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Author SHA1 Message Date
delangel be75b087ec a) Add input argument (-ncrate) to BeagleOutputToVCFWalker. If the genotype posterior error probability is higher than this threshold, we declare No-call at this genotype. 
b) Add "OG" annotation to genotypes. If Beagle changes genotypes, this annotation gets the original genotype call, to ease performance  comparisons. If not, this annotation gets an empty value.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3723 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-06 18:33:28 +00:00
hanna 4213e05aeb Fix for sharding ref walkers via monolithic sharding. Introduces the potential bug (for 
monolithic sharding only) that when traversing by read, map() function will not be called for loci
off the end of the reference.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3722 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-06 04:34:38 +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
ebanks e7220bc885 Variant Context simple merging routine should keep ID if one of the VCs has it 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3718 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-05 01:10:15 +00:00
delangel 3016e1cf80 Fixes to increase robustness in vcf4 writer. We assume that only at most 1 base was clipped from beginning of allele encoding by reader, and improve the way we find if bases were clipped. We still cant deal with some corner cases, and duplicate records may follow, for example if a snp location is followed at the next base by an indel. Also, if we are reading form a 3.3 vcf and the reference is null (ie we have an insertion), the reference base is not computed correctly. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3717 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-04 20:22:04 +00:00
ebanks 07945040f8 Set VariantFiltration's JEXL engine to silent for warning messages 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3716 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-04 18:11:19 +00:00
ebanks be8740b00d Another edge case in left alignment for indels: deal with cases when insertions are ambiguously placed at ends of reads 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3715 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-04 17:26:38 +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
weisburd f7593435eb Implemented decodeLoc(..) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3713 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-02 21:01:36 +00:00
depristo cd2e4b0a1e merging now very close to working. Bug todo in writer and vcf infrastructure. Can almost create merged snp and indel files 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3712 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-02 20:09:25 +00:00
delangel b6bdd61283 a) Fix bug when multi-base reference is homopolymeric when writing a VCF4.0 variant context: computation of number of trailing bases was incorrect and we ended up with incorrect position. 
b) Updated VCF4WriterTestWalker to take either VCF3 or VCF4 as inputs (this walker can also be used to convert from 3.3 to 4.0).
 


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3711 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-02 15:19:42 +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
hanna cab8394103 The sharding system now buffers reads, with a size determined by command-line argument. Will investigate whether/how this 
impacts performance on low-pass data and, if it works well, will create a more automatic version of the tool.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3709 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-01 22:28:55 +00:00
aaron f967cae1aa tiny comment change 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3708 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-01 22:04:25 +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
delangel 61c07c6f90 Fixes for missing key values that can create null pointer exceptions when reading from 3.3-generated variant contexts. Also, chop missing genotype fields correctly from right to left 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3706 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-01 20:17:03 +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 4903d1fb4f fix for a parallelization issue: moving the creation of iterators outside of the sync block so we don't wait for RMD tracks to seek to the correct location. Thanks to Ben for providing the test case! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3703 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-01 16:37:02 +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
hanna c9d5345150 Redo StratifiedAlignmentContext to use ReadBackedPileup's stratification options. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3699 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-01 02:46:05 +00:00
delangel dc4715c9c6 Permit empty fields in INFO and FORMAT structures - not fully tested yet but at least failing cases before now pass. Also, corrected a bug where in case we were reading 3.3 VCF's, or VCFs with no original allele encodings, we'd always print 2 bases per allele. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3698 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-01 01:56:07 +00:00
depristo 5f2b2d860e Final stage of renaming 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3696 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-30 21:39:07 +00:00
depristo 6e7927a47d Continuing the renaming nightmare... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3695 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-30 20:25:01 +00:00
depristo 9d7d5f1747 Continuing the renaming nightmare... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3694 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-30 20:24:27 +00:00
depristo aa20c52b88 deleting vcf 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3693 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-30 20:19:15 +00:00
depristo 4195fc5c4e renaming part 2... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3692 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-30 20:18:11 +00:00
depristo 6c9da5525d renaming starting 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3691 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-30 20:16:51 +00:00
depristo b8d6a95e7a Preliminary commit of new VCFCombine, soon to be called CombineVariants (next commit) that support merging any number of VCF files via a general VC merge routine that support prioritization and merging of samples! It's now possible to merge the pilot1/2/3 call sets into a single (monster) VCF taking genotypes from pilot2, then pilot3, then pilot1 as needed. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3690 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-30 20:13:03 +00:00
kshakir 178cf64a0c Refactored ArgumentDefinition to absorb functionality from ArgumentDefinition and ArgumentTypeDescriptor. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3688 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-30 18:37:58 +00:00
chartl 569456850d Mark pointed out there's differentiation in the filter field. Rolling back. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3687 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-30 17:05:53 +00:00
chartl 52a474b27d Fixed an issue with VCF combine in sites like the following: 
Broad: Filtered     BC: No call

