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  • 3aabc144c6 Added functionality to allow for a contract between LocusWindowTraversalEngine and LocusWindowWalker which allows the Walker to act upon reads outside of the provided intervals. (Really, all we want to do is spit out all reads, but this allows the Walker to do other things with the reads if it wants) ebanks 2009-05-08 17:28:16 +0000
  • de1c282e62 Reference-ordered data relies on bugs in the old command-line argument system to work. Update the ROD system to from -B track1 type1 file1 track2 type2 file2 to -B track1,type1,file1 -B track2,type2,file2. hanna 2009-05-08 15:28:19 +0000
  • 483a58627b More cleanup -- pushing shared functions down into the traversal engine. hanna 2009-05-08 14:12:45 +0000
  • 7a9cfe1f75 Push reduceInit down a level so that the walker can call into it without weird casts. hanna 2009-05-08 13:46:28 +0000
  • a5154d99a3 Haven't heard any complaints, so I'm deleting the original implementation of TraverseByLociByReference. All TbyLbyR's will now go through the new sharding code. hanna 2009-05-08 13:37:00 +0000
  • 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... aaron 2009-05-08 01:25:26 +0000
  • 226edbdef6 Hypen-style xml output. Much sexier. hanna 2009-05-08 01:04:40 +0000
  • 4c269b8496 Cleanup LinearMicroScheduler in preparation for TraverseByLoci inclusion. hanna 2009-05-08 00:58:37 +0000
  • 21536df308 Change the sample XML marshalling code over to simple XML, and take out the castor lines in the ivy.xml aaron 2009-05-08 00:08:25 +0000
  • 5d9536d2b4 Added simple xml to replace castor (at least for now) aaron 2009-05-07 23:57:18 +0000
  • 7f8850a8a2 Argument validation. hanna 2009-05-07 20:28:56 +0000
  • a3d8febbf2 Error message cleanup. hanna 2009-05-07 19:31:32 +0000
  • c241d386a7 Beefed up command-line usage string. hanna 2009-05-07 19:08:19 +0000
  • 5a6892900e fixing oddities in duplicates depristo 2009-05-07 18:55:45 +0000
  • 4a26f35caa new default syntax depristo 2009-05-07 18:16:53 +0000
  • 283a4d1b54 Fix some special-case cleaner issues. We now do the same as brute force in all examples to date. ebanks 2009-05-07 18:16:35 +0000
  • 93211c1cd8 template for windowmaker utility -- total non-functional depristo 2009-05-07 18:13:03 +0000
  • 2204be43eb System for traversing duplicate reads, along with a walker to compute quality scores among duplicates and a smarter method to combine quality scores across duplicates -- v1 depristo 2009-05-07 18:06:02 +0000
  • 71e8f47a6c boundQual function for capping qual values depristo 2009-05-07 18:04:18 +0000
  • e848f34896 countOccurances of char in string and max of a list of bytes depristo 2009-05-07 18:03:49 +0000
  • 5a4bb76cc3 More capabilities for the pileup depristo 2009-05-07 18:03:13 +0000
  • 89a26a7078 Utilities for handling duplicates depristo 2009-05-07 18:02:24 +0000
  • 4f85062004 Cleanup parsing method to make it less generic. hanna 2009-05-07 16:21:17 +0000
  • d725c6cf1c Added unit tests for parsing failures that I encountered during integration testing. hanna 2009-05-07 14:01:54 +0000
  • 2f3ab53888 Oops. Arguments didn't load into applications with non-plugins (basically everything except the GATK). hanna 2009-05-07 13:37:19 +0000
  • 4177560543 Mutually exclusive options. hanna 2009-05-07 13:27:48 +0000
  • 752928df94 Switch to better mechanism for supplying a default. hanna 2009-05-07 01:22:01 +0000
  • dc944ec69b First stage of ROD plumbing for MicroScheduler. hanna 2009-05-06 23:26:21 +0000
  • 5136724884 Added code to the schedulers, one step closer to turning on the new reads traversals aaron 2009-05-06 22:36:25 +0000
  • 9c0b81e946 Default flags to 'not required'. hanna 2009-05-06 22:09:49 +0000
  • 072808858e added COUNT_CUTOFF arg: it is nor possible to tell the code to try to realign all read piles over trains of nearby indels with at least one indel observed in COUNT_CUTOFF or more different alignments (set the arg to 1 to realign around all indels); also, some diagnostic printouts added to the output (time spent on loading the reference, time spent on scrolling through the input bam file, counts of discarded reads) asivache 2009-05-06 21:59:33 +0000
  • 1fe8155111 Some critical fixes for cases where argument values directly abut argument names and for arguments with missing short names. hanna 2009-05-06 21:47:34 +0000
