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Author SHA1 Message Date
ebanks a4f8d70d8d oops, forgot to update this integration test 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3788 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-14 11:38:33 +00:00
ebanks 460283f6d2 No more manually converting VariantContexts to VCFRecords. You should be utilizing VCs and not VCFRecords. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3787 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-14 05:21:28 +00:00
ebanks 6b5c88d4d6 The GATK no longer writes vcf3.3; welcome to the world of vcf4.0. Needed to fix a few output bugs to get this to work, but it's looking great. Much more still to come. Guillermo: hopefully this doesn't break your local build too badly. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3786 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-14 04:56:58 +00:00
ebanks 9a05e8143d Move to 4.0 and away from VCFRecord. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3780 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-13 15:54:54 +00:00
ebanks 7e7da75d27 Moving over to 4.0 and away from VCFRecord 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3778 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-13 14:07:10 +00:00
ebanks d896d03554 Moving VF to vcf 4.0. Still need to fix genotype filters. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3777 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-13 11:39:51 +00:00
ebanks 76b3b39720 Technically, Mark broke this with his commit earlier. But since I had an outstanding broken test, I lose and have to fix this one too... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3776 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-13 03:58:38 +00:00
ebanks 1bef7dd170 git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3775 348d0f76-0448-11de-a6fe-93d51630548a 2010-07-13 00:56:12 +00:00
ebanks 52c534a8f2 Updating to VCF 4.0 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3770 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-12 20:18:30 +00:00
ebanks e50627a49e 1. Updated tests and added integration test for liftover code. 
2. Updated liftover code (and scripts) to emit vcf 4.0 and no longer depend on VCFRecord.
3. Beagle walker now also emits vcf 4.0.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3767 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-12 17:58:18 +00:00
ebanks 221e01fb27 deleting/archiving as instructed 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3765 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-12 16:59:45 +00:00
ebanks e75b3e13bd updating unit test for previous fix 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3761 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-12 03:23:53 +00:00
ebanks fb717fe128 First pass needed to remove old VCF code: moving all VCF-related constants into a single unified class 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3759 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-11 07:19:16 +00:00
chartl ea8fd506bf Update to PickSequenomProbes: Option to ignore mask sites within X bp of a variant (very useful for indels where dbSNP entries near the indel are almost always false SNP calls). Also fixed an integration test where the variant site itself, being in dbSNP, was represented as [N/C] rather than [A/C]. Added integration test for 1bp no-mask window. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3753 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-09 04:03:19 +00:00
depristo 45fb614296 Fixes to VE for obscure bug, as well as disabled integration test for CombineVariants 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3749 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-09 00:13:07 +00:00
ebanks 6e6ad36523 reallow MNP events through 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3740 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-08 06:26:52 +00:00
ebanks 9a81f1d7ef Fixed this tool for chartl so that it now properly handles deletions. Added deletion case to integration tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3737 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-08 04:45:59 +00:00
hanna 9fc05ac2ae eagerDecode is now false. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3733 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-07 22:51:48 +00:00
ebanks 4bc3ad2194 Shame on me: UG was emitting negative QUALs (-0) in all_bases mode. Thanks, Matt. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3732 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-07 20:30:22 +00:00
ebanks 30714ec8d9 As per quick chat with Richard Durban, don't increase the mapping quality of realigned reads too much; for now, arbitrarily increase the MQ by 10. We need to figure out a better solution. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3731 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-07 20:12:59 +00:00
aaron 86031f4034 part two: todo's in combine variants, fixes for InferredGeneticContext, and some other tests and clean-up. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3721 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-05 21:07:53 +00:00
ebanks 36edc60ccc Connected UG to the new comp track annotation system in VA. Also, when emit confidence is lower than call confidence (so that we emit records filtered with LowQual), add a corresponding FILTER header field to the VCF so that the validator doesn't complain. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3720 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-05 13:04:24 +00:00
aaron 3347d1ca7c part one of combining format and info header lines code into a single abstract class for Mark; plus some 'm' removals from access methods for Eric. Adding fixes for CombineVariants next. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3719 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-05 05:57:58 +00:00
weisburd 9ec393bfce Updated md5 - vcf header line change 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3714 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-02 21:02:09 +00:00
depristo 61e2b2e39b Nearly finalize merging capabilities for CombineVariants. Support for dealing with inconsistent indel alleles at loci. Improvements to Allele and removal of addAllele to MutableGenotype. We are close to being able to merge all of 1000 genomes -- snps and indels -- into a single combined vcf 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3710 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-02 13:32:33 +00:00
aaron 3093a20a55 fixing VCF header format and info fields so that they propery emit the unbounded count value correctly for vcf4 or vcf3. Eric we should update the vcf4 spec page to indicate format fields are allowed to use the unbounded count as well (if this is true). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3707 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-01 22:02:16 +00:00
rpoplin 255b036fb5 Variant Recalibrator MLE EM algorithm is moved over to variational Bayes EM in order to eliminate problems with singularities when clustering in higher than two dimensions. Because of this there is no longer a number of Gaussians parameter. Wiki will be updated shortly with new recommended command. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3704 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-01 18:51:07 +00:00
aaron 43ca595d15 VCF headers now can be set to a particular VCF version after creation, which converts the header lines to the appropriate encoding on output. Plus some clean-up of the code. 
Also commented out the Tribble index out-of-date tests, the timing seems to be troublesome from the farm.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3702 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-01 05:32:14 +00:00
hanna 4995950d04 IndexedFastaSequenceFile is now in Picard; transitioning to that implementation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3701 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-01 04:40:31 +00:00
ebanks 944dbb94ce Refactored and generalized the database/comp annotations in VariantAnnotator. Now one can provide comp tracks as with VariantEval (e.g. compHapMap, comp1KG_CEU) and the INFO field will be annotated with the track name (without the 'comp') if the variant record overlaps a comp site (e.g. ...;1KG_CEU;...). This means that you can now pass 1kg calls to the Unified Genotyper and automatically have records annotated with their presence in 1kg. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3684 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-30 16:37:31 +00:00
ebanks 12c0de6170 Added ability to clean using only known indels. Added integration test for it. Fixed vcf->vc conversion for indels which was busted. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3678 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-30 01:20:56 +00:00
aaron 844cb2ed33 fixing a bug that Eric found with RODs for reads, where some records could be omitted. Sorry Eric! 
Also putting more tolerance into the timing on the tibble index tests (that check to make sure we're deleting out of date indexes, and not deleting perfectly good indexes).  It seems that some of the farm nodes aren't great with a stopwatch.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3674 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-29 21:38:55 +00:00
ebanks baf9479c35 An addition for Sendu since he can't seem to tell when his CountCovariate jobs die in the middle of writing the CSVs. We now write an EOF marker at the end of the covariates table and look for it when reading in the file in TableRecalibrationWalker. By default, we warn the user if the EOF marker isn't present, but we exception out if the user provides the --fail_with_no_eof_marker option. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3670 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-29 18:50:07 +00:00
ebanks 4a451949ba add parallel option to target creator for masking out reads with bad mates 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3663 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-28 22:13:25 +00:00
ebanks 6a23edd911 Fix performance tests 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3662 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-28 21:51:48 +00:00
aaron 62d22ff1aa adding the original allele list to a variant context (as the annotation ORIGINAL_ALLELE_LIST), in the case where the set alleles are the result of clipping. Added tests for both cases. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3658 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-28 17:23:46 +00:00
ebanks 1292c96e29 The cleaner now adds the OC (original cigar) and OS (original alignment start) tags as appropriate to reads that get realigned; this feature can be turned off. Also, improved integration tests (sorry, Kiran!). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3657 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-28 16:46:47 +00:00
ebanks bf5cbad04c Make the target creator a rod walker (that allows reads) so that we can easily trigger the cleaner on only known indel sites. Adding an integration test to cover this case. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3651 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-28 13:28:37 +00:00
ebanks 8e848ccd84 SAMFileWriters can now write to /dev/null without throwing exceptions, so we can remove the try/catch blocks. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3648 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-27 03:59:10 +00:00
aaron 09ccdf83b2 fixing a broken test 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3647 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-25 21:59:00 +00:00
aaron 5f8a3f95ef The GT field once again reigns supreme (it must be the first genotype field). Thanks for the catch Eric. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3645 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-25 21:03:05 +00:00
aaron b3edb7dc08 two fixes for the VCF 4 parser: 
- Allow the "GT" field in genotypes at any point in the genotype string (before we required they be the first key-value pair).
- Fix a bug with the phasing value put into the VariantContext, thanks for the catch Guillermo!

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3638 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-25 18:01:23 +00:00
weisburd e15fe6858e Disabling test - Will need to update big-tables soon.. will re-enable after updating md5 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3637 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-25 15:43:41 +00:00
aaron 682f9b46c6 Two fixes together: 
1) Some improvements to the VCF4 parsing, including disabling validation.
2) Reimplemented RefSeq in the new Tribble-style rod system.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3630 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-24 22:17:03 +00:00
aaron 62bc7651a8 fix for PSPW with DbSNP mask. Added an integration test for this case. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3628 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-24 19:31:32 +00:00
aaron 8a9b2f4256 removing the GLF ROD. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3624 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-23 22:51:45 +00:00
aaron 611d834092 a couple of VCF 4 improvements: 
-Validation of INFO and FORMAT fields.
-Conversion to the the correct type for info fields (i.e. allele frequency is now stored as a float instead of a string).
-Checks for CNV style alternate allele encodings( i.e. <INS:ME:L1>), right now we exception out.  Maybe we should just warn the user?
-Tests for the multiple-base polymorphism allele case.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3622 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-23 20:21:43 +00:00
ebanks b6bceb39b0 Fixing up output for performance tests 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3619 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-23 17:00:17 +00:00
hanna 003dd4de3e Rev Picard with performance enhancements. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3615 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-22 22:54:23 +00:00
aaron 0cafd3d642 clip VCF alleles for indels: only a single left base, and as many right bases as align before converting to variant context. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3614 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-22 22:42:38 +00:00
aaron 9872b65803 clip to the null allele on the reference string in VCF 4, instead of stopping to perserve one reference base. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3613 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-22 20:52:19 +00:00
ebanks b5df2705c9 -Remove Nway output option 
-Remove in-memory sorting
-Default to name-sorting (although we allow coordinate sorting with the --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe flag).

Cleaner, faster code.  Wiki has been updated (including how to use FixMateInformation.jar from Picard).  More changes coming soon.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3612 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-22 20:31:55 +00:00
aaron a6d3e4bd47 Add code to allow reference alleles with 'N' in VariantContext, but not in the alternate allele(s). Also more updates to the VCF 4 code (fixed parsing for files without genotypes). 
This check-in will temperarly break the build (I need to see if Bamboo is correctly returning the log file for the failed builds).  

