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46 Commits (b0cdba8bb321dcc487559e37c0b954bfafedbca0)

Author SHA1 Message Date
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
aaron 887adcfc7f Some minor fixes to the last check-in 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@387 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-13 18:24:51 +00:00
hanna cf929a8275 Get rid of test case's dependence on transient methods. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@381 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-13 15:16:42 +00:00
hanna 9c37400c4f Added basic performance testing so I can make sure concurrent access doesn't slow down overall fasta access. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@367 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-12 18:05:56 +00:00
kcibul ce72932a45 * refactored GenomeLoc to use contigIndex internally for performance and fixed several calling classes 
* added basic unit test for GenomeLoc
* fixed bug when parsing genome locations like chr1:5000 the start position was being left as maxint rather than being set to the same as the stop position.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@365 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-12 02:25:17 +00:00
hanna 49fd951d8c Initial test suite for FastaSequenceFile2, so I can add parallelism support with abandon. 
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
aaron 9afa101465 Add interval support to the 
.__            __    __                
  _____|  |__ _____ _/  |__/  |_  ___________ 
 /  ___/  |  \\__  \\   __\   __\/ __ \_  __ \
 \___ \|   Y  \/ __ \|  |  |  | \  ___/|  | \/
/____  >___|  (____  /__|  |__|  \___  >__|   
     \/     \/     \/                \/       

classes!



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@352 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-09 21:23:43 +00:00
aaron 8e2f5471a1 Some cleanup to the data source, and another JUnit test case. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@344 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-09 14:58:05 +00:00
aaron d517245beb Fixes for shattering, added JUnit test case 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@332 348d0f76-0448-11de-a6fe-93d51630548a
 2009-04-08 16:37:34 +00:00
hanna b17a03abbd Fix argument parser test case. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@215 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-27 16:05:18 +00:00
aaron c2b2ed8e1d added our first junit test, for the argument parser 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@176 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-24 21:14:30 +00:00