  • 0aba688e6f Added a interface that all our SAMRecord iterators should try to code to. This is in the effort to keep our code generic aaron 2009-05-06 21:40:41 +0000
  • 62e7e46754 Miscellaneous cleanup. Better display of help output. Better exception subtyping. More thought-out access routines. hanna 2009-05-06 21:16:01 +0000
  • 5be75e0ae6 First version of indel cleaner walker that works on intervals ebanks 2009-05-06 20:20:48 +0000
  • 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. hanna 2009-05-06 19:38:05 +0000
  • f5eae98af2 Fixed a bug where we could ask for a read when there were none in the pool (that's a bad thing). aaron 2009-05-06 18:40:55 +0000
  • ef211f96b1 Remove old Apache CLI-based arg system. hanna 2009-05-06 18:37:51 +0000
  • 521aa40baa Bring new command-line argument parsing system live. hanna 2009-05-06 18:16:11 +0000
  • 98f4920739 Added BCEL and some basic instrumenation code to the test library. aaron 2009-05-06 17:18:23 +0000
  • bfd6dfe36c Added real-world tests and tests for conditional validation. hanna 2009-05-06 13:38:46 +0000
  • 4ac9e72739 Migrate default and GATK arguments over to new attribute system in preparation for conversion. hanna 2009-05-05 23:57:48 +0000
  • 2ee9374975 Check for proper error output in case of boolean args with parameter specified. hanna 2009-05-05 23:08:48 +0000
  • b0cdba8bb3 Acting on Kiran's suggestion to make the doc tag in the @Argument annotation required.x hanna 2009-05-05 22:43:40 +0000
  • 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. hanna 2009-05-05 22:08:00 +0000
  • 70afda12c4 Cut the test time down aaron 2009-05-05 22:05:51 +0000
  • 89344ccc0f Not sure why junit is so excited about running inner classes with no @Tests. Omit inner classes from the fileset of tests to run. hanna 2009-05-05 21:56:34 +0000
  • f5880109a7 Added TraverseReads test, some bug fixes discovered in the traversal test aaron 2009-05-05 20:36:00 +0000
  • daa2163ee8 Made the MergingSamIterator2 peekable. This iterator is being a ducktaped together swiss army knife, the iterators could use a redo soon. aaron 2009-05-05 19:15:07 +0000
  • 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. aaron 2009-05-05 18:17:07 +0000
  • 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. hanna 2009-05-04 22:41:23 +0000
  • 8925df2e1e More information from the duplicate combiner quality metrics depristo 2009-05-04 21:51:01 +0000
  • 2b6466ea00 coverage calculator based on Gabor's Pilot 3 Coverage Metrics kcibul 2009-05-04 14:18:16 +0000
  • 4f2ccda56a Interface skeleton for a new command line argument parser. Nowhere near the point of being a drop-in replacement for apache cli yet. hanna 2009-05-04 00:11:42 +0000
  • 6e38966349 Rename some key classes. hanna 2009-05-01 22:01:04 +0000
  • 5bdf653919 Cleanup: prepare for better output handling. hanna 2009-05-01 21:40:46 +0000
  • fd496159a8 Added convenience functions for RefHanger depristo 2009-05-01 21:14:40 +0000
  • 7ed496b859 JUnit test for RefHanger depristo 2009-05-01 20:11:14 +0000
  • 9f5f6f9bc7 N-way parallelism. Works for small test cases. Untested for large test cases. hanna 2009-05-01 19:34:09 +0000
  • df88c4d6b0 Added some code to determine the on-genotype and off-genotype secondary base distributions (which, at the moment, is commented out). kiran 2009-05-01 06:48:19 +0000
  • e7534b292f Optionally applies secondary base distribution priors to normal single-sample genotyper posteriors. kiran 2009-05-01 06:36:32 +0000
  • 58c80d8d87 For on and off-genotype primary bases, optionally compute the concordance of the secondary bases to their expected distributions. Each genotype has slightly different profiles. kiran 2009-05-01 06:33:48 +0000
  • 16467ae7cf A better (less overflow-y) implementation of multinomialProbability(). kiran 2009-05-01 06:28:16 +0000
  • 4f818f5c1c Choose a random base to stick in the pileup if the 2nd-best base matches the best base. kiran 2009-05-01 06:27:37 +0000
  • 9800d09608 A more thorough test for multinomialProbability. kiran 2009-05-01 06:27:05 +0000
  • 84dae06d5a Initial version of ByDuplicates traversal, as well as a duplicate quality score estimator depristo 2009-04-30 22:16:21 +0000
  • ff420f5f6f Enabled iterator() function depristo 2009-04-30 22:15:14 +0000
  • 12d6edfe7c Only prints about first contig info setting depristo 2009-04-30 22:14:26 +0000
  • 1cc5e74435 More ways to access quality utils depristo 2009-04-30 22:12:07 +0000