Will be fixed once Bamboo starts building.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3609 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-22 18:26:37 +00:00
ebanks 824c2bbac0 Finishing previous checkin 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3608 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-22 17:21:38 +00:00
aaron 32f324a009 incremental changes to the VCF4 codec, including allele clipping down to the minimum reference allele; adding unit testing for certain aspects of the parsing. Not ready for prime-time yet. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3604 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-22 06:31:05 +00:00
bthomas 300a18b85f Updating the way reference data is processed, so GATK creates the .fasta.fai and .dict files automatically. If either (or both) don't exist, GATK will create them in the same folder as the fasta file. If it can't write the file, GATK will fail with a message to create them manually. 
Note that this functionality will only work if the directory with the fasta is writeable. GATK will fail if directory is read only and and either the .fasta.fai or .dict files don't exist. In the future, we could have these references be created in memory, but we decided against it this time. 

Locking was also added to ReferenceDataSource so no issues come up while running multiple GATKs on the same reference: we don't want one process to be half-finished and another try to read it. So, you could see error messages related to locking. See ReferenceDataSource.java for explanation of the locking strategy. 



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3601 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-21 21:42:42 +00:00
hanna c806ffba5f Switching over DownsamplingLocusIteratorByState -> LocusIteratorByState. Some operations 
will not be as fast as they could be because the workflow is currently merge sam records (sharding)
-> split sam records (LocusIteratorByState) -> merge records (LocusIteraotorByState) -> split
records (StratifiedAlignmentContext), but this will be fixed when StratifiedAlignmentContext
is updated to take advantage of the new functionality in ReadBackedPileup.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3599 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-21 02:11:42 +00:00
depristo 57a13805da GATK now uses a optimized indexing scheme in Tribble. 5x or more performance gain on files with many genotypes. Updated integrationtest that was failing and was clearly wrong. DB=; isn't a valid annotation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3596 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-19 21:36:41 +00:00
kiran 8ff93f77e6 Added evaluation module to count functional classes (missense, nonsense, etc.). At the moment, it only understands Cancer's MAF annotations. Added integration test for the functional class counting. Added better description for VariantEval. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3595 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-18 21:51:40 +00:00
ebanks 1e06d2bf68 Initial HLA Caller integration tests. Kind of painful, but will improve with code refactoring. 
This baby is now officially ours.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3593 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-18 20:35:27 +00:00
rpoplin 724affc3cc Major bug fixes for the Variant Recalibrator. Covariance matrix values are now allowed to be negative. When probabilities are multiplied together the calculation is done in log space, normalized, then converted back to real valued probabilities. Clustering weights have been changed to only use HapMap and by-1000genomes sites. The -nI argument was removed and now clustering simply runs until convergence. Test cases seem to work best when using just two annotations (QD and SB). More changes are in the works and are being evaluated. Misc fixes to walkers that use RScript due to CentOS changes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3590 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-18 17:37:11 +00:00
aaron c3434493b0 fixed integration test for VCF Header changes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3589 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-18 16:31:48 +00:00
aaron 42e7ff4f28 forgot to update a test, the md5sum of the underlying file changed (which is recorded in the ROD tests). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3586 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-18 13:27:56 +00:00
aaron b978d5946b adding changes for VCF 4, mostly in the way we handle VCF headers. The header fields are now aware of the differences between different VCF formats. There was also a bunch of clean-up of out-of-spec VCF used in the tests (mismatched VCF file format fields, etc), and updates to the associated integration tests. Also some logging statements for BTI. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3584 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-18 08:23:23 +00:00
weisburd e26a273ef5 Turned the test back on 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3582 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-17 22:57:42 +00:00
hanna 48cbc5ce37 Merging the sharding-specific inherited classes down into the base. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3581 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-17 22:36:13 +00:00
hanna 612c3fdd9d First pass at eliminating the old sharding system. Classes required for the original sharding system 
are gone where I could identify them, but hierarchies that split to support two sharding systems have
not yet been taken apart.
@Eric: ~4k lines.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3580 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-17 20:17:31 +00:00
aaron 3d049204ed some refactoring for the variant eval output system 
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 2010-06-17 05:34:31 +00:00
hanna db1383d0b2 Rev the latest version of Picard. 
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 2010-06-16 23:55:07 +00:00
weisburd 5b370ffc62 git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3574 348d0f76-0448-11de-a6fe-93d51630548a 2010-06-16 20:42:58 +00:00
ebanks 01ffa307c2 When going NWay out in the cleaner, use the new *merged* header (instead of the original one) for each bam file so that it matches the new uniquified read group ids in the reads. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3569 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-16 19:36:36 +00:00
ebanks 7a91dbd490 Renamed some of the column names in Ti/Tv and Concordance modules so that they are clearer. Removed ValidationRate module (it was busted). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3564 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-16 15:53:06 +00:00
asivache 671ac00748 A simple utility class that implements a merging Iterator<GenomeLoc> built over an interval or bed file (this is NOT a rod, but rather a direct line-by-line file reader that converts strings to genome locs on the fly and merges overlapping intervals) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3546 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-14 15:54:37 +00:00
ebanks 8c28be5933 Fixing a VCF bug for Sendu: we weren't emitting flags (booleans) correctly in VCF3.3 (rev'ed tribble for this). 
Updated dbsnp/hapmap membership info fields to be flags now instead of ints.
While I was there, I added the change in the Annotator for Jan to force reads to be from a specific sample.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3536 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-11 16:42:06 +00:00
bthomas 99b684ea89 Adding new support for reference data. ReferenceDataSource is a new class that manages reference data, and allows IndexedFastaSequenceFile to be a simple reader. This checkin also includes FastaSequenceIndexBuilder, which reads a fasta file and creates an index, like samtools faidx. Right now this is not enabled, because we are still working out thread safety. So the only new UI change is that GATK can be run without a fai file. Soon, we will enable 1) GATK to be run without a dict file too, and 2) both dict and fai files will be saved on disk for future program executions. For more info, see ReferenceDataSource.java 
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 2010-06-10 20:10:23 +00:00
ebanks ca4eab1d23 Now annotations that require reads return null if there's no alignment context, so that running without reads adds annotations only for the appropriate fields. 
Added an integration test for the read-less case.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3525 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-09 20:36:46 +00:00
ebanks 9b2fcc4711 Refactoring of the annotation system: 
1. VA is now a ROD walker so it no longer requires reads (needs a little more testing)
2. Annotations can now represent multiple INFO fields (i.e. sets of key/value pairs)
3. The chromosome count annotations have been pulled out of UG and the VCF writer code and into VA where they belong.  Fixed the headers too.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3513 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-09 17:05:51 +00:00
aaron 6d5556939d updating Tribble with a couple of important Tabix fixes, and updating the variant eval integration tests to run each test with both plain vcf and gzipped tabix (added the tabix version 
to the vlidation directory), using the same md5sum.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3509 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-09 01:47:04 +00:00
depristo 6eeb1693ca JEXL2 upgrade. Improvements to JEXL processing including dynamically resolving variable -> value bindings instead of up front adding them to a map. Performance improvements and code cleanup throughout. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3494 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-07 00:33:02 +00:00
depristo 3ea506fe52 No more new Allele() -- must use create. Allelel simple alleles are now cached for efficiency reasons. VCF4 codec optimizations -- 4x performance in general. Now working in general but hooked up to the ROD system now as VCF4. WARNING -- does not actually work with indels, genotype filters, etc. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3489 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-04 23:03:55 +00:00
aaron 0b03e28b60 updating the tribble library to include the reference dictionary reading / writing. We now check the dictionaries of any tracks that have them against the reference (all new tribble tracks and out-of-date tracks will have this). Also renamed some classes to be more reflective of their function. 
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 2010-06-04 06:34:26 +00:00
depristo e2b41082af GATK now does automatic adaptor filtering in locus iterators (but not expt. downsampling iterator). General support for LocusIteratorFilters just like read filters but only applying at particular bases. Updated tools with new MD5 sums due to adaptor bases in their integrationtest data. Not that as a side effect here reads close to each other with odd orientations are also filtered out. Updated minor argument to VariantRecalibrator to change the qStep value on the command line 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3481 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-02 22:26:32 +00:00
aaron 8ec091d6d2 re-enabling regeneration of the tribble index if it's out of date. Also moved the class that can detect text in the log4j stream (useful in testing to make sure appropriate messages are generated). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3480 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-02 17:45:51 +00:00
depristo 21427211c0 Personal MD5 database system now live. WalkerTest now maintains a database of result files associated with MD5 results in integrationtest/, and provides command lines for diff-ing expected to current md5 results when encountering failed intergration tests. The suite currently takes 200Mb to store. Update and run intergrationtest to build your very own expectation database for future development work. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3466 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-31 16:06:16 +00:00
depristo 2b02324587 Support for detecting and automatically excluding reads reading into the adaptor sequence and, if desired, also only showing the first pair when two reads overlap in the fragment. Not enabled, an intermediate check in before updating and verifying the impact on locus walkers everywhere. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3465 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-30 18:00:12 +00:00
ebanks ffeb3fd80d Thanks to Guillermo, I found a bug in the Unified Genotyper output: GL was posteriors instead of likelihoods. Not a huge deal because the 
priors were flat, but fixed nonetheless.
Also, needed to update Tribble.
Minor updates to the Beagle input maker.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3461 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-28 19:28:26 +00:00
rpoplin 4e268ef6ac Removing the Variant Recalibration Performance test because it isn't ready yet. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3460 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-28 18:27:25 +00:00
rpoplin 522dd7a5b2 Adding the variantrecalibration classes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3459 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-28 18:21:27 +00:00
rpoplin 2014837f8a VariantOptimizer package is moved to core, renamed as VariantRecalibration, and added to the binary release package. VariantOptimizer walker is renamed to GenerateVariantClustersWalker and ApplyVariantClustersWalker renamed to VariantRecalibrator. Integration tests added, performance tests still to be done. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3458 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-28 18:20:18 +00:00
aaron 871cf0f4f6 Call out ROD types by there record type, instead of the codec type (which was clumsy). So instead of: 
@Requires(value={},referenceMetaData=@RMD(name="eval",type= VCFCodec.class))

you'd say:

@Requires(value={},referenceMetaData=@RMD(name="eval",type= VCFRecord.class))

