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104 Commits (0feee9cdfde4bf5c2c8de90d8fd7d0d506b63c40)

Author SHA1 Message Date
aaron 5b41ef5f70 rod DBSNP had a bug where the reference wasn't calculated correctly under certain conditions. Fixed getRefBasesFWD and getRefSnpFWD so that they were more in line with getAltBasesFWD and getAltSnpFWD. Also updated Variant Eval tests to reflect this change. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1609 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-13 23:48:58 +00:00
depristo 6e13a36059 Framework for ROD walkers -- totally experiment and not working right now 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1600 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-12 19:13:15 +00:00
ebanks e24c8d00d5 So, the VCF spec allows for an optional meta field in the header representing the date. However, using this field means that integration tests run on the vcf file will fail the MD5 test (which is what happened to the VariantFiltration test this morning after working just fine yesterday). 
After consulting our resident expert (Aaron), we're going to (temporarily) remove the date from the vcf output until we can come up with a better solution.  However, this shouldn't cause any short-term problems because the data truly is optional.
VF test's MD5s are updated.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1580 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-10 14:28:43 +00:00
aaron 5a64a80ab5 changes to the variation class, updates to SSG, updated tests based on changes to the SSGenotypeCall, and added the ability to run a single integration test from using the build script. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1577 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-10 04:31:33 +00:00
ebanks 1362a56227 Added fasta tests and small fix to cleaner test 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1575 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-10 03:13:11 +00:00
ebanks 8ca89279aa Added a test for VariantFiltration and the VECs 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1574 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-10 02:21:14 +00:00
ebanks bed646e4f6 Adding cleaner test 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1561 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-09 16:05:56 +00:00
depristo d9588e6083 bug fixes to LIBS and LIBH following ultra-aggressive regression testing across 454, solid, and solexa 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1558 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-09 15:36:12 +00:00
aaron 0df6a9da5c -Seperating out normal (unit) tests and integration tests. From now on if your test are more of an integration test (i.e. you're testing a walker and all the subunits it relies on) please name the test "______IntegrationTest.java" instead of "______Test.java". 
-Bamboo will now run the integration tests once a day, and the normal units tests on each check-in.

-Also added a bunch of unit tests for VariantEval walker

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1555 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-09 15:01:40 +00:00
depristo eeb9b6eb13 GenotypeLikelhoods now support a cache per subclass, avoiding genotyping clashes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1554 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-09 10:39:14 +00:00
ebanks 0cc219c0df -Added unit test for walkers dealing with intervals for cleaning 
-I also uncovered a corner case in the cleaner that for some reason was commented out but shouldn't have been.  Hooray for unit tests!



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1553 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-09 02:35:17 +00:00
depristo ec0f6f23c7 LocusIterationByState is now the system deafult. Fixed Aaron's build problem 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1552 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-09 01:28:05 +00:00
depristo 1c3d67f0f3 Improvements to the CountCovariates and TableRecablirator, as well as regression tests for SLX and 454 data 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1539 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-04 22:26:57 +00:00
depristo 2b0d1c52b2 General WalkerTest framework. Includes some minor changes to GATK core to enable creation of true command-line like GATK modules in the code. Extensive first-pass tests for SSG 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1538 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-04 19:13:37 +00:00
aaron 0cc634ed5d -Renamed rodVariants to RodGeliText 
-Remove KGenomesSNPROD
-Remove rodFLT
-Renamed rodGFF to RodGenotypeChipAsGFF
-Fixed a problem in SSGenotypeCall
-Added basic SSGenotype Test class
-Make VCFHeader constructors public

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1536 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-04 18:40:43 +00:00
depristo a08c68362e Renaming error to getNegLog10PError(); added Cached clearing method to GL; SSG now has a CallResult that counts calls; No more Adding class to System.out, now to logger.info; First major testing piece (and general approach too) to unit testing of a walker -- SingleSampleGenotyper now knows how many calls to make on a particular 1mb region on NA12878 for each call type and counts the number of calls *AND* the compares the geli MD5 sum to the expected one! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1530 348d0f76-0448-11de-a6fe-93d51630548a
 2009-09-04 12:39:06 +00:00
depristo 49a7babb2c Better organization of Genotype likelihood calculations. NewHotness is now just GenotypeLikelihoods. There are 1, 3, and empirical base error models available as subclasses, along with a simple way to make this (see the factory). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1481 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-30 19:16:30 +00:00
depristo 8e129d76fd Support for original quality scores OQ flag. pQ flag in TableRecalibation to preserve quality scores below a threshold (defaulting to 5) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1474 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-28 14:14:21 +00:00
depristo 37a9b84276 corresponding test 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1470 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-28 00:17:42 +00:00
hanna ccdb4a0313 General-purpose management of output streams. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1454 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-23 00:56:02 +00:00
aaron d101c20b30 added the ability to pass in a csv file of ROD triplets (one triplet per line) to the -B option 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1412 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-11 22:10:20 +00:00
aaron d69ae60b69 fixed two tests affected by my previous commit 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1408 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-11 17:57:50 +00:00
hanna dd228880ed Partially implemented NewHotnessGenotypeLikelihoodsTest caused the tests to fail. 
Ouch!  So hot it burned me.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1403 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-10 20:45:44 +00:00
depristo a864c2f025 Updated polarized reference priors, need DiploidGenotypePriors class that is directly used by the NewHotness genotypelikelihoods, more bug fixes and refactoring, etc. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1390 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-07 19:00:06 +00:00
depristo bbd7bec5db Continuing cleanup of SSG. GenotypeLikelihoods now have extensive testing routines. DiploidGenotype supports het, homref, etc calculations. SSG has been cleaned up to remove old garbage functionality. Also now supports output to standard output by simply omitting varout 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1387 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-05 22:25:30 +00:00
hanna 48713e154c Windowed access to the reference. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1383 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-05 16:29:15 +00:00
hanna 21d1eba502 Cleaned division of responsibilities between arguments to map function. Reference has been changed 
from an array of bases to an object (ReferenceContext), and LocusContext has been renamed to reflect
the fact that it contains contextual information only about the alignments, not the locus in general.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1376 348d0f76-0448-11de-a6fe-93d51630548a
 2009-08-04 21:01:37 +00:00
aaron bca894ebce Adding the intial changes for the new Genotyping interface. The bullet points are: 
- SSG is much simpler now
- GeliText has been added as a GenotypeWriter
- AlleleFrequencyWalker will be deleted when I untangle the AlleleMetric's dependance on it
- GenotypeLikelihoods now implements GenotypeGenerator, but could still use cleanup