  • 63403d32cd Changes to the interface to the simple data source rippled out to a bunch of files. aaron 2009-04-30 20:35:56 +0000
  • 19e4e97f21 Add tag to ignore node class. hanna 2009-04-30 20:27:34 +0000
  • 7f173af2ea Encapsulate output tracking a bit. hanna 2009-04-30 15:12:13 +0000
  • 3bf3c21ddd Changed the assert code in the genome loc to throw exceptions, and deleted a function no one seems to be using. aaron 2009-04-30 13:54:51 +0000
  • b630f2f2f1 More tables output by CovariateCounterWalker AND made CovariateCounterWalker and LogisticRecalibration aware of positive and negative strandedness of data which changes the regression output significantly. andrewk 2009-04-30 01:22:50 +0000
  • f7a877bfeb Changed Sting exception from a base exception to a runtime exception. This makes it so you can throw it without the consumer having to check it, and hopefully people will be more inclined to use it. aaron 2009-04-29 22:09:41 +0000
  • ba9a0b5da8 Break out some of the weird inner classes out of the HierachicalMicroScheduler. hanna 2009-04-29 21:07:07 +0000
  • 95d10ba314 Sketch of hierarchical reduce process, with unit tests for some core classes. Requires breakout of inner classes, testing. hanna 2009-04-29 20:26:16 +0000
  • 0a707a887b Added ability to evaluate best + random base. kiran 2009-04-29 20:05:36 +0000
  • 334f158e5a added parameters for mapping quality and duplicate filters kcibul 2009-04-29 18:05:34 +0000
  • 30218ee31a Better validation scripts and data depristo 2009-04-29 17:40:07 +0000
  • 7de5da7065 Start getting the cleaner working in Walker ebanks 2009-04-29 14:59:53 +0000
  • 4c5f640eb7 Tweak the arguments passed to the command-line arguments parser so that it fails less often for invalid arguments. hanna 2009-04-29 14:36:27 +0000
  • b6a7ebd3c4 You can now test a single JUnit test from the command line, by specifying the test with the command line parameter -Dsingle=myTestName. aaron 2009-04-29 13:30:47 +0000
  • f557da0a78 Calculate interval-based statistics for Hybrid Selection kcibul 2009-04-29 04:01:24 +0000
  • 6ecc43f385 Provide a default logger, some config settings, and some doc updates. hanna 2009-04-29 02:06:05 +0000
  • b836761104 removed the test cases from the bottom of this file aaron 2009-04-28 21:50:22 +0000
  • 6b02248298 moved the test cases out of the GenomeAnalysisTK code and into a JUnit test case aaron 2009-04-28 21:49:17 +0000
  • a573b8ede1 Bumped sam-jdk version to fix bug unzipping bam files. hanna 2009-04-28 20:02:05 +0000
  • d4de68e260 added changes for the readsTraversal to accomidate design changes aaron 2009-04-28 19:49:58 +0000
  • b6874f30cb Added changes to bounded read iterator, it now explicitly takes a MSRI2 instead of the interfaces ClosableIterator<SAMRecord>. It would be good to fix this in the future with an interface that lets you get the (possibly merged) header. aaron 2009-04-28 17:57:54 +0000
  • 395aaf48b0 Added the new by reads traversal, still needs to be sewn into the micromanager code. aaron 2009-04-28 17:55:08 +0000
  • 58b2578c44 Several changes to CovariateCounter walker to print more tables (called vs. observed Q scores), bug fixes to LogisticRecalibrationWalker and LogisticRegressor, and print string functionality added to Pair. andrewk 2009-04-28 00:37:48 +0000
  • a0a581171b print out the last interval ebanks 2009-04-27 20:43:06 +0000
  • a343f3eab7 Fixed bug where we weren't setting the reads group correctly. Also added code to set the printMetrics field of the singleSampleGenotyper from the Pool caller, it was null excepting out for me without that set. aaron 2009-04-27 15:17:20 +0000
  • 1daf8e0987 A utility to compare the results of the SingleSampleGenotyper in 1-base and 4-base mode. kiran 2009-04-27 15:10:08 +0000
  • 444bc18183 Removed binomialProb() method. Set better values for qHom, qHet, and qHomNonRef and allowed those to be set from the command-line. kiran 2009-04-27 15:09:02 +0000
  • b9c9dbb1d7 Added multinomialProbability method. kiran 2009-04-27 15:03:50 +0000
  • eeb0b78cce Added another assert to testBinomialProbability() and added a test method for testMultinomialProbability(). kiran 2009-04-27 14:59:11 +0000
  • 60fe2e06d1 Revert accidental checkin of hacked picard build. hanna 2009-04-27 09:47:10 +0000
  • 9a8902571c Placeholder for parallel MicroManager. hanna 2009-04-26 23:08:12 +0000