These were being treated the same as

Broad: Call         BC: No call

Added some verbosity to separate them.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3686 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-30 16:49:31 +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 47c4a70ac1 It turns out that it is legitimately possible for there to be reads that won't overlap within a target interval for cleaning. While we don't want to attempt cleaning, we also don't want to fail. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3682 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-30 15:50:44 +00:00
ebanks ae33d8a2f2 I just wanted one more vote. It's settled: we die. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3681 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-30 14:00:56 +00:00
ebanks 8fb37f5f7a For Kiran: warn the user when the actual and vcf ref bases differ so that if an exception is generated later, he knows why. All: should we generate the actual exception here? Is there any reason to allow cases where the vcf record has a different ref base than the actual reference? I'd vote that we die here. Thoughts? 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3680 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-30 13:56:16 +00:00
delangel d932322190 More necessary fixes for VCF4.0 - now results look more sensible in realistic, bigger VCF files produced by say Dindel and not just the small test VCF: 
- Fixed and cleaned code to produce trailing and padding bases in alleles around indels.
- Deal better with missing fields.
Pending:
- Chopping missing fields at end of genotypes.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3679 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-30 02:59:30 +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
chartl 610cc7ae2b Cool package trick Kiran showed me. VariantEvaluator no longer public, AAT specifies the core package even though it lives in oneoffs. Disabled so integration tests pass. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3677 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-29 22:42:04 +00:00
chartl 4c6f4e41c6 Include making VariantEvaluator public within the package so my oneoffs can be seen (not included in previous submit specifically because I didn't want to break the build by changing anything in core...the road to hell is paved with good intentions) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3676 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-29 22:26:52 +00:00
chartl 9ac13b8f5d Name and body change for this module to reflect local code. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3675 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-29 21:45:26 +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
chartl 101c27294d Comment this guy out so we build again. (Hate it when my repository goes all funky.) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3673 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-29 21:16:33 +00:00
chartl 3017f82550 Initial commit of items for analyzing amino acid transitions in variant eval. Blew up my subversion by coding locally while i did not have internet. I hope this doesn't bust any integrationtests since I changed no existing code but...who knows. Crossing my fingers. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3672 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-29 20:57:18 +00:00
delangel e3fb4d5c70 Intermediate checkin, just to fix null pointer exception that happened when merging implementation with latest VCF4 decoder - field ORIGINAL_ALLELE_LIST in vc shouldn't be written in infoFields structure since this won't be output to file and there is no legal structure under this key. 
Base encoding for complex events is still brittle and most probably still has issues, fixes upcoming.
 


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3671 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-29 20:57:09 +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
delangel 3ca2b7374b Fixes to better deal with the "Type" and "Number" field in the INFO and FORMAT header lines in VCF4.0. We now record these fields and provide appropriate conversions. This is the first version that passes fully the VCF validator. 
Also, moved the flag indicating VCF4.0 to the VCFWriter constructor.

 


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3669 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-29 16:43:00 +00:00
ebanks 801b47c6e9 For Sendu: a similar addition to the Indel Genotyper allowing it to emit a metrics file (which for now consists only of # of normal/tumor calls made) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3668 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-29 13:19:17 +00:00
ebanks ddf87e61c2 For Sendu: optionally emit a metrics file with callability info (including number of actual calls made) from UG 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3667 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-29 12:57:28 +00:00
ebanks 929e5b9276 Fix possible null pointer exception 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3666 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-29 09:01:18 +00:00
hanna 2953c9f069 Efficiency improvement requested by the Picard team in IndexedFastaSequenceFile: improve the memory efficiency 
(and loading time) of long reference sequences by better controlling the input buffer size.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3665 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-29 07:22:07 +00:00
delangel ed71e53dd4 1) Initial complete version of VCF4 writer. There are still issues (see below) but at least this version is fully functional. It incorporates getting rid of intermediate VCFRecord so we now operate from VariantContext objects directly to VCF 4.0 output. 
See VCF4WriterTestWalker for usage example: it just amounts to adding
vcfWriter.add(vc,ref.getBases()) in walker.

add() method in VCFWriter is polymorphic and can also take a VCFRecord, lthough eventually this should be obsolete.
addRecord is still supported so all backward compatibility is maintained.

Resulting VCF4.0 are still not perfect, so additional changes are in progress. Specifically:
a) INFO codes of length 0 (e.g. HM, DB) are not emitted correctly (they should emit just "HM" but now they emit "HM=1").
b) Genotype values that are specified as Integer in header are ignored in type and are printed out as Doubles.

Both issues should be corrected with better header parsing.

