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Author SHA1 Message Date
aaron 4ce3feba4d my move ended up being a copy, so this is to delete dupplicate files. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@651 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-11 02:10:26 +00:00
aaron 898f65547e Added code to split GenomeAnalysisTK.java into an object concerned with loading command line args, and one that runs the engines. This will allow us to run the GATK from other tools (like Matlab). Also some cleanup to seperate out the legacy traversals and the new style traversals. This is not live yet, and any modifications you need should be made to GenomeAnalysisTK.java for now. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@650 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-11 02:07:20 +00:00
hanna 6e394490cb Cleanup in preparation for ByLoci traversal. Also did some work minimizing unit tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@643 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-08 21:27:54 +00:00
aaron bae4256574 Started the process to make the GATK engine into a runnable object so we can call it from other processes. Step 1: make a configuration object that can serialize to and from an XML file. This way we can store the information everyone uses shell scripts for. Also we can now pull the list of params out of the GenomeAnalysisTK.java. More to come... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@636 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-08 01:25:26 +00:00
hanna 7f8850a8a2 Argument validation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@631 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-07 20:28:56 +00:00
hanna d725c6cf1c Added unit tests for parsing failures that I encountered during integration testing. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@618 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-07 14:01:54 +00:00
hanna 4177560543 Mutually exclusive options. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@616 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-07 13:27:48 +00:00
aaron 0aba688e6f Added a interface that all our SAMRecord iterators should try to code to. This is in the effort to keep our code generic 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@609 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-06 21:40:41 +00:00
hanna 98716138e9 Cleanup: add support for non-public fields. Track matches as state of parsing engine as well as definitions. 
Made fields of command-line argument system non-public by default.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@606 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-06 19:38:05 +00:00
hanna ef211f96b1 Remove old Apache CLI-based arg system. 
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
hanna 521aa40baa Bring new command-line argument parsing system live. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@603 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-06 18:16:11 +00:00
aaron 98f4920739 Added BCEL and some basic instrumenation code to the test library. 
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
hanna bfd6dfe36c Added real-world tests and tests for conditional validation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@601 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-06 13:38:46 +00:00
hanna 2ee9374975 Check for proper error output in case of boolean args with parameter specified. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@599 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-05 23:08:48 +00:00
hanna b0cdba8bb3 Acting on Kiran's suggestion to make the doc tag in the @Argument annotation required.x 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@598 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-05 22:43:40 +00:00
hanna ec0261275b Lots of command line argument validation. Catches all common validation problems, including missing required arguments, invalid arguments, and several types of misplaced argument value errors. 
Still pending:
- Help system.
- Mutually exclusive arguments.
- Design includes too many classes per file.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@597 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-05 22:08:00 +00:00
aaron 70afda12c4 Cut the test time down 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@596 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-05 22:05:51 +00:00
aaron f5880109a7 Added TraverseReads test, some bug fixes discovered in the traversal test 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@594 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-05 20:36:00 +00:00
aaron 09b0b6b57d Fixes to try and speed up unmapped read traversals. Still not nearly as fast as they should be, but the next step would be to modify samtools code. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@592 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-05 18:17:07 +00:00
hanna 6550fe6f97 Another pass of command-line arguments. Revised parser supports all types 
of arguments that the existing parser supports, but does a poor job with
validation.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@591 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-04 22:41:23 +00:00
hanna 4f2ccda56a Interface skeleton for a new command line argument parser. Nowhere near the point of being a drop-in replacement for apache cli yet. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@588 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-04 00:11:42 +00:00
depristo 7ed496b859 JUnit test for RefHanger 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@584 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-01 20:11:14 +00:00
hanna 9f5f6f9bc7 N-way parallelism. Works for small test cases. Untested for large test cases. 
-Needs more comprehensive unit testing.
-Needs some basic refactoring.
-Needs rethink of interface boundaries.