Which is more in-line with what was done before.  All instances in the existing codebase should be switched over.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3457 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-28 14:52:44 +00:00
depristo cc2bf549c8 Removing my unnecessary optimization. 10 lines later in the code the same optimization was applied. A monumental waste of time. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3455 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-28 14:10:48 +00:00
aaron a4d834cc01 fixing the test I broke 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3454 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-28 02:06:20 +00:00
depristo f2e7582cfc Reorganization of SW code for clarity. Totally failure at raw optimization. Discovered that ~50% of reads being cleaned were perfect reference matches. New code comes with flag to look at NM field and not clean perfect matches. Can we turned off with command line option (needed for 1KG bams with bad NM fields). Going to rerun cleaning jobs due to accidentally rebuilding of stable codebase and loss of 2 days of runtime. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3452 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-27 23:16:00 +00:00
ebanks 058441fa39 Trivial renaming of test 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3441 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-26 16:56:42 +00:00
aaron a2fab07258 fixed the build problem: there were two copies of the AnnotatorInputTable Codec and Feature in two different spots. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3439 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-26 14:47:15 +00:00
chartl 88a06ad81f Changes to Depth of Coverage: 
- For speedup in large number of samples, base counts are done on a per read group level, then
   merged into counts on larger partitions (samples, libraries, etc)
   + passed all integration tests before next item
- Added additional summary item, a coverage threshold. Set by (possibly multiple) -ct flags,
   the summary outputs will have columns for "%_bases_covered_to_X"; both per sample, and
   per sample per interval summary files are effected (thus md5s changed for these)

NOTE:

This is the last revision that will include the per-gene summary files. Once DesignFileGenerator is sufficiently general, and has integration tests, it will be moved to core and the per-gene summary from Depth of Coverage will be retired.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3437 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-26 03:39:22 +00:00
ebanks 0607f76a15 commenting out this test until I can figure out what the hell is going on with the codecs. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3436 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-26 01:12:10 +00:00
ebanks ae6c014884 Fixed UG parallelization bug. Better integration test to catch this in the future. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3432 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-25 21:03:45 +00:00
ebanks 434e920da9 Oops, forgot to update integration tests 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3431 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-25 20:37:45 +00:00
delangel a280a0ff0d a) Made HaplotypeScore default annotation. This changed several integration tests, whose MD5 is now updated. 
b) Disabled BaseQualRankSumTest, the returned p-values differ wildly from Matlab/R-provided ones, cause TBD.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3419 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-21 22:25:17 +00:00
chartl 745d7c582f added integration test for intervals with no coverage due to filtering 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3414 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-21 16:52:42 +00:00
chartl 88cb93cc3c Changes to Depth of Coverage (added maximum base and mapping quality flags; with new integration tests -- because they use b36, and the other test uses hg18, it's in a different class (integration test system can't change refs on the fly). Initial change to VariantAnnotator to allow it to see extended event pilups; you currently have to throw the -dels flag; and it's specified as "very experimental". Yet,all the integration tests pass. 
Homopolymer Run now does the "right" thing (e.g. single bases are represented as HRun = 0 rather than HRun = 1) for indels. AlleleBalance now does something close enough to correct.

Added a convenience method to VariantContext that will return the indel length (or lengths if a site is not biallelic).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3409 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-21 13:02:01 +00:00
depristo 6faf101c6c Minor improvements to Callable Loci for public consumption 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3408 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-21 12:50:11 +00:00
depristo a10fca0d5c Genotyper now is using bytes not chars. Passes all tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3406 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-20 21:02:44 +00:00
depristo 6ce3835622 Removing unused methods in QualityUtils; ReferenceContext now converting all bases to upper case, but can be disabled with static boolean 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3399 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-20 12:38:06 +00:00
depristo 5abac5c057 A few more char -> byte cleanups 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3398 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-20 00:02:06 +00:00
depristo 8a725b6c93 Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3397 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-19 23:27:55 +00:00
aaron ca386439be only emit a warning if the tribble index is out of date, don't remove and replace it for them. Added a test case where the log4j appender checks the logging messages for the appropriate output. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3393 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-19 15:12:48 +00:00
hanna 017ab6b690 Experimental versions of downsampler and Ryan's deduper are now available either 
as walker attributes or from the command-line.  Not ready yet!  Downsampling/deduping 
works in a general sense, but this approach has not been completely optimized or validated.
Use with caution.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3392 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-19 05:40:05 +00:00
aaron 7cfb9ff3dc updates for Tribble 82, fixes for Ryans case where multiple processes would attempt to read/write to the same index, and a couple other Tribble-centric bug fixes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3382 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-18 19:34:45 +00:00
chartl e016491a3d Major refactoring of Depth of Coverage to allow for more extensible partitions of data (now can do read group, sample, and library; in any combination; adding more is fairly easy). Changed the by-gene code to use clones of stats objects, rather than munging the interval DoCs. (Fix for Avinash. Who, hilariously, thinks my name is Carl.) Added sorting methods to ensure static ordering of header and body fields. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3377 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-18 16:58:13 +00:00
hanna 0791beab8f Checking in downsampling iterator alongside LocusIteratorByState, and removing 
the reference implementation.  Also implemented a heap size monitor that can
be used to programmatically report the current heap size.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3367 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-17 21:00:44 +00:00
chartl b7d21627ab Changes to DepthOfCoverage (JIRA items) and added back an integration test to cover it. Alterations to the design file generator to output all transcripts (rather than choosing one at random). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3366 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-17 17:23:00 +00:00
ebanks 32389dc0a9 Fixed GQ estimate when chosen genotype isn't the most likely according to the GLs. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3362 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-14 19:17:46 +00:00
hanna 88bd7a2045 Reenabling UG parallelization performance tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3360 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-13 16:28:08 +00:00
hanna 0490909285 Fixed epic generic paths fail. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3359 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-13 15:59:57 +00:00
hanna 7ef87e5126 An integration test based on validating pileup to test parallelism in reads, reference, and RODs. This test runs in less 
than a minute and fell over instantly in the case of the Tribble parallelism issue.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3358 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-13 15:40:43 +00:00
hanna ceec525420 Got rid of stray unicode characters in copyright message. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3357 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-13 14:47:39 +00:00
ebanks c81b910f73 Commenting out the parallelization test which is failing 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3354 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-12 18:39:53 +00:00
aaron cac98ba5ef a couple of small documentation fixes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3353 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-12 17:40:27 +00:00
aaron 2c55ac1374 fixes for parallel processing problems with Tribble, a small bug in the resource pool, and some more documentation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3349 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-12 06:13:26 +00:00
ebanks 34969f304c Adding dbsnp to all UG performance tests 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3347 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-11 15:48:05 +00:00
ebanks 140e43b93b Checking in to see whether it fails. If I start getting bombarded with Bamboo error reports, I'm commenting it out... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3346 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-11 15:39:42 +00:00
ebanks 572b383fe2 Make VA annotate dbsnp again 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3345 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-11 14:06:53 +00:00
depristo 64ccaa4c6a Walkers and integration tests that calculate and compare callable bases 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3328 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-07 21:33:47 +00:00
aaron 7d2df3f511 example windowed ROD walker for Kristian, and updates to Tribble 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3325 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-07 17:12:50 +00:00
rpoplin 57f254b13a VE integration test 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3324 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-07 13:58:25 +00:00
aaron 78409dca0d turned off the progress output from tribble when making an index, and fixing a case where the index file isn't writable so we instead make the index in memory. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3312 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-06 16:36:58 +00:00
aaron a0d71540df speed-up for VCF, adding code to the VCF reader to automagically make an index if one doesn't already exist, and a change to the VCF writer unit test 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3305 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-05 20:19:42 +00:00
aaron a68f3b2e9c VCF moved over to tribble. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3302 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-05 17:28:48 +00:00
aaron ad11201235 adding more ROD pile-up tests 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3301 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-05 16:01:11 +00:00
aaron f497213933 DbSNP moved over to tribble 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3288 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-03 06:02:35 +00:00
ebanks 9dff578706 Added PG tag to bam header to let people know it's been cleaned. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3284 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-30 17:30:30 +00:00
ebanks 850f36aa61 Changes to the Unified Genotyper's arguments: 
1. User can specify 4 confidence thresholds: for calling vs. emitting and at standard vs. 'trigger' sites.
2. User can cap the base quality by the read's mapping quality (not done yet).
3. Default confidence threshold is now Q30.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3281 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-30 16:44:24 +00:00
aaron cbed0b1ade Adding GeliText tribble track as the first enabled Tribble track. This mean 'Variants' is no longer valid for a ROD type, use GeliText instead. I've updated all the references in the codebase. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3271 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-29 22:50:17 +00:00
aaron 7fbfd34315 adding the GELI ROD validation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3270 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-29 21:43:00 +00:00
depristo 5dce16a8f1 Better genotype concordance module. Code refactoring for clarity (please see below/after for educational purposes). Now reports variant sensitivity, concordance, and genotype error rate by default. Also aggregates this data across all samples, so you get a per sample and overall stats for each of these in the allSamples row. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3265 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-28 13:10:11 +00:00
ebanks df31eeff9f minor change 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3259 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-26 06:05:29 +00:00
depristo 7f4d5d9973 Ti/Tv by AC 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3252 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-23 17:56:29 +00:00
rpoplin e7c0ded40e Fixed long-standing bug in GenotypeConcordance module of VariantEval which caused incorrect numbers to be displayed in the concordance table. The format of the concordance table has changed. Added a concordance summary table which gives overall genotype concordance summary stats by sample. None of the VE integration tests contained genotype information so I added a comp track with genotypes to one of the tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3247 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-23 15:48:41 +00:00
aaron f050beada6 make sure we do delete the temp file we create 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3244 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-23 05:32:49 +00:00
aaron 536f22f3bd adding VC adaptor for GELI, along with unit tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3243 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-23 05:28:39 +00:00
hanna 32d86cf457 Rev the reservoir downsampler to support partitioning through a functor. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3232 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-21 19:50:26 +00:00
ebanks e9e844fbf5 1. Reverting: dbsnp automatically is a comp 
2. Fixing logic for min Qscore calculation


