops. Failed to add DbSnpMatchMetrics to Picard private jar. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5994 348d0f76-0448-11de-a6fe-93d51630548a
 2011-06-14 15:14:19 +00:00
hanna 1b1aefc385 Move fingerprinting metrics reader into our Picard private extract. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5990 348d0f76-0448-11de-a6fe-93d51630548a
 2011-06-14 00:13:10 +00:00
droazen 480598842c Updated the tribble jar 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5982 348d0f76-0448-11de-a6fe-93d51630548a
 2011-06-13 18:00:09 +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 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 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
hanna c2e8c460cb Factor out all testing dependencies into a separate test configuration and 
only download that test configuration when running unit/integration tests.
This means that the build will (hopefully) never break because it can't
fetch a file that isn't required for the GATK to run.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5775 348d0f76-0448-11de-a6fe-93d51630548a
 2011-05-05 22:42:11 +00:00
hanna 45d8634522 Intermediate commit: bring Google Caliper into our private repository (even 
though sonatype is back up).  This will tide us over until I figure out how
to add caliper to test configuration, so that it's only swapped in when we
actually run our unit / performance tests.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5770 348d0f76-0448-11de-a6fe-93d51630548a
 2011-05-05 14:33:14 +00:00
hanna 6d5e45b5c6 Revbump Picard dependencies at Tim/Kathleen's request. Exclude anonymous 
classes from PluginManager.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5699 348d0f76-0448-11de-a6fe-93d51630548a
 2011-04-27 20:38:05 +00:00
hanna 57a4700299 Ported small BAM performance test suite to the Google Caliper microbenchmarking suite. Looks promising, 
but I'm still not sure that GC is a good long-term solution.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5683 348d0f76-0448-11de-a6fe-93d51630548a
 2011-04-22 22:09:17 +00:00
kshakir 4f8411f4b5 Revved Picard to access new flag to disable mmap for bam indices. Only added a 3% speed boost but the mmap was added to the heap count, making it harder to specify/restrict the total resident memory size in LSF. Specifying -Xmx4g will now stay much closer to 4g resident memory usage versus bumping up to 9g when accessing 900 x ~8Mb bai's. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5549 348d0f76-0448-11de-a6fe-93d51630548a
 2011-04-01 01:40:41 +00:00
hanna 8d2c14b29c Update Picard / sam-jdk at Tim's request. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4925 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-03 02:17:25 +00:00
kshakir 56433ebf6b Switched from LSF command line wrappers to JNA wrappers around the C API. Side effects: 
- bsub command line is no longer fully printed out.
- extraBsubArgs hack is now a callback function updateJobRun.
Updated FullCallingPipelineTest to reflect latest changes to fullCallingPipeline.q.
Added a pipeline that tests the UGv2 runtimes at different bam counts and memory limits.
Updated VE packages that live in oneoffs to compile to oneoffs.
Added a hack to replace the deprecated symbol environ in Mac OS X 10.5+ which is needed by LSF7 on Mac.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4816 348d0f76-0448-11de-a6fe-93d51630548a
 2010-12-10 04:36:06 +00:00