2) Check in ability of Beagle to mask an additional percentage of genotype likelihoods (0 by default), for testing purposes.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3664 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-28 23:54:38 +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
chartl 20f5fdbcf7 Changes to MVC to make the the header of its output VCF compliant with spec (give expected # of values for info field annotations) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3660 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-28 18:33:23 +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
asivache cc8d8eaedb Now that we always reserve space for two read ends when collecting stats stratified by libraries, we need to check that the second end was indeed present; otherwise the pointer is null and this was causing an exception 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3656 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-28 16:40:16 +00:00
ebanks 9a24598a98 By default, don't clean reads with mates mapped to other chromosomes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3654 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-28 15:14:20 +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 464ac63a22 Allowing N's in ALT field 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3650 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-28 11:41:32 +00:00
hanna 3a9d426ca8 Added hasPileupBeenDownsampled() boolean to ReadBackedPileup, so that a pileup can report whether or not (but not how much) it's been downsampled. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3649 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-28 04:56:33 +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
depristo d6cbe4d0ad Bug fixes to support haploid genotypes, optimization for indexing, now tracks the line of the VCF and catches errors to tell you the line no and line when a parsing error occurred. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3646 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-25 21:08:41 +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
kshakir 75c98c42b8 Started path of deprecation of Sting's @Argument by splitting the annotation into @Output and @Input. Anything that's not an @Output should be an @Input. 
Checked in example qscripts that are basically todo integration tests.
Replaced use of queue @Input/@Output with Sting's new @Input/@Output.  This means you'll now have to doc-ument the annotations.
More work on dependency resolution cycles being created in the graph during scatter/gather.
Filtering nulls to avoid NPE exceptions in scala's 'Collection'.hashCode.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3643 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-25 20:51:13 +00:00
weisburd 147ba68441 Fixed bug with mrnaCoord field - made it count exon positions only, rather than introns & exons 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3642 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-25 19:53:32 +00:00
aaron d3848745ab moving VCF 3.3 back into the GATK so Guillermo can make changes for VCF 4 output 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3639 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-25 18:20:06 +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 f9c7803d4e this got left off my last commit 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3635 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-25 02:42:44 +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 f0fc34bb8e Bug fix: N's are allowed in the ref so don't fail when e.g. dbsnp has an N! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3620 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-23 17:49:14 +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
chartl 75d4736600 Committing changes to comp overlap for indels. Passes all integration tests; minor changes to MVC walker. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3618 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-23 15:49:13 +00:00
ebanks 9b8775180e Turn on the memory improvement by default (assume the target interval list is sorted, since it is 99.9% of the time). Make the user throw a flag when it's specfically not sorted. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3617 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-23 15:44:55 +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
kshakir 30cf78fdc0 Refactoring for a first version of scatter gather api with basic shell script implementations. 
Modified build script so that queue is cleaned during "ant clean".



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3611 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-22 18:39:20 +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
ebanks 4727bcda24 Removing Beagle output from UG. Use ProduceBeagleInput walker instead (since it can be run post-filtration and respects the FILTER column). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3607 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-22 16:56:37 +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 de9f1f575f Fixing command line parsing to accept negative number arguments. Command line definitions must now start with a letter or underscore; previously, they could start with a digit. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3603 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-21 21:54:31 +00:00
bthomas 9d6a341d15 Fixing the error messages thrown with bad interval arguments. I simplified the exception handling and made the messages more verbose. 
Note: the -L argument takes both interval strings and filenames. If you specify an interval string that is also a file, an error will be thrown to move the file: ie. if you have a file "chr1" in the parent directory, GATK will ask you to move/delete it. But, this only happens with interval string arguments, NOT with intervals that are contained in files, which is a majority of the use case. 



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3602 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-21 21:49:41 +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
ebanks df1cadc4c9 Fix NullPointerException when priority list is left out 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3600 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-21 13:46:54 +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
hanna 1d50fc7087 Misc bug fixes: fix tracking of nInsertions with sample-split pileup constructor. Fix performance 
issue building up pileups from pileups of individual sample data.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3598 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-20 20:32:27 +00:00
hanna f18ac069e2 A refactoring / unification of ReadBackedPileup and ReadBackedExtendedEventPileup. 
Provides a cleaner interface with extended events inheriting all of the basic RBP
functionality.  Implementation is still slightly messy, but should allow users to
provide separate implementations of methods for sample split pileups and unsplit
pileups for efficiency's sake.
Methods not covered by unit/integration tests have not been sufficiently tested yet.
Unit tests will follow this week.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3597 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-20 04:42:26 +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
chartl f44d8b150f Mendelian Violation Classifier now filters violations on the fly via command line arguments; and closes unterminated homozygous regions at the end of a chromosome (so we see arms falling off in the file, rather than in the log) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3592 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-18 19:32:24 +00:00
ebanks aa1852575e Add -noVerbose flag to stop output of INFO data. 
Cuts runtime by 30% and output from 65Mb to 1Kb.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3591 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-18 18:53:35 +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
hanna 52477bd9e6 Add some missing methods to the pileup architecture. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3588 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-18 15:03:08 +00:00
hanna 5050b19457 We're unable to make the naive deduper more worldly, so we're killing it instead. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3587 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-18 13:54:27 +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
delangel b694ca9633 Cleanup: Don't require likelihood ROD in Beagle parameters when generating output VCF. Likelihoods file is only an input to Beagle but the Walker that generates a VCF doesn't need it, so it's silly to ask for it and it's error-prone. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3579 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-17 17:45:48 +00:00
hanna c1595a383a More bugfixes for cases where no sample name is present. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3578 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-17 16:46:02 +00:00
aaron 3d049204ed some refactoring for the variant eval output system 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3576 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-17 05:34:31 +00:00
hanna db1383d0b2 Rev the latest version of Picard. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3575 348d0f76-0448-11de-a6fe-93d51630548a
 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
hanna 5972ad1199 Fixes to mrl integration. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3573 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-16 20:40:10 +00:00
ebanks b75ded61b8 Removing obsolete rod; no longer needed given previous addition to SampleUtils. 
JIRA GSA-318