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3230 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-21 18:51:35 +00:00
asivache 532263ea25 Oooops, forgot to update the test 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3229 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-21 18:38:24 +00:00
ebanks 4abd3b0b7b Fixing known/novel calc now that dbsnp isn't a default comp track 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3223 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-21 05:43:59 +00:00
ebanks 3b5673d967 1. Removed -all; by default all modules are used; use -none for no modules. 
2. Don't make dbsnp track be a comp by default (to cut back on output). Please let me know if someone wants this back for some reason.
3. Cleaned up dbsnp module output to print the right numbers.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3220 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-21 02:46:42 +00:00
aaron 4e18c54bb8 fixing a couple of commented out portions of the VCFReader test 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3219 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 22:20:35 +00:00
aaron 80c4f88a72 removing the Variation interface. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3216 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 18:56:45 +00:00
hanna c1e53d407d The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had 
unicode quote characters embedded in it.  These characters were invisible inside
IntelliJ but cause compile warnings for Ryan and Aaron, who for whatever reason
have a different default charset.  Fixed.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3203 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 15:26:32 +00:00
aaron b5f6f54968 Almost done removing any trace of the old Variation and Genotype interfaces. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3202 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 14:52:15 +00:00
hanna 1bc26f69e9 An attempt to cleanup the Utils directory. Email to follow. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3198 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-19 23:00:08 +00:00
hanna c08936d6f4 Added a reservoir downsampler which can sample elements in an iterator uniformly 
from a stream (see Vitter 1985).  Thanks to Eric and Andrey for the pointer.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3197 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-19 20:48:14 +00:00
ebanks c44f63c846 Fixing the performance tests: we need to catch the RuntimeException (not samtools' RuntimeIOExcpetion). Also, CountCovariates doesn't need the catch. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3196 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-19 14:28:12 +00:00
ebanks abf48cee05 Moving over to VariantContext from Variation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3195 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-19 06:56:29 +00:00
ebanks d73c63a99a Redoing the conversion to VariantContext: instead of walkers passing in a ref allele, they pass in the ref context and the adaptors create the allele. This is the right way of doing it. 
Also, adding some more useful integration tests.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3194 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-19 05:47:17 +00:00
aaron be7cbf948b adding a catch for the exception thrown by samtools when it attempts to close /dev/null in the performance tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3186 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-16 17:41:48 +00:00
ebanks 7adff5b81a Renaming for consistency 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3180 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-15 20:36:19 +00:00
ebanks e702bea99f Moving VE2 to core; calling it "VariantEval" (one more checkin coming) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3179 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-15 20:25:47 +00:00
chartl ac6f6363ce Execs() temporarily disabled after removal of bam file. New tests forthcoming. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3178 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-15 20:11:56 +00:00
ebanks ac9dc0b4b4 Removing VariantEval (v1); everyone should be using VE2 now. Docs coming ASAP. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3177 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-15 19:53:02 +00:00
ebanks 5f7564bf0a Better naming of output columns 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3175 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-15 18:08:07 +00:00
aaron e682460c1f add a fix so that XL arguments won't cancel out -BTI arguments, fixed a bug for Ben where the ROD -> interval list conversion was throwing an exception, and some old code removal. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3174 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-15 16:31:43 +00:00
ebanks 04909fa6ad Removing arbitrary selects 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3169 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-14 17:46:39 +00:00
weisburd b930dc52a5 Integration test for GenomicAnnotator 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3167 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-14 14:43:25 +00:00
ebanks dde092fb61 Added the ability in VE2 to select which eval modules to run, so that you aren't forced to use all of them. You can use --list to list all of the possible modules to run. 
Heads up everyone: by default, *no* modules are run.  Please add "-all" to your scripts to maintain the previous behavior.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3161 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-13 22:15:58 +00:00
hanna 8573b0bc6f Refactoring intervals, separating the process of parsing interval lists, 
sorting and merging interval lists, and creating RODs from intervals.  This
gives Doug the ability to keep using our interval list parsing code when
sorting intervals on our behalf.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3159 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-13 15:50:38 +00:00
ebanks e413882302 Generalizing the SequenomValidationConverter to be able to take in any arbitrary rod type (provided it can be converted to VariantContext). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3155 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-12 20:42:18 +00:00
ebanks d06c7835d8 Adding performance tests for the indel realigner; should take ~3 hours. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3151 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-11 04:45:22 +00:00
ebanks 961ca05abc Removed outdated Sequenom rod and renamed HapMapGenotypeROD to HapMapROD. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3149 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-11 01:43:07 +00:00
ebanks fa01876255 UnifiedGenotyper performance tests (WG, WEx); currently takes just over an hour. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3148 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-09 19:42:29 +00:00
rpoplin c2a37e4b5c Variant Quality Score modules in VariantEval2 no longer create huge lists which hold all of the quality scores encountered and instead cast the quality score to an integer and use hash tables. Bug fix for files in which all the quality scores are set to -1. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3146 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-09 18:36:06 +00:00
ebanks 71f38a9199 Adding performance tests for the recalibrator (Whole Genome and Whole Exome tests). 
Should take ~3 hours to run.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3145 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-09 18:30:59 +00:00
ebanks fba48b515a Heads up everyone: 
For consistency, these tools should be writing to the walker's output stream and no longer use the -vcf argument.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3140 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-09 05:37:25 +00:00
chartl 7025f5b51d Added an auxiliary table to DepthOfCoverage, which is the cumulative equivalent of the locus table (got tired of doing the calculation by hand). Also took care of a trailing tab in the per-locus output table. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3138 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-08 19:37:17 +00:00
aaron 9f6377f7fb added a performance test build option (for the upcoming performance test suite), and added a sample performance test for VariantEval. 
IMPORTANT: it was really redundant that we had -Dsingle and -Dsingleintegration to run single unit tests and integration tests, now you can just use -Dsingle to run a single test for performance, unit, and integration tests.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3136 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-08 15:37:15 +00:00
aaron 4014a8a674 A long overdue correction; all unit tests now end in 'UnitTest'. This was something we wanted to do for a while, and now with the performance tests coming, it was a good time to clean-up. Please label any new test appropriately: *UnitTest and *IntegrationTest are the two valid file name patterns for tests. 
Thanks!



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3135 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-08 06:14:15 +00:00
aaron 8fd59c8823 Modified the report system based on Ryan's feedback: tables are now created independently to avoid the permutation problem when they were all compressed in rows, and removed our dependency on FreeMarker. The Grep format stays the same. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3130 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-07 20:39:55 +00:00
depristo 918b746798 More detailed validation output. Fixes for genotyping overflow -- these are temporary and need to be properly resolved 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3129 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-07 16:38:28 +00:00
rpoplin 60c227d67f Added new VE2 module to create a plot of titv ratio by variant quality score 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3125 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-06 15:19:27 +00:00
chartl d7880ef7ad Forgot to uncomment the AlignerIntegrationTest before committing. And yes, matt, commenting it out is, in fact, easier than just setting my classpath. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3110 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-01 17:17:16 +00:00
chartl f7d1b8f5de CoverageStatistics has now replaced DepthOfCoverage -- old DoC is in the archive. 
Also, I can't be bothered to fix the spelling of "oldepthofcoverage" to contain the necessary number of D's. Be content that it does, however, contain the requisite number of O's.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3109 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-01 16:27:23 +00:00
aaron 585cc880a2 changed jexl expressions to jexl names in the VariantEval2 output, fixed integration test, and fixed a problem where a line was getting dropped in CSV output 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3108 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-01 16:23:14 +00:00
bthomas b4f6f54502 Reorganizing the way interval arguments are processed 
Most of the changes occur in GenomeAnalysisEngine.java and GenomeLocParser.java: 
-- parseIntervalRegion and parseGenomeLocs combined into parseIntervalArguments
-- initializeIntervals modified
-- some helper functions deprecated for cleanliness
Includes new set of unit tests, GenomeAnalysisEngineTest.java

New restrictions: 
-- all interval arguments are now checked to be on the reference contig
-- all interval files must have one of the following extensions: .picard, .bed, .list, .intervals, .interval_list



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3106 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-01 12:47:48 +00:00
aaron 3d3d19a6a7 the last-mile commit for Tribble integration. The system is now ready for Tribble to be turned on, as soon as we've removed any dependencies in the ROD code on interfaces that aren't in the Tribble library (i.e. the Variation or Genotype interface on RODs). All of the walkers should be up to date. 
a caveat: for anyone asking for all of the ROD's back from the RefMetaDataTracker (if your not using the facilities to get the track by name), you'll now be getting back a collection of GATKFeature objects.  This object will contain the track name, and a method for getting the underlying object (getUnderlyingObject()), which will be the traditional RodVCF, rodDbSNP, etc.  This layer is needed so we can integrate Tribble tracks (which don't natively have names).  Calls that ask for RODs by name will still get back the traditional reference ordered data objects (RodVCF, rodDbSNP, etc).

Sorry for the inconvenience!  More changes to come, but this is by far the largest (as has the greatest effect on end users).


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3104 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-31 22:39:56 +00:00
chartl dc802aa26f Moved CoverageStatistics to core. This will be (soon) renamed DepthOfCoverage; so please use CoverageStatistics 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3090 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-29 13:32:00 +00:00
depristo 8ea98faf47 Deleting the pooled calcluation model -- no longer supported. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3088 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-29 11:44:27 +00:00
aaron 074ec77dcc First go of the new output system for VE2. There are three different report types supported right now (Table, Grep, CSV), which can be 
specified with the reportType command line option in VE2.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3083 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-27 03:59:32 +00:00
kshakir 20e3ba15ca Added an optional argument -rgbl --read_group_black_list to filter read groups. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3079 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-26 19:38:57 +00:00
ebanks 73a14a985b Moving VariantsToVCF to core. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3078 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-26 18:55:12 +00:00
ebanks 14bf6923a8 HapMap-to-VCF now works fine within Variants-to-VCF. Added integration test for it and removed old code. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3077 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-26 18:34:59 +00:00
ebanks 4398a8b370 Updated. Now uses VariantContext and is truly "variants" to vcf (i.e. not just GELI to vcf). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3074 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-25 04:53:31 +00:00
aaron 5079f35e40 better method names for read based reference ordered data access. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3069 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-24 16:13:31 +00:00
aaron 7462a0b2d1 cleaned-up of VariantContextAdapter tests, fixed the double comparisons in equals() in RodGeliText (nice MathUtils.compareDoubles Kiran) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3064 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-23 15:18:30 +00:00
aaron a69b8555dd Geli to variant context. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3063 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-23 06:45:29 +00:00
aaron eafdd047f7 GLF to variant context. Added some methods in GLF to aid testing; and added a test that reads GLF, converts to VC, writes GLF and reads back to compare. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3062 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-23 03:43:25 +00:00
asivache ee1dc6092f Test updated. Now we do not throw an exception when locus interval is out of bounds, we just return silently a reference context trimmed to the current shard boundaries. New test checks for trimming. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3058 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-22 17:37:52 +00:00
aaron 439c34ed38 clean-up before annotating VariantEval2 for output. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3055 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-22 07:39:20 +00:00
ebanks 4c4d048f14 Moving VariantFiltration over to use VariantContext. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3048 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 18:35:23 +00:00
ebanks c88a2a3027 Fixing/cleaning up the vcf merge util 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3047 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 15:13:32 +00:00
ebanks 03480c955c And now the UnifiedGenotyper can officially annotate genotype (FORMAT) fields too. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3039 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 04:58:37 +00:00
ebanks 0311980668 The VariantAnnotator can now officially annotate genotype (FORMAT) fields. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3037 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 03:30:14 +00:00
aaron 8a5f0b746e some cleanup for the output system. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3032 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-18 12:54:39 +00:00
ebanks 0247548400 Fixed one test and (temporarily) punted on another 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3030 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-18 06:22:48 +00:00
ebanks ee0e833616 Some significant changes to the annotator: 
1. Annotations can now be "decorated" with any arbitrary interface description - not just standard or experimental.
2. Users can now not only specify specific annotations to use, but also the interface names from #1.  Any number of them can be specified, e.g. -G Standard -G Experimental -A RankSumTest.
3. These same arguments can be used with the Unified Genotyper for when it calls into the Annotator.
4. There are now two types of annotations: those that are applied to the INFO field and those that are applied to specific genotypes (the FORMAT field) in the VCF (however, I haven't implemented any of these latter annotations just yet; coming soon).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3029 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-18 05:38:32 +00:00
ebanks 4340601c26 -Pushed base quals back down into SAMRecord; if -OQ is used, the SAMRecord quals get updated automatically 
-Better integration test