There is still a lot more work to do, but this is a good initial check-in.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1335 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-29 19:43:59 +00:00
hanna 7a13647c35 Support for specifying SAMFileReaders and SAMFileWriters as @Arguments directly. *Very* 
rough initial implementation, but should provide enough support so that people can stop
creating SAMFileWriters in reduceInit.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1332 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-29 16:11:45 +00:00
hanna 2db86b7829 Move the cleaned read injector test from playground to core. Remove CovariateCounterTest's dependency on the CleanedReadInjector. Start doing a bit of cleanup on the CLP's FieldParsers. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1312 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-24 19:44:04 +00:00
aaron 0b16253db3 an iterator to fix the problem where read-based interval traversals are getting duplicate reads because reads span the two intervals. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1305 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-23 23:59:48 +00:00
aaron b4adb5133a GLF rod as a AllelicVariant object. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1282 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-21 00:55:52 +00:00
aaron 9ecb3e0015 adding GLFRods with tests and some other code changes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1251 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-15 15:30:19 +00:00
aaron d86717db93 Refactoring of the traversal engine base class, I removed a lot of old code. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1209 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-09 21:57:00 +00:00
hanna da4d26b1ea Enum support for command-line argument system, and some cleanup for hacks to the CleanedReadInjector that were required because Enum support was missing. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1199 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-08 20:26:16 +00:00
hanna 433ad1f060 Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1196 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-08 18:49:08 +00:00
hanna d8fbb2b62c Refactoring; make a better home for the MalformedReadFilteringIterator. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1194 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-08 16:54:20 +00:00
aaron f6a273a537 other fixes for some broken unit tests 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1181 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-07 05:53:13 +00:00
aaron 033bafe7a1 fixed sam by reads test for the new filtering code 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1180 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-07 05:45:50 +00:00
depristo b9d533042e Two-tailed HardyWeinberg test implemented. VariantEval now separate violations from summary outputs for clarity; Fixing problems with CovariateCounterTest and TabularRodTest 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1177 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-06 22:02:04 +00:00
aaron bc17ff567a When you get the reference string for a read that is mapped partially off the end of a contig, the string is masked with X's for base positions without corresponding reference positions. Now with a test case! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1156 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-02 14:15:50 +00:00
hanna 9b182e3063 Prep for documenting command-line arguments: delete some arguments that don't make sense any more given 
the state of the traversals and GATK input requirements: all_loci (replaced by walker annotation), max
OTF sorts (bam files must be sorted and indexed), threaded io (replaced by data sharding framework).


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1144 348d0f76-0448-11de-a6fe-93d51630548a
 2009-07-01 18:23:35 +00:00
aaron 03f8177a53 When you get the reference string for a read that is mapped partially off the end of a contig, the string is masked with X's for base positions without corresponding reference positions. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1121 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-29 20:51:55 +00:00
aaron 1dcababad1 a fix to make the test run 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1120 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-29 20:24:32 +00:00
depristo 5289230eb8 Version 0.2.1 (released) of the TableRecalibrator 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1108 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-25 22:50:55 +00:00
hanna ad3a3aa350 First pass at passing lists of files / lists of interval arguments work. Note that the interval 
ROD system will throw up its hands and not deal with intervals at all if multiple interval files 
are passed in (see JIRA GSA-95). 


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1105 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-25 20:44:23 +00:00
aaron 0a16519aa2 a couple of additions to the tests, plus a change to the artificial resource pool to support the queryContained flag 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1099 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-25 18:30:32 +00:00
aaron 5b1c23a7f2 changes to fix and test the interval based traversals 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1095 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-25 17:54:15 +00:00
hanna ef546868bf Pooling of unmapped reads -- improves runtime of files with tons of unmapped reads by an order of magnitude. 
Desperately needs cleanup.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1080 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-23 23:48:06 +00:00
aaron bcb64d92e9 Aaron: 1, GenomeLoc: 0. I changed our GenomeLoc class, seperating the creation of a genome loc (with the reference setup) to a parser class. GenomeLoc now just represents the actual genomic postion. The constructors are now package-protected (to enforce using the parser), but we may want to expose some constructors in the future. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1069 348d0f76-0448-11de-a6fe-93d51630548a
 2009-06-22 14:39:41 +00:00