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3572 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-16 20:03:14 +00:00
kshakir c671864228 Re-allowing blacklist by read group id. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3571 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-16 19:45:44 +00:00
ebanks f003703912 Allow specification of particular rods for pulling out sample names. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3570 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-16 19:37:09 +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
kshakir 05c2f96bb4 Small update to the command line docs for read_group_black_list. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3568 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-16 19:23:34 +00:00
ebanks d7f3102c3f Fixed read group blacklist filter to look only at readgroups (and not the read's themselves). Otherwise, it fails when attribute tags with different meanings show up in both places (e.g. SM). Added performance improvement. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3567 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-16 19:14:37 +00:00
hanna e77f76f8e1 Reenabled downsampling by sample after basic sanity testing and fixes of the 
new implementation.  Hard testing and performance enhancements are still
pending.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3566 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-16 17:23:27 +00:00
kshakir c44fd05aa1 Fix for a reflection issue with generic types. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3565 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-16 15:58:38 +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
delangel 8cb16a1d45 a) Cleanup, remove -input argument from BeagleOutputToVCFWalker since it's not needed. 
b) Added back old Beagle ROD to maintain backward compatibility (does anyone even use this???)



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3563 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-16 02:13:08 +00:00
delangel d319a28be7 Complete rewrite of the Beagle functionality to read from Beagle output files and produce VCF with modified genotypes. Now, a new ROD system using Tribble is in place. Beagle inputs are set using -B beagleType,Beagle,pathToBeagleFile, where beagleType can be either beagleR2, beagleLike, beaglePhased or beagleR2 (BeagleOutputToVCFWalker requires all of the above). Only pending items: -input argument is now unused and can be removed, will be cleaned later. Wiki will be updated with new usage shortly. 
We can now run with a reduced memory footprint, and output VCF is exactly identical to previous version. Drawback is increased runtime because Tribble has to create an index for all the Beagle files when starting if the idx files are missing.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3562 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-16 02:01:35 +00:00
aaron d265397bf6 removing a reference to a unused internal Sun class 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3560 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-15 15:27:57 +00:00
asivache 42b8a8f295 slight change in output format 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3559 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-15 14:52:04 +00:00
kshakir 32fc221ffe Replaced pattern matched pipeline spec with annotated objects. 
Old version is no longer available.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3558 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-15 04:43:46 +00:00
sjia b99a5e06f3 Added option to only consider alleles of > specific allele frequency. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3557 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-15 02:09:35 +00:00
hanna 8a895f481f Proper exception chaining for troubleshooting Sendu's issue. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3556 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-15 01:38:36 +00:00
sjia 8defb30796 Documentation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3555 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-14 21:31:01 +00:00
weisburd c1046653a2 Fixed handling of records where gene-names are identical (eg. as in refseq NR_030638 in chr20) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3554 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-14 20:00:49 +00:00
weisburd 1e42984a16 Improved buffer-size arg handling 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3553 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-14 19:59:15 +00:00
sjia b3c3023c3c Allows callers to handle HLA reference files as input (rather than hard-coded paths) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3552 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-14 18:56:08 +00:00
asivache 9666d47d17 ooops, debug print now removed 
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 2010-06-14 18:07:12 +00:00
sjia abdc8521ea Added debug options for FindClosestHLAWalker 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3549 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-14 17:52:03 +00:00
sjia c38390eabb Added option for min number of matches between reads and alleles required to consider reads. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3548 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-14 16:08:49 +00:00
asivache 4ab1f440c3 A new argument: --targetIntervalsSorted (boolean flag). If specified, the interval file is assumed to be sorted (duh!) and it is NOT slurped into the memory but instead traversed directly on disk as needed. If the file turns out to be unsorted, an exception will be thrown at the point where inconsistency occurs (can be late into the processing!). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3547 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-14 16:00:22 +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
asivache f137bf8f85 now adaptor silently skips empty lines in the underlying string iterator 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3545 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-14 15:35:07 +00:00
sjia d8c963c91c Remove PhaselikelihoodsWalker.java 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3544 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-14 15:21:43 +00:00
sjia 5704294f9d HLA caller updated - now searches all (common and rare) alleles, more efficient read filtering and allele comparison runs. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3543 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-14 15:14:40 +00:00
asivache d51e6c45a7 a utility class; turns string iterator into GenomeLoc iterator 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3542 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-14 14:07:44 +00:00
asivache 7b7d3341f0 trivial refactoring: isFile renamed to isIntervalFile and made public 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3541 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-14 14:02:23 +00:00
hanna c3b68cc58d Rethinking DownsamplingLocusIteratorByState with a flattened read structure. Samples are kept 
independent while processing, and only merged back in a priority queue if necessary in a special
variant of the ReadBackedPileup.  This code is not live yet except in the case of naive deduping.
Downsampling by sample temporarily disabled, and the ReadBackedPileup variant is sketchy and
not well integrated with StratifiedAlignmentContext or the walkers.  Cleanup to follow.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3540 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-13 01:47:02 +00:00
kiran 804facb0cc Removing these utilities as part of a hostage negotation with Matt. Can I have my journal club paper now?! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3539 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-11 21:41:29 +00:00
asivache e6d8faf293 making 'parseLocation' public static - as simple as the logic is, it's better kept in one place and I need it! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3537 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-11 18:19:59 +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
ebanks 22620ba95c Adding "abi_solid" to the list of known platforms. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3534 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-11 13:37:19 +00:00
ebanks 63ad71cca6 Fix busted code. Note for all: 
String.valueOf(byte[]) doesn't work.  You must use new String(byte[]).