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 2010-03-17 16:00:10 +00:00
hanna 2525ecaa43 Oops. Commented out some tests to improve performance and then checked in the commented out tests. Reverted. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3012 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-16 16:34:50 +00:00
hanna 6dd5f192e7 Performance improvements for RODs in conjunction with new sharding system. 
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 2010-03-16 14:54:12 +00:00
aaron 10e76abbbc adding some VE2 report infrastructure; work-in-progress. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3008 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-16 03:57:42 +00:00
ebanks 202231141c -Push the --use_original_qualities argument into the engine. 
-Check that base and qual strings are the same lengths
-Fix one more bug in the clipper.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3006 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-16 02:06:11 +00:00
ebanks 411d25c8d1 -Integration tests for walkers that use original quals. 
-framework for pushing -OQ into GATK (not done)


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3004 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-15 18:46:31 +00:00
aaron e365d308d4 add a new JEXLContext that lazy-evaluates JEXL expressions given the VariantContext. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3003 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-15 16:00:55 +00:00
ebanks 73d6167bd6 Fixing broken integration tests 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2998 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-14 23:18:49 +00:00
depristo 4dd7c5972c Unit tests for -XL arguments; expt. annotation calculating the GC content within 100 bp of the current SNP 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2997 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-14 21:08:14 +00:00
aaron ecb59f5d0d removed old tests and old code 
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 2010-03-12 22:57:01 +00:00
aaron 88a48821ea removed the dependence on removeRegion() in GenomeLocSortedSet 
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 2010-03-12 22:35:49 +00:00
depristo b39b5edca8 Bug fix in variant eval 2. Preliminary (slow and buggy) support for -XL exclude lists. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2991 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-12 19:23:12 +00:00
aaron 1eb5f97255 fixed dropping single base intervals from deleteRegion, moving onto performance fixes. 
(stop - start is length-1 on closed intervals, so we need to check greater than OR equals to zero)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2990 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-12 19:14:21 +00:00
aaron 661a043cef adding methods to get RODs by name or type in read traversals, performance improvements to RODs for Reads in general, and some more Tribble infrastructure. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2984 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-11 21:13:39 +00:00
hanna a7ba88e649 Rework the way the MicroScheduler handles locus shards to handle intervals that span shards 
with less memory consumption.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2981 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-11 18:40:31 +00:00
aaron dde9fd8a15 some rods-for-reads cleaning and performance improvements. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2979 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 22:54:58 +00:00
depristo 4f4555c80f PPV and Sensitivity added to validation tool output; support for arbitrary -sample arguments to subset variant contexts by sample 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2978 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 22:28:31 +00:00
ebanks 40d305bc7e Added test of Nway cleaning for Matt; thanks to Aaron for the help. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2977 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 21:00:41 +00:00
depristo 486bef9318 Support for validationRate calculation in variant eval 2; better error messages for failed genome loc parsing; tolerance to odd whitespace in plinkrod, and fix for monomorphic sites in vcf2variantcontext. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2976 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 16:25:16 +00:00
ebanks 7ddd45d059 Hmm. I thought I removed this already. 
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 2010-03-10 03:09:13 +00:00
ebanks 1a576525e9 misc improvements 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2972 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 03:00:28 +00:00
ebanks 6e855809e1 Renaming and moving relevant tools into a sequenom directory 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2971 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-10 02:31:10 +00:00
chartl 0a49dffa8f Row/Column names are now R-friendly 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2966 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-09 19:01:03 +00:00
ebanks e5475a7ba9 re-enabling PlinkToVCF integration tests 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2964 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-09 17:35:49 +00:00
ebanks 5a20bf0e64 3 changes to UG which break integration tests: 
1. emit AA,AB,BB likelihoods in the FORMAT field for Mark
2. remove constraint that genotype alleles (in the GT field) need to be lexigraphically sorted.
3. Add bam file(s) used by genotyper to header for Kiran


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2963 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-09 17:16:47 +00:00
ebanks 9f3b99c11b Moving UnifiedGenotyper and VariantAnnotator over to VariantContext system. 
Removing obsolete genotyping classes.
First stage of removing dependence on old Genotype class.
More changes to come.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2960 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-09 03:41:07 +00:00
chartl bca9bdcc68 Add integration test for quartiles overflowing on interval reduce 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2957 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-08 16:18:45 +00:00
hanna a7fe07c404 A few stopgap fixes to get the GATK to the point where the old sharding 
infrastructure can be torn down:
1) New sharding system emulates old MonolithicSharding mechanism.
2) Better awareness of differences between fasta and BAM files when creating
   shards.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2948 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-07 21:01:25 +00:00
hanna dd6122f682 Fixed another bug in the original sharding system. Updated integration tests 
as appropriate.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2947 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-07 15:32:18 +00:00
hanna ee2ec7ced9 Fix off-by-one error in original implementation of read sharding. Tested by 
awking output of BamToFastq vs. samtools until the outputs matched exactly.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2945 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-06 18:52:53 +00:00
depristo ee913eca07 Forgot to check in fix this morning 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2943 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-05 21:07:19 +00:00
chartl 8738c544f1 Minor refactoring of CoverageStatistics to allow simultaneous output of per-sample and per-read group statistics. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2940 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-05 17:06:52 +00:00
hanna 7104a3a96c Fix for accumulator exception when running reduce by interval walkers without 
intervals.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2935 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-05 01:04:08 +00:00
aaron 366771d5a6 another test-with-multiple outputs fix 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2934 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-04 22:46:15 +00:00
chartl 706d49d84c Commit for Aaron 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2932 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-04 21:29:07 +00:00
aaron 54f04dc541 forgot to uncomment the auto-deletion of temp files... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2930 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-04 20:29:42 +00:00
aaron 80cc6bbeb4 add a way to test files generated by a walker that aren't command-line arguments; added some example code in CoverageStatisticsIntegrationTest for Chris. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2929 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-04 20:20:58 +00:00
ebanks 0dd65461a1 Various improvements to plink, variant context, and VCF code. 
We almost completely support indels. Not yet done with plink stuff.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2926 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-04 17:58:01 +00:00
aaron c8077b7a22 Waypoint check-in: a couple of changes to for Tribble, and adding some options to the integration test for passing in auxillary files that aren’t “%s” command line options. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2925 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-04 16:02:21 +00:00
aaron ca2cd9d4f5 a little clean-up: move setting the bases of generated reads into Artificial SAM Utils now that the clean read injector test is gone. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2919 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-03 16:31:45 +00:00
aaron 790d2a7776 adding the initial ROD for Reads support; more convenience methods in ReadMetaDataTracker to come. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2918 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-03 15:56:44 +00:00
ebanks 0e9a6826b0 Update to VCF code to get it up to spec. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2917 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-03 06:12:42 +00:00
ebanks 74a5223b11 oops - didn't mean to check this in 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2914 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-02 20:28:22 +00:00
ebanks 5f3c80d9aa 1. To make indel calls, we need to get rid of the SNP-centricity of our code. First step is to have the reference be a String, not a char in the Genotype. Note that this is just a temporary patch until the genotype code is ported over to use VariantContext. 
2. Significant refactoring of Plink code to work in the rods and use VariantContext.  More coming.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2913 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-02 20:26:40 +00:00
aaron d8fedd59be docs, cleanup, and some improvements to the iterators. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2901 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-26 22:36:04 +00:00
chartl 87f8fb7282 Quick commit in advance of Aaron's. Just a bunch of refactoring (private classes separated out, put in proper package). Also support added for coverage by read group rather than sample. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2897 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-26 16:39:47 +00:00
depristo 9a6b384adb Support for no qual fields in VCF; better support for Mendelian violation calculations 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2893 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-26 00:29:17 +00:00
aaron 246fa28386 RODs for reads phase 2: modified RODRecordList to implement List<ReferenceOrderedDatum> so I could stub it out for testing, added a FlashBackIterator which is needed to prevent the ResourcePool from opening infinity+1 iterators, and some other interfaces to make unit testing much smoother. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2892 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-25 22:48:55 +00:00
chartl 3d92e5a737 Initial commit of integration test(s) for CoverageStatistics, currently in progress [midway commit is for Matt] 
Modifications to CoverageStatistics - now includes and extends much of the behavior of DepthOfCoverage (per-base output, per-target output).