-Needs to play more nicely in the /tmp sandbox.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@583 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-01 19:34:09 +00:00
kiran 9800d09608 A more thorough test for multinomialProbability. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@577 348d0f76-0448-11de-a6fe-93d51630548a
 2009-05-01 06:27:05 +00:00
aaron 63403d32cd Changes to the interface to the simple data source rippled out to a bunch of files. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@572 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-30 20:35:56 +00:00
hanna 19e4e97f21 Add tag to ignore node class. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@571 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-30 20:27:34 +00:00
hanna 7f173af2ea Encapsulate output tracking a bit. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@570 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-30 15:12:13 +00:00
aaron 3bf3c21ddd Changed the assert code in the genome loc to throw exceptions, and deleted a function no one seems to be using. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@569 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-30 13:54:51 +00:00
hanna ba9a0b5da8 Break out some of the weird inner classes out of the HierachicalMicroScheduler. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@566 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-29 21:07:07 +00:00
hanna 95d10ba314 Sketch of hierarchical reduce process, with unit tests for some core classes. Requires breakout of inner classes, testing. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@565 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-29 20:26:16 +00:00
aaron 6b02248298 moved the test cases out of the GenomeAnalysisTK code and into a JUnit test case 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@555 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-28 21:49:17 +00:00
kiran eeb0b78cce Added another assert to testBinomialProbability() and added a test method for testMultinomialProbability(). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@544 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-27 14:59:11 +00:00
hanna e50ae97fe1 Introduce new index-based fasta reader. Clean up MicroManager code, pushing necessary code back into TraversalEngine. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@531 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-24 19:40:21 +00:00
kiran 305584b69e Test class for MathUtils with a test for binomialProbability(). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@519 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-24 03:31:02 +00:00
hanna 45d962e491 I understood the contig index incorrectly when I initially wrote this code. Fixed. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@517 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-23 22:31:43 +00:00
aaron 0720d248ce Adding the test case for by reads sharding of BAM data sources 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@509 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-23 18:01:22 +00:00
hanna 56f6847456 Changed interface from contig,pos,length to more common contig,start,stop interface. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@441 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-16 00:04:41 +00:00
aaron 180ff13290 Added a bunch of changes to support the new MicroManager code 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@431 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-15 18:29:38 +00:00
hanna 26e84d7fd6 Added index iteration for ReferenceSequenceFile interface compatibility. 
Added better error checking for querying past the end of a contig.
Lots more testing.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@429 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-15 17:17:11 +00:00
aaron 6db9127f90 Added changes to shattering, refactored SAMBAM into SAM 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@426 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-15 13:52:56 +00:00
hanna 182626576f Basic indexed fasta POC in place. Requires a more complete implementation of the ReferenceSequenceFile interface, 
and much more testing.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@425 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-15 13:46:56 +00:00
aaron e6fb122d7d Added some fixes and new iterator tests 
--This lin e, and those below, will be ignored--

A    gatk/iterators
AM   gatk/iterators/BoundedReadIteratorTest.java
M    gatk/dataSources/simpleDataSources/SAMBAMDataSourceTest.java


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@420 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-14 22:19:36 +00:00
aaron 96248cdec4 Added some output to all the classes, including build in runtime analysis 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@411 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-14 19:14:53 +00:00
hanna 0629f79049 Moved fasta support files into their own package. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@408 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-14 18:13:23 +00:00
hanna 7a4a5a17c0 Made sequence index compatible with Aaron's junit changes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@407 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-14 17:53:20 +00:00
aaron 88ebf1a05b Fied some documentation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@406 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-14 17:41:38 +00:00
hanna 186c799ffc Class to read an .fai file. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@405 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-14 17:37:18 +00:00
aaron 704f1bd634 It helps if I check the new base class in with my changes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@404 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-14 17:18:16 +00:00
aaron 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. 
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
aaron eb4b4a053b A bunch of updates to the SAM/BAM data source, along with test cases for the merging of multiple files (it works!). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@399 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-14 14:19:20 +00:00