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3533 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-11 05:01:48 +00:00
weisburd 338bb9adf4 CommandLineProgram for measuring java I/O speeds for large plain-text or gzipped files. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3532 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-10 21:34:37 +00:00
weisburd 06fc5eecf8 Implemented TreeReducible - if num threads > 1, the output will be accumulated in memory and written to a vcf file at the end - in onTraveralDone(..). If num threads == 1, things will work as before - where vcf records are written to disk as soon as they are computed with map(..). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3530 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-10 20:57:23 +00:00
weisburd 3b375cb237 Sped up parseGenomeLoc(..) by replacing regexp with String.indexOf(..) - attempt 2 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3529 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-10 20:54:36 +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 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3527 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-10 20:10:23 +00:00
hanna f55f32d4ee Bug fix. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3526 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-10 01:53:26 +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
aaron 6941c81bfa reverting revision 3522 to the old code until we fix the tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3524 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-09 19:25:02 +00:00
hanna dbee21a50f Bugfixes for the case when no read groups / no samples are available. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3523 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-09 18:47:05 +00:00
weisburd adc4c4e577 Sped up parseGenomeLoc(..) by replacing regexp with String.indexOf(..) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3522 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-09 18:11:43 +00:00
chartl 20167fd411 Final changes to MVC -- associates variants with regions of homozygosity in child and parents, corrects for genotype errors, and prints out a separate file with informationf or each region of homozygosity. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3521 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-09 18:05:37 +00:00
weisburd fdded73861 Improved error reporting 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3520 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-09 17:52:48 +00:00
aaron 4f00e265a8 quick update for a change I implemented for Ryan 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3519 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-09 17:23:31 +00:00
aaron ad98512f6c adding changes so that we look at the headers already loaded by the engine for samples and other VCF utils, and not create readers for each file to get them (this caused Tribble to regerenate indices if the index file can't be written to disk). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3518 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-09 17:21:12 +00:00
weisburd c1b7bcc786 Fixed handling of mitochondrial genes - added special cases such as ATT being a start codon in mitochondria. Added warning if a gene doesn't start with Met or end in a stop codon 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3517 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-09 17:15:47 +00:00
weisburd 4f1181974b Added toString() method 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3516 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-09 17:12:57 +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
hanna 84563b37e5 Partial flattening of the hanger data structure. Hanger data structure is 
not currently as flat as it could / should be, but it's already comparable
to the speed of the reference implementation.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3512 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-09 16:28:49 +00:00
chartl 8f9e3e8ad7 Commit for Kiran; but this is now working, barring little exceptions that I've yet to run across... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3511 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-09 14:21:19 +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
hanna c2858c8988 Minor performance enhancement. Checkpoint commit before major performance 
overhaul.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3504 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-08 21:39:39 +00:00
chartl 5ed2818ffb Forgot to commit code i relied upon 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3503 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-08 21:01:35 +00:00
chartl 736098b58d A quick commit before running home. This is a re-factored version of the OppositeHomozygoteClassifier which will work with deNovo violations as well. Some code still needs to be migrated from OHC which is wy that walker isn't yet deleted. This'll be up and running tonight. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3502 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-08 20:47:01 +00:00
delangel de134c226d Removed ability of users to specify annotations to recompute, cleanups. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3501 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-08 19:17:59 +00:00
ebanks 4d1a6b3d99 quick changes for G 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3500 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-08 16:33:27 +00:00
delangel 907931c902 a) Update annotations when creating new vcf with Beagle's imputed data. Since genotypes may (will) change based on imputation, several annotations need to be updated. By default, AC, AF, AN and AB will be updated. User can force extra annotaqtions to be updated with -A <annotation> argument. 
b) Several cleanups and beautifications.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3499 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-08 15:12:04 +00:00
chartl 933133ee28 Initial commit of the opposite homozygote classifier. Currently does the following, given a trio vcf: 
+ Identifies opposite homozygote sites
 + Identifies the parent from whom it is expected that a null allele was inherited (or whether it was a putative genotype error; e.g. mom=homref, dad=homref, child=homvar)
 + Labels each opposite homozygote with its homozygous region in the child (e.g. region 1, region 2)
 + Labels each opposite homozygote with the size of the homozygous region in which it was found, the number of child homozygotes in the region, and the number of opposite homozygote violations within that region