Additional functionality (coverage without deletions, base counts, by read group instead of by sample) is upcoming.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2888 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-25 20:25:07 +00:00
hanna 553d39bb00 Clean up the code a bit following the introduction of reduceByInterval. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2887 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-25 01:20:22 +00:00
hanna 199b43fcf2 Reduce by interval alterations to interface with new sharding system. This checkin with be followed by a 
simplification of some of the locus traversal code.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2886 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-25 00:16:50 +00:00
aaron fef1154fc8 starting on RODs for Reads: made RODRecordList implement list<RODatum> (so we can sub in fake lists during testing), and removed unnecessary generic-ness. Removed BrokenRODSimulator, which isn't being used. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2884 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-24 22:11:53 +00:00
aaron 5546aa4416 adding code to deal with the off-spec situation where our minimum likelihood is above the GLF max of 255. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2871 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-22 22:27:39 +00:00
ebanks 8b555ff17c Killed the old cleaner code. Bye bye. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2868 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-22 20:49:58 +00:00
rpoplin 3e0e7aad2d Removing debug statement. oops. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2858 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-19 15:26:22 +00:00
rpoplin 7f19ff1fa1 Added a new option in the recalibrator to be used by people who have SOLiD data in which only a few of the reads have no-calls in the color space. These reads will be skipped over and left in the bam file untouched. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2857 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-19 15:25:23 +00:00
aaron b1a4e6d840 removing non-ascii characters from my Copyright and from VariantEval2Walker 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2856 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-18 18:54:36 +00:00
aaron 33ae256186 a start to some of the infrastructure for Tribble, including dynamic detection of new RMD; not nearly wired in or complete yet. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2855 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-18 18:43:52 +00:00
ebanks 79ab7affda - Change sortOnDisk option to sortInMemory 
- Fix horrible cleaner bug
- Trivial optimizations to cleaner code - more significant ones coming soon.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2850 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-17 20:52:57 +00:00
aaron 653f70efa2 added methods to validate an interval before you try to make a GenomeLoc: boolean validGenomeLoc(). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2846 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-16 20:35:35 +00:00
depristo 8072e9aed5 should never commit without running intergration tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2838 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-12 23:42:37 +00:00
depristo 5f74fffa02 Massive improvements to VE2 infrastructure. Now supports VCF writing of interesting sites; multiple comp and eval tracks. Eric will be taking it over and expanding functionality over the next few weeks until it's ready to replace VE1 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2832 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-12 15:26:52 +00:00
depristo 197dd540b5 added root GATKData variable 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2831 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-12 15:25:34 +00:00
depristo c66861746a improvements to ve2, including more meaningful mendelian violation counting. Support for VCF emitted interesting sites, annotated according to the evaluations themselves. Basic intergration test for VE2 started 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2819 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-10 16:12:29 +00:00
rpoplin 0b1e243a7b CountCovariates now sorts the list of standard covariate classes coming from PackageUtils.getClassesImplementingInterface(). As a result some of the integration tests now make use of -standard 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2817 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-10 15:52:20 +00:00
depristo 934d4b93a2 VariantContext to VCF converter. BeagleROD, and phasing of VCF calls. Integration tests galore :-) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2814 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-09 19:02:25 +00:00
depristo 94f892ad42 VCF->beagle and VCF phasing using beagle input. Appears to work fairly well. VariantContexts now support phased genotypes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2812 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-09 01:22:05 +00:00
kshakir fc810a1800 Updated VCF Reader to parse VCFs according to the VCFv3.3 spec. Column headers are tab separated since sample names might have spaces. 
Updated test files in /humgen/gsa-scr1/GATK_Data/Validation_Data/*.vcf to remove spaces except for when they are supposed to be in the sample name.
Added @Test before VCFReaderTest.testHeaderNoRecords()

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2809 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-08 22:55:59 +00:00
chartl 935e76daa1 Minor changes to oneoff walkers. PlinkRod altered but still commented. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2808 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-08 18:49:56 +00:00
ebanks ca1917507f Various improvements and fixes: 
In indel cleaner:

1. allow the user to specify that he wants to use Picard’s SAMFileWriter sorting on disk instead of having us sort in memory; this is useful if the input consists of long reads.

2. for N-way-out mode: output bams now use the original headers from the corresponding input bams - as opposed to the merged header.  This entailed some reworking of the datasources code.

3. intermediate check-in of code that allows user to input known indels to be used as alternate consenses.  Not done yet.

In UG: fix bug in beagle output for Jared.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2805 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-07 04:21:04 +00:00
depristo 3b1ab86d11 Added generic interfaces to RefMetaDataTracker to obtain VariantContext objects. More docs. Integration tests for VariantContexts using dbSNP and VCF. At this stage if you use dbSNP or VCF files only in your walkers, please move them over to the VariantContext, it's just nicer. If you've got RODs that implemented the old variation/genotype interfaces, and you want them to work in new walkers, please add an adaptor to VariantContextAdaptors in refdata package. It should be easy and will reduce burden in the long term when those interfaces are retired. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2803 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-06 16:26:06 +00:00
hanna c7e006a996 Bug fixes for interval batching in sharding system. Sharding system now batches intervals and passes 
basic tests for small and large intervals and intervals that cross bin boundaries.  Currently works
only with a single BAM file.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2800 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-05 21:47:54 +00:00
rpoplin be33d1852c Reverting 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2792 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-05 15:57:09 +00:00
rpoplin 0d8d6e0a14 Ti/Tv module in VariantEval shows known and novel ratios if possible 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2790 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-05 15:37:40 +00:00
depristo 1494dc875f fixing up tests. Moves are complete 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2789 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-05 14:24:00 +00:00
depristo c6d86da4b8 almost managed to move things around perfectly in move go 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2788 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-05 14:18:26 +00:00
depristo 1d86dd7fd1 Interface changes following Matt's advice. VariantContexts are now immutable, and there are special mutable versions, in case you need to change things. AttributedObject now a InferredGeneticContext and package protected. VariantContexts are now named, which makes them easier to use with the rod system 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2780 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-04 20:55:49 +00:00
aaron af7cd9cf58 some very old tests relied on cancer data that got moved. Reset one to use data in the validation directory, the other to the artificial sam utils (the best approach). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2767 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-02 23:13:10 +00:00
hanna 9dbdfff786 Moved VariantEval to core. Updated integration test md5s to reflect new Analysis class names. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2762 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-02 00:22:15 +00:00
depristo d9671dffba Documentation for VariantContext. Please read it and start using it. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2756 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-01 17:49:51 +00:00
ebanks e0808e6c37 Moved old EM model to archive 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2754 348d0f76-0448-11de-a6fe-93d51630548a
 2010-02-01 02:55:32 +00:00
ebanks f6da57dc79 1. For Matt: JIRA GSA-270. Other walkers needing to call into the Unified Genotyper now use static methods (e.g. runGenotyper()) instead of calling initialize and map. 
2. Set the default confidence cutoff to 50 (instead of 0).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2752 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-31 21:14:57 +00:00
depristo 62a80f2b6f fixed out of date tests. Also, tests uncovered a subtle bug in new implementation that was also fixed 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2741 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-29 20:03:48 +00:00
hanna e7f5c93fe5 Cleaning up the inheritance hierarchy from the previous commit. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2738 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-29 19:13:36 +00:00
depristo 1993472b38 Just like VariantFiltration but lets you match info fields out of the VCF instead of annotating them. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2736 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-29 15:38:03 +00:00
depristo 5aaf4e6434 VariantFiltration now accepts any number of --name --filter expressions, and annotates the VCF file with each name that matches. Very useful 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2732 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-29 12:13:08 +00:00
hanna 3d922a019f Basic support for very simple index-driven locus traversals. Interface has been changed to 
support batched intervals in a single shard, but intervals are not yet compressed into a single
shard.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2730 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-29 03:14:26 +00:00
depristo 956b570c8e V5 improvements to VariantContext. Now fully supports genotypes. Filtering enabled. Significant tests throughout system. Support for rebuilding variant contexts from subsets of genotypes. Some code cleanup around repository 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2721 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-28 18:37:17 +00:00
depristo f6bca7873c V3 of VariantContext. Support for Genotypes and NO_CALL alleles. QUAL fields fully implemented. Can parse VCF records and dbSNP. More complete validation. Detailed testing routines for VariantContext and Allele. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2718 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-28 04:10:16 +00:00
depristo 3399ad9691 Incremental update 2 -- refined allele and VariantContext classes; support for AttributedObject class; extensive testing for Allele class, and partial for VariantContext. Now possible to easily convert dbSNP to VariantContext. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2705 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-27 17:19:37 +00:00
ebanks 476d6f3076 RealignerTargetCreator is officially live 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2697 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-27 03:41:52 +00:00
ebanks 47440bc029 - Removed max_coverage argument from UG; Aaron will set it up so that we don't call when the GATK had to drop reads. 
- Reimplemented optimization in UG to not call when there are no non-ref bases.
- Compute reference confidence accurately in UG for ref calls.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2693 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-26 21:56:33 +00:00
rpoplin a1054efe8a Default platform and default read group are no longer set to values by default. The recalibrator throws an exception if needed values are empty in the bam file and the args weren't set by the user. This is done to make it more obvious to the user when the bam file is malformed. Similarly, the recalibrator now refuses to recalibrate any solid reads in which it can't find the color space information with an exception message explaining this. The recalibrator no longer maintains its own version number and instead uses the new global GATK version number. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2690 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-26 18:47:40 +00:00
depristo c231547204 Refactoring and migration of new allele/variantcontext/genotype code into oneoffprojects. NOT FOR USE. PlinkRod commented out due to dependence on this new, rapidly changing interface. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2687 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-26 13:53:29 +00:00
chartl d6b9b788a8 Renamed -- PlinkRodWithGenomeLoc --> PlinkRod 
Since binary files do not need encoded locus information in the SNP names there's no need to suggest that it is so in the name of the rod



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2671 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-23 18:19:28 +00:00
chartl ac983e7a0b Ran the rod on a binary plink file with indels and it just worked. Love it when that happens! Unit test to ensure this behaviour is maintained. 
****** PLINK ROD IS NOW READY TO GO ********




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2670 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-23 18:13:05 +00:00
chartl ae22d35212 PlinkRod now correctly parses binary files without indels; unit test added for this behavior. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2669 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-23 17:34:06 +00:00
chartl 94dc09c865 PlinkRod now successfully instantiates on the binary ped file trio (.bim, .bam, .fam) for non-indel files. 
Upcoming: Test that the instantiation is correct, do it for indel-containing files.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2668 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-23 16:13:24 +00:00
chartl 01db93299c PlinkRodWithGenomeLoc now properly handels indels. 
There is now a DELETION_REFERENCE allele type to allow for the storage of multi-base references rather than point-mutation references.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2667 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-23 07:34:52 +00:00
chartl 42fb85e7f3 PlinkRodWithGenomeLoc now properly parses text plink files. Unit test added to test this functionality. Indels and binary files to come. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2666 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-23 06:19:26 +00:00
aaron 2ea768d902 ant clean is your friend....fixed test code dependent on an interface change. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2660 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-22 20:07:46 +00:00
ebanks c1e09efb23 - Fixed output for beagle header 
- Better description for QualByDepth annotation



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2655 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-21 21:25:56 +00:00
chartl 5b2a1e483e Renamed SequenomToVCF as PlinkToVCF. Wiki will be changed accordingly. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2649 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-21 17:35:20 +00:00
ebanks 9c7b281b4f Set default value for max_coverage to be 100K (since 10K is too small). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2646 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-20 20:15:25 +00:00
aaron 8d1d37302c a quick change to GLF to keep as much precision in our likelihoods as long as possible, before we put it into byte space. Sanger was doing a diff at low coverage and noticed our calls didn't contain as much precision as theirs. Updated the MD5 for unified genotyper output. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2644 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-20 19:36:49 +00:00
aaron a1b4cc4baf changes to intelligently log overflowing locus pile-ups. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2640 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-20 08:09:48 +00:00
ebanks 4ac9eb7cb2 - Smarter strand bias calculation 
- Better debug/verbose printing



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2639 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-20 03:01:26 +00:00
depristo 9e0ae993c7 -B 1kg_ceu,VFC,CEU.vcf -B 1kg_yri,VCF,YRI.vcf system supported to allow 1KG % (like dbSNP%) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2632 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-19 21:33:13 +00:00
rpoplin c98df0a862 Updated solid_recal_modes to work with bfast aligned data. Added an integration test that uses the BFAST file provided by TGen. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2630 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-19 21:18:02 +00:00
ebanks 12453fa163 Misc cleanup of UG args 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2620 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-17 04:38:52 +00:00
depristo d8e74c5795 Update to MD5s for old tests and added extensive VCF testing 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2615 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-16 20:22:58 +00:00
ebanks b911b7df82 Fixing the AC annotation to be in line with the VCF spec 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2593 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-15 18:28:52 +00:00
rpoplin f2e539c52f As per discussions with Tim we are reverting the previous change regarding PairedReadOrderCovariate. The CycleCovariate now differentiates between first and second of pair by multiplying the cycle by -1. PairedReadOrderCovariate has been removed completely. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2592 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-15 18:18:59 +00:00
rpoplin df998041a8 Minor change to solid warning message. Added note for a future solid recalibration integration test when we get the required data file. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2590 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-15 16:31:25 +00:00
hanna b19bb19f3d First successful test of new sharding system prototype. Can traverse over reads from a single 
BAM file.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2587 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-15 03:35:55 +00:00
aaron db9570ae29 Looks bigger than it is: 
* Moved GATKArgumentCollection into gatk.arguments folder to clean up the main folder, also added some associated argument classes (most of the changes).
* Added code the argument parsing system for default enums, we needed this so we could preserve the current unsafe flag, and at the same time allow finer grained control of unsafe operations.  You can now specify:

"-U" (for all unsafe operations), "-U ALLOW_UNINDEXED_BAM" (only allow unindexed BAMs), "-U NO_READ_ORDER_VERIFICATION", etc.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2586 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-15 00:14:35 +00:00
asivache cff8b705c0 Oh, and the test would not work anymore... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2585 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-14 17:47:09 +00:00
rpoplin 9bf0d7250a Fixing the testOtherOutput UG integration test so it will run. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2580 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-14 13:40:14 +00:00
chartl 424d1b57f7 Sequenom to VCF now allows user to specify filters for QC, and they will appear in the filter field of the output VCF 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2577 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-13 23:22:37 +00:00
rpoplin f96b2b211e My last checkin updating R code broke an unrelated UnifiedGenotyper integration test. Eric says that I should take out the verbose test. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2576 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-13 22:28:10 +00:00
rpoplin 49c44e7b36 PairedReadOrderCovariate is now a standard covariate and because of this CycleCovariate no longer multiplies by negative one for second of pair reads. Added PairedReadOrderCovariate to some of the integration tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2574 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-13 20:09:10 +00:00
ebanks 8ca5bba738 We emit genotype data in the VCF record if the format string instructs us to (regardless of whether or not genotypes are provided - this was the wrong test). 
SequenomToVCF now correctly has no-calls when probes fail.
Re-enabled SequenomToVCF integration test.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2572 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-13 15:40:27 +00:00
chartl 6d1107a4ed Update to SequenomToVCF 
Output changing slightly so integration test disabled temporarily



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2571 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-13 15:32:05 +00:00
ebanks f99586f91b Added integration test for beagle and verbose output in UG. 
Minor cleanup of VCFRecord code.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2570 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-13 03:55:24 +00:00
rpoplin 189829841b The recalibrator now uses all input RODs when looking for known polymorphic sites not just the one named dbsnp. Added an integration test which uses both dbsnp and an input vcf file and skips over the union of the two. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2564 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-12 18:50:39 +00:00
aaron 16777e3875 more fixes for the empty interval list problem; you can now run LocusWindow traversals with an empty interval list, but the GATK will give you a warning (unless you're running in unsafe mode). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2563 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-12 18:47:43 +00:00
ebanks 03b7d5f5c7 1. Fixed small but embarrassing bug in weighted Allele Balance annotation calculation. 
2. Made RankSumTest abstract; added 2 subclasses: BaseQualityRST and MappingQualityRST (the latter based on a suggestion from Mark Daly).  Untested so they're still experimental.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2561 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-12 18:33:53 +00:00
ebanks 040fdfee61 Cleaned up the interface to VCFRecord. It's now possible (and easy) to create records and then write them with a VCFWriter. 
I've updated HapMap2VCF to use the new interface; Chris agreed to take care of Sequenom2VCF.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2558 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-11 21:42:12 +00:00
ebanks 42aff1d2c3 Annotator in general should be able to annotate monomorphic or tri-allelic sites. 
It's up to the individual annotations to decide whether they want to annotate or not.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2556 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-11 19:52:18 +00:00
chartl dfa3c3b875 Added: 
SequenomToVCF - Takes a sequenom ped file and converts it to a VCF file with the proper metrics for QC. It's currently a rough draft,
but is working as expected on a test ped file, which is included as an integration test.

Modified:

VCFGenotypeCall -- added a cloneCall() method that returns a clone of the call

Hapmap2VCF -- removed a VCFGenotypeCall object that gets instantiated and modified but never used
(caused me all kinds of confusion when I was basing SequenomToVCF off of it)



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2554 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-11 17:17:21 +00:00
rpoplin 62dd2fa5be Fixing another bug in solid recal regarding negative strand reads. The isInconsistentColorSpace method incorrectly used the inconsistent tag added by parseColorSpace, the inconsistent tag is in the direction of the read like the color space tag, and not in the direction of the reference like everything else. This affects the recalibrated quality scores but the improvment in SNP calling performance is minor when using the default UG settings (min base quality 10). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2553 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-11 14:28:52 +00:00
rpoplin 9cbae53ee1 Bug fixes for both SET_Q_ZERO and REMOVE_REF_BIAS solid recal modes regarding proper handling of negative strand reads. These changes yield a minor improvment in HapMap sensitivity. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2548 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-08 15:19:22 +00:00
ebanks dfcd5ce25b Fixed broken test 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2547 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-08 06:13:01 +00:00
ebanks d5ab002449 Curiously, it seems I never set the default base quality used by the Genotyper to 10. It's done now. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2546 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-08 06:02:01 +00:00
ebanks b468369dfa -UG's call into VariantAnnotator now uses the full alignment context (as opposed to the filtered one) 
-MQ0 annotation is now standard again
-Added AC and AN annotations to VCF output



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2545 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-08 05:40:42 +00:00
rpoplin f587ff46af Tile is now a standard covariate. By default the TileCovariate returns -1 if tile can't be derived from the read's name. Added a new command line option -throwTileException which will force TileCovariate to throw an exception if tile can't be derived for a read. Singleton covariates, such as any read group without tile info, must be skipped over in TableRecalibration so that the sequential formulation doesn't apply the same correction more than once. TileCovariate class has been added to the Early Access package. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2544 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-07 22:51:41 +00:00
rpoplin 5f58492401 A rogue QualityUtils.MAX_REASONABLE_Q_SCORE managed to get through my previous bug fix. It should instead check the command line -maxQ argument. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2540 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-07 21:17:39 +00:00
ebanks c7a8dffa89 Check for division by 0 in annotations 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2539 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-07 19:27:15 +00:00
ebanks b643a513bb Minor interface change for VCFGenotypeRecord. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2537 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-07 16:48:09 +00:00
depristo 076481f786 Fixes to mergeVCF -- now correctly supports merging of filter fields. Also removed incorrect hasFilteringCodes() function. Updated intergration tests 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2535 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-07 14:50:13 +00:00
rpoplin cea544871d Fixed an issue with recalibrating original quality scores above Q40. There is a new option -maxQ which sets the maximum quality score possible for when a RecalDatum tries to compute its quality score from the mismatch rate. The same option was added to AnalyzeCovariates to help with plotting q scores above Q40. Added an integration test which makes use of this new -maxQ option. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2534 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-07 13:50:30 +00:00
ebanks 6c739e30e0 1. Removing an old version of the Genotype interface which is no longer being used. Needed to do this now so that the naming conflicts would cease. 
2. Adding a preliminary version of the new Genotype/Allele interface (putting it into refdata/ as the VariantContext really only applies to rods) with updates to VariantContext.  This is by no means complete - further updates coming tomorrow.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2533 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-07 05:51:10 +00:00
depristo 7215526810 Fix to isReference() in VCFRecord. Change to VariantCounter to correctly counter only non-genotype variants, as well as update to VariantEvalWalker 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2531 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-07 00:03:29 +00:00
andrewk 6c4ac9e663 Updated HapMap2VCF to use the VCFGenotypeWriterAdapter interface; fixed bug in VCFParameters that affects VariantsToVCF and HapMap2VCF when reference is lower-cased; added integration test for HapMap2VCF that checks for the lower-case issue by testing against Hg18 region that has lower-cased bases 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2530 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-06 21:27:11 +00:00
depristo 8d13597a27 Temporary command-line support to enable rod walkers, if you know what you are doing this is safe. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2505 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-06 12:15:36 +00:00
rpoplin 0a6bd5a270 CycleCovariate is now one-based so that 0 and -0 don't collide with each other. Solid recal modes now only change the inconsistent base and the previous base (along the direction of the read) instead of both the bases before and after. Removed estimatedNumberOfBins from the Covariate interface because it wasn't being used. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2498 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-04 20:52:15 +00:00
ebanks ed2fff13aa -Misc improvements to VCF code 
-Small fix to callset concordance