To come:
 + Classification of sites as likely tri-allelic


Note that this is very experimental



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3498 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-08 03:56:07 +00:00
hanna 199e4208cd Bug fixes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3497 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-08 00:30:33 +00:00
hanna 52ab9f2417 Feature parity between LocusIteratorByState, DownsamplingLocusIteratorByState, including pushing mrl / 
the LocusOverflowTracker into LocusIteratorByState.  Note that the 'Matt Hanna exception', is still enabled
because I haven't yet validated the performance of the DownsamplingLocusIteratorByState when running
without downsampling.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3496 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-07 22:58:21 +00:00
hanna 5c4d070566 Push Mark's changes in LocusIteratorByState into DownsamplingLocusIteratorByState 
in preparation for merging the two into one.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3495 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-07 17:29:30 +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
hanna c1ecf75dd5 Update to the latest rev of the picard sharding patch. Includes updates reflecting 
the imminent move of IlluminaUtil into picard public.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3493 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-06 20:33:21 +00:00
delangel c503f01dcf More cleanup 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3492 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-06 17:41:38 +00:00
delangel d4c66d6191 a) Small cleanup 
b) Fix major issue with Beagle likelihood converter: if likelihood triplets from UG end up being too low, then Beagle input file will be produced with 0.00,0.00,0.00 triplet. If all samples at a marker have this issue, Beagle will effectively produce junk. To fix, likelihoods are renormalized before converting to linear space.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3491 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-06 17:31:59 +00:00
depristo cfa18f6743 Fixing missed update with new Allele in it 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3490 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-04 23:56:34 +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
delangel ef47a69c50 a) First fully functional (sort of) version of walker that parses Beagle imputation output files and produce a vcf with imputed genotypes. 
More doc/info to follow shortly. Issues still to be solved:
a) Walker changes all genotypes based on Beagle data, but annotations on the original VCF are unchanged. They should in theory be recomputed based on new genotypes.
b) Current implementation is ugly, dirty unwieldy and will necessitate a refactoring soon so I can keep my pride. Most aesthetically affronting issue right now is that we read the full Beagle files at initialization and keep them in memory, but a more delicate implementation would just read from files on a marker by marker basis. Issue that currently prevents this is that BufferedReader() instances don't seem to play nice when called from the map() function.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3488 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-04 20:37:25 +00:00
depristo b811e61ae1 Optimized, nearly complete VCF4 reader 2-4x faster than the previous implementation, along with a VCF4 reader performance testing walker that can read 3/4 files, useful for benchmarking 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3487 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-04 18:11:38 +00:00
aaron 6482b87741 adding the super experimental, half-broken, generally crippled, awkwardly commented, header ignoring vcf4 code. Don't use this, unless you're a developer for VCF4. If so, remove the exception from the constructor so that it won't always exception out. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3486 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-04 07:38:46 +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. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3485 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-04 06:34:26 +00:00
hanna 3d055e3d16 Fail fast if users try to parallelize a read walker. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3484 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-03 18:14:33 +00:00
hanna 7d79848f40 Better error message when bam file / list file with wrong extension is 
supplied.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3483 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-03 17:52:48 +00:00
ebanks 597b3744ab Always use phasing info when converting genotypes to strings 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3482 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-03 17:50:50 +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
asivache f0c379dde8 Unconsequential changes in report formatting 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3479 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-02 17:43:25 +00:00
weisburd 3ab936181c Supports the join feature of GenomicAnnotator 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3478 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-02 16:29:57 +00:00
weisburd f5f7217413 Implemented joins 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3477 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-02 16:28:53 +00:00
weisburd 09c3b15af3 Implemented joins 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3476 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-02 16:28:06 +00:00
weisburd e14ae471a0 Refactored some of the small utility methods 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3475 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-02 16:26:00 +00:00
weisburd 898a78e97d Added toString() 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3474 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-02 16:24:25 +00:00
weisburd 12c3e3ecda Added back the check for values.size() != header.size(). Now exception will be thrown if number of columns in a record doesn't equal number of columns in the header 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3473 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-02 16:23:05 +00:00