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2497 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-04 02:28:47 +00:00
ebanks b668d32cf1 Updated the min mapping quality and min base quality defaults to be 10 in both cases (and updated all integration tests) as suggested by Mark. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2494 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-03 21:31:04 +00:00
hanna b6ecc9e151 Support for ad-hoc reference sequences. Also reenabled BWA/Java integration test, which was commented out 
and the data backing it up deleted without my knowledge.  Unfortunately, since the data was deleted, I had
to regenerate the data and a new md5.  Hopefully the aligner output is still correct.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2493 348d0f76-0448-11de-a6fe-93d51630548a
 2010-01-02 20:19:14 +00:00
asivache ad549eacfd Now that we changed how deletions are represented, got to update MD5... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2491 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-30 22:00:58 +00:00
asivache 9c41ac252f Disable testSingleBPFailure - getReferenceContext() now whould agree to accept length > 1 genome locs as its argument, so there's nothing to test... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2486 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-30 21:12:00 +00:00
asivache 4aeb50c87d Added: integration test for extended pileup (with indels included) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2481 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-29 23:02:23 +00:00
rpoplin 96c4929b3c Recalibrator now uses NestedHashMap instead of NHashMap. The keys are now nested hash maps instead of Lists of Comparables. These results in a big speed up (thanks Tim!). There is still a little bit of clean up to do, but everything works now. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2474 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-29 21:01:32 +00:00
depristo 7826e144a1 forgot to update md5s 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2473 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-29 20:31:29 +00:00
depristo 87e863b48d Removed used routines in duputils; duplicatequals to archive; docs for new duplicate traversal code; general code cleanup; bug fixes for combineduplicates; integration tests for combine duplicates walker 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2468 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-29 19:46:29 +00:00
ebanks 5fdf17fccb Removed the VCF "NS" annotation (which wasn't working for pooled calls anyways) since it's ambiguous and not useful. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2465 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-29 17:30:47 +00:00
aaron a34c2442c0 moved hard-coded file paths to the oneKGLocation, validationDataLocation, and seqLocation variables setup in the BaseTest. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2460 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-29 07:40:48 +00:00
depristo 9d263b2565 Integration tests for count duplicates walker validated on a TCGA hybrid capture lane. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2459 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-28 23:57:25 +00:00
depristo fcc80e8632 Completely rewritten duplicate traversal, more free of bugs, with integration tests for count duplicates walker validated on a TCGA hybrid capture lane. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2458 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-28 23:56:49 +00:00
hanna 4617052b3c For Alec, and others at the Broad who want to run our unit/integration tests off of gsa1/gsa2: put a ceiling on the amount of memory that integration tests can use. Reduce the memory footprint of the fasta reader test. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2457 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-28 23:42:46 +00:00
alecw b5e5e27225 New versions of picard-private, sam and picard jars for TileCovariate and regeneration of NM tag 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2456 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-28 22:18:55 +00:00
rpoplin 562db45fa5 Sites that were marked NO_DINUC no longer get dinuc-corrected but are still recalibrated using the other available covariates. Solid cycle is now the same as Illumina cycle pending an analysis that looks at the effect of PrimerRoundCovariate. Solid color space methods cleaned up to reduce number of calls to read.getAttribute(). Polished NHashMap sort method in preparation for move to core/utils. Added additional plots in AnalyzeCovariates to look at reported quality as a function of the covariate. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2451 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-28 20:19:37 +00:00
ebanks 12990c5e7a Added qual-by-depth annotation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2445 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-25 02:30:30 +00:00
ebanks 438d21842a The new recalibrator had been mimicking the behavior of the old one in that if there was no dinuc available (following a no-call base or at either end of a read), it didn't try to recalibrate. Now that Ryan has modularized the system, we no longer need to skip the base completely (we just need to skip the dinuc value)... which is good because the Picard people complained after realizing that cycle #1 never got recalibrated. 
The major effects of this commit are as follows:
1. We no longer skip any good bases (of course, this change alone breaks every single integration test).
2. The dinuc covariate returns a "no dinuc" value for the first base of a read (but not for the last base anymore, since there is a valid dinuc) or if the previous base is a bad base (e.g. 'N').

I've done a bunch of testing on real data and everything looks right; however, let's wait until the recalibrator guru gets back from vacation next week and can double-check everything before shipping this out in another early access release.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2443 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-24 20:41:29 +00:00
ebanks 6df40876a3 Un-reverted Matt's previous changes and fixed integration tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2441 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-24 02:47:00 +00:00
hanna 2bd0b1bbf7 After further review, it's unclear that my patch in RecalDataManager was the right choice. Reverting. 
Also updating other IntervalCleanerIntegrationTest failures that were masked by my first patch.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2440 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-24 00:32:33 +00:00
hanna 98c268483e Fixed issues with the integration tests: 
1) sam-jdk apparently no longer supports custom tags with type int[] values.
2) BAM output for indel cleaner integration test changed in a way that's so subtle it can't be seen after converting the output to .sam.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2439 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-23 23:12:22 +00:00
aaron b134e0052f added changes to the code to allow different types of interval merging, 
1: all overlapping and abutting intervals merged (ALL), 
2: just overlapping, not abutting intervals (OVERLAPPING_ONLY), 
3: no merging (NONE).  This option is not currently allowed, it will throw an exception.  Once we're more certain that unmerged lists are going to work in all cases in the GATK, we'll enable that.  

The command line option is --interval_merging or -im


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2437 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-23 21:59:14 +00:00
ebanks 770093a40e Oops - forgot to check this one in. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2433 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-23 19:53:28 +00:00
ebanks dc96879861 2 separate changes which both affect lots of UG integration md5s, so I'm committing them together: 
1. allele balance annotation is now weighted by genotype quality (so we don't get misled by borderline het calls)

2. Updates to the Unified Genotyper for parallelization:
   a. verbose writing now works again; arg was moved from UAC to UG
   b. UG checks for command that don't work with parallelization
   c. some cleanup



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2432 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-23 19:03:56 +00:00
ebanks 872a9d1c7b I'm making this change now (as opposed to waiting until Monday) to honor Tim's request. 
The cycle covariate is now first/second of pair aware.  I'm taking it on faith from both Chris Hartl (waiting on slides from him) and Tim that this is the right thing to do.  We'll have Ryan confirm it all next week.
The only change is that if a read is the second of a pair, we multiple the cycle by -1 (a simple way of separating its index from that of its mate).
Of course, this broke all integration tests.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2431 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-23 16:26:43 +00:00
ebanks cf303810d3 VCF reader now creates the correct type of header line for each header type 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2423 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-21 20:39:06 +00:00
ebanks 87e5a41964 Fixed a bug that accounted for a bunch of my remaining mis-cleaned indels. 
Also, slightly optimized the cleaner by using readBases (instead of readString) and caching cigar element lengths.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2419 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-21 05:46:16 +00:00
hanna 9e53c06328 First revision of command-line argument support for GenotypeWriter. Also, fixed the damn build. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2416 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-20 19:19:23 +00:00
aaron 7e0f69dab5 Changed the GLF record to store it's contig name and position in each record instead of in the Reader. Integration tests all stay the same. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2410 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-18 22:54:56 +00:00
hanna 80b3eb85fa Fixed curiously epic failure in read-backed pileup: size() mismatched the numReads-numDeletions at that locus in the case where includeReadsWithDeletionsAtLoci == false, causing failures including bad output from pileup walker. Also fixed up ValidatingPileup to run with the new ReadBackedPileup instead of just compiling successfully. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2409 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-18 22:52:44 +00:00
rpoplin fdf542c214 The CycleCovariate for 454 data is now the TACG flow cycle. That is, each flow grabs all the T's, A's, C's, and G's in order in a single cycle. This is changed from incrementing the cycle whenever there is a discontinuous nucleotide along the direction of the read. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2408 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-18 22:39:51 +00:00
ebanks 4ea31fd949 Pushed header initialization out of the GenotypeWriter constructors and into a writeHeader method, in preparation for parallelization. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2406 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-18 19:16:41 +00:00
ebanks 1cde4161b7 Fixed another test 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2399 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-18 05:05:03 +00:00
ebanks 94f5edb68a 1. Fixed VCFGenotypeRecord bug (it needs to emit fields in the order specified by the GenotypeFormatString) 
2. isNoCall() added to Genotype interface so that we can distinguish between ref and no calls (all we had before was isVariant())
3. Added Hardy-Weinberg annotation; still experimental - not working yet so don't use it.
4. Move 'output type' argument out of the UnifiedArgumentCollection and into the UnifiedGenotyper, in preparation for parallelization.
5. Improved some of the UG integration tests.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2398 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-18 04:14:14 +00:00
rpoplin 6fbf77be95 Updating the two solid_recal_mode options to also change the previous base since solid aligner prefers single color mismatch alignments over true SNP alignments. COUNT_AS_MISMATCH mode has been removed completely. The default mode is now SET_Q_ZERO. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2394 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-17 20:07:26 +00:00
hanna 07f1859290 Added integration test for running the recalibrator with no index. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2393 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-17 19:10:53 +00:00
ebanks c75ec67f84 When called as a standalone, VariantAnnotator now emits samples in sorted (as opposed to random) order in VCFs. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2392 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-17 19:01:08 +00:00
hanna b863fffdf6 Fix 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2390 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-17 17:55:00 +00:00
asivache e6cc7dab26 fixing md5 sum; new version of IndelIntervalWalker does the right thing... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2388 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-17 01:04:13 +00:00
ebanks b626fc0684 Joint Estimate is now the default calculation model. 
Reworked all of the integration tests so that they're now more comprehensive, cover more of what we wan to test, and don't take forever to run.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2376 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-16 19:41:02 +00:00
ebanks bb312814a2 UG is now officially in the business of making good SNP calls (as opposed to being hyper-aggressive in its calls and expecting the end-user to filter). 
Bad/suspicious bases/reads (high mismatch rate, low MQ, low BQ, bad mates) are now filtered out by default (and not used for the annotations either), although this can all be turned off.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2373 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-16 17:28:09 +00:00
ebanks 874552ff75 Pull the genotype (and genotype quality) calculation out of the VCF code and into the Genotyper. 
[Also, enable Mark's new UG arguments]



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2355 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-15 04:29:28 +00:00
chartl 1389ac6bdf Hurrr -- this uses power as part of its output. Changes to the power calculation broke the md5s RIGHT AFTER I HAD FIXED THEM arghflrg. 
Will fix again.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2351 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-14 22:42:50 +00:00
chartl b42fc905e8 Added - new tests (Hapmap was re-added) 
Modified - Hapmap now takes a -q command to filter out variants by quality
Modified - MathUtils - cumBinomialProbLog now uses BigDecimal to handle some numerical imprecisions
Modified - PowerBelowFrequency - returns 0.0 if called with a negative number (can't be done from inside the walker itself, but since it's called elsewhere one can't be too careful)



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2350 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-14 21:57:20 +00:00
rpoplin 8e44bfd2ef CycleCovariate and PrimerRoundCovariate now correctly handle negative strand 454 and SOLID reads. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2349 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-14 21:52:30 +00:00
ebanks 97618663ef Refactored and generalized the VCF header info code. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2346 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-13 21:02:45 +00:00
ebanks bd2a46ab4c I want to move over to hpprojects tonight, so I'm checking in various changes all in one go: 
1. Initial code for annotating calls with the base mismatch rate within a reference window (still needs analysis).
2. Move error checking code from rodVCF to VCFRecord.
3. More improvements to SNP Genotype callset concordance.
4. Fixed some comments in Variation/Genotype



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2341 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-13 02:52:18 +00:00
aaron 09811b9f34 Now that we always output the VCF header, make sure that we correctly handle the situation where there are no records in the file. Added unit tests as well. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2333 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-11 19:51:05 +00:00
ebanks 2ea7632b76 The SNP genotype concordance module is now more comprehensive. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2330 348d0f76-0448-11de-a6fe-93d51630548a
 2009-12-11 18:34:33 +00:00