rpoplin 290771a8c2 Automatic cutting of recalibrated variant calls using ApplyVariantCuts. VariantRecalibrator produces the tranches plot alongside the optimization curve. Specify the levels using -tranche 1.0 -tranche 5.0 etc 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3472 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-02 15:03:00 +00:00
ebanks 4a555827aa Removing more toUpperCase sanity checks 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3471 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-02 14:38:39 +00:00
ebanks 56e504789a trivial change: toUpperCase no longer necessary 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3470 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-02 14:00:47 +00:00
rpoplin 87fe60fe4f Fix for Sendu. new Process and p.waitFor() don't seem to work on his farm. Throws an IOException. This was a problem way back with AnalyzeCovariates too. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3469 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-02 11:37:10 +00:00
ebanks 7f0c638653 Fix for the indel cleaner: I forgot to "unclip" the cigar string (even though the clipped bases were removed) before using it as an alternate consensus in a particular instance. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3468 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-01 02:07:20 +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 eb25e41111 minor update to new tribble name 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3462 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-28 20:23:25 +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 6485e8383d Trivial change to retrigger broken build that really isn't broken 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3453 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-27 23:33:46 +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
aaron e1b0aefb29 fix for parallelism bug 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3451 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-27 22:16:14 +00:00
aaron cded9ec985 adding a command line option, -etd (enable threaded debugging), that uses a custom thread pool class to catch exceptions thrown inside of a thread. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3450 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-27 21:57:56 +00:00
ebanks e2674671e7 The liftover code needs to *hard filter* records whose reference changes (since they no longer adhere to the VCF spec as they don't match the new reference - and can't be converted to VariantContext). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3448 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-27 19:22:47 +00:00
chartl ff4a0764df Read error rate is now parallelizable 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3447 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-27 19:00:09 +00:00
depristo dfc36c1e95 Restructuring of the mandatory read filters for traversals. Now everything uses ReadFilters, even for the required filters like being mapped for LocusWalkers. Statistics now tracked for each read filter used during the traversal and info emitted in INFO at the end. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3445 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-26 22:12:25 +00:00
delangel 3873dccb35 First fully functional (though preliminary) version of walker that takes an input VCF and outputs a Beagle .bgl file that can be used for missing genotype calls/haplotype imputation. For now, only supported input format is likelihood format for unrelated individuals. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3444 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-26 21:03:23 +00:00
chartl f9efc1248c VariantEvalWalker now takes indels if you throw the -dels flag. IndelLengthHistogram appears to be working properly, it is turned off by default (as it is experimental) but you can turn it on in your own repository. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3443 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-26 20:03:14 +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
chartl 0265199ce4 First pass at an IndelLengthHistogram module for variant annotator. Off by default. Will be tested shortly (have to commit, so I can check out in another directory, so that compiling won't kill all my jobs running on LSF) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3440 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-26 15:04:39 +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
depristo 5928047d8b Optimization of reference window calculation to us bytes not char and no uppercasing since reference and read bases are always uppercase now. Should remove some ~5% of runtime of UG. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3438 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-26 14:10:26 +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
rpoplin 062b316881 Better Exception message when can't find annotation value in variant recalibrator. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3434 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-25 21:15:50 +00:00
rpoplin bf530d23de Variant Recalibrator now makes use of a prior on known/novel status as well as on allele frequency spectrum. The VariantOptimizer walker now clusters with all variants but gives more weight to knowns / hapmap / 1KG / MQ1 sites. The weights are all optional command line arguments. We no longer assign default values to annotations that are malformed. The walkers will crash with exception so as to not cover up potential issues. We only produce titv-less clusters now, and so the titv argument in VO was removed and the WithoutTiTv string that gets added to the cluster file is removed. The wiki is updated to show new example commands. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3433 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-25 21:08:31 +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
ebanks 772f558ae0 Massive change to the indel realigner code. We now properly deal with soft-clipped reads. Also, improved left-alignment code. 
Small change for Ryan to get hard-clipped reads working for the recalibrator.

PLEASE DO NOT RELEASE THIS WEEK.  I still have some more testing to do and need Mark to run WG jobs.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3430 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-25 20:04:33 +00:00
aaron f3e2aae570 add experimental support for tabix files (for any of our Tribble rod types), as long as they end in .gz and can be read by the tabix reader. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3429 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-25 04:44:46 +00:00
weisburd 8db7c97c4d Moved AnnotatorInputTableFeature and Codec to org.broadinstitute.sting.gatk.refdata.features.annotator 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3427 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-24 14:38:54 +00:00
weisburd 4aa749c709 Moved AnnotatorInputTableFeature and Codec to org.broadinstitute.sting.gatk.refdata.features.annotator 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3426 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-24 14:38:07 +00:00
weisburd aca3bcb193 Moved AnnotatorInputTableFeature and Codec to org.broadinstitute.sting.gatk.refdata.features.annotator 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3425 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-24 14:37:17 +00:00
weisburd 64ed770250 Moved AnnotatorInputTableFeature and Codec to org.broadinstitute.sting.gatk.refdata.features.annotator 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3424 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-24 14:36:28 +00:00
hanna ee3f2eb1d0 Don't output traversal reduce result in the logger. In many cases, the reduce 
result is tangential to the product of the analysis and having the logger always
emit it can confuse the output (such as in the new reduceByInterval 
DepthOfCoverage walker).  If users want to emit it, they can choose not override
onTraversalDone, or override onTraversalDone and write results to the output
stream / logger / whatever their choice.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3422 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-23 22:41:43 +00:00
hanna a40e64e47b A downsampling validator. Compares the generated pileup passed in from the alignment context to the reads, 
passed in as a Tribble SAM text feature.  If the generated pileup contains a valid set of reads according to
the downsampling rules, the test passes.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3421 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-23 21:49:54 +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
hanna b10950c691 Simple performance optimization -- cache the number of reads in the locus hanger. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3417 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-21 19:26:16 +00:00
delangel 355396109b Bug fix to avoid build failure (class changed under me??) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3416 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-21 18:48:56 +00:00
delangel 1753d07b02 Added AnnotationByAlleleFrequencyWalker - walker takes an input vcf, a reference vcf and a list of annotations (with the -A argument). For each site present in both VCF's, it outputs the given annotations into the screen as well as allele frequency. Since HapMap vcf reference doesn't include AF in annotations, it computes it from Chromosome, Het and HomVar counts. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3415 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-21 18:31:34 +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 7fb3f2d3eb Annotator now buffers indel calls (prevents double-output from double-calls to map) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3413 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-21 16:34:34 +00:00
chartl 4e834b5e35 VFW now uses a ref window and thus is compatible with indels. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3412 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-21 15:59:42 +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
hanna 388dd8d64d Fixing bugs in downsampler introduced when I added Ryan's dup eliminator. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3407 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-21 02:53:12 +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
hanna 7389077b3b A few misc usability fixes: 
- Clarify the message emitted when -XL is supplied so I don't spend another half day chasing a bug that doesn't exist.  
- Crash with a helpful message when running -nt with non-TreeReducible walkers.
- Crash with a helpful message when running -nt with reduceByInterval walkers.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3405 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-20 19:02:02 +00:00
aaron b543dd4ac4 more aggressive checks for the locking, and some more documentation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3404 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-20 16:16:36 +00:00
depristo 1ab00e5895 Retiring multi-sample genotyper 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3401 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-20 14:10:56 +00:00
depristo 727822adb4 BaseUtils has more clear distinction between byte and char routines. All char routines are @Depreciated now. Please use bytes. Better organization of reverse(), now in Utils not BaseUtils. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3400 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-20 14:05:13 +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 02cc1afdc8 remove RodBed and all it's dependencies. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3396 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-19 19:12:30 +00:00
chartl ffb1b46166 Added a GCCalculatorWalker for a oneoff analysis for Mark Daly (GC content of agilent 1.1 targets) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3395 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-19 18:49:51 +00:00
aaron 0036df7b03 adding a convenience method for getting at the RODs that overlap a specific locaiton as GATKFeatures. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3394 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-19 17:40:20 +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
weisburd 46ba88018d Updated to the new readHeader(..) api 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3391 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-19 04:06:34 +00:00
weisburd 984c51efd3 Updated to use Tribble-based GATKFeature instead of TabularROD 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3390 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-19 03:42:12 +00:00
weisburd 42ee16f256 Updated to use Tribble-based GATKFeature instead of TabularROD 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3389 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-19 03:41:37 +00:00
weisburd d8469e2fba Updated to use Tribble-based GATKFeature instead of TabularROD 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3388 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-19 03:40:47 +00:00
weisburd d65b2d32d1 Removed AnnotatorROD which has been ported to Tribble 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3387 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-19 03:39:34 +00:00
weisburd b82116f488 Removed AnnotatorROD which has been ported to Tribble 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3386 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-19 03:39:20 +00:00
weisburd 6b96f025f5 Tribble integration for indexing the AnnotatorInputTable format 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3385 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-19 03:37:54 +00:00
weisburd 2f3933148d Added fast split(str, delimiter) methodf 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3384 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-19 03:37:26 +00:00
hanna aedb9f6734 Bring SAMPileupCodec into compliance with new interface. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3383 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-19 01:23:29 +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 635f61c22d Clone the other guy too 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3381 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-18 18:56:01 +00:00
rpoplin 9e15299475 Misc cleanup in variant recalibrator. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3380 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-18 17:37:01 +00:00
chartl eb200e4cce Hrumph. Don't just add pointers to the same objects, actually clone the underlying arrays. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3379 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-18 17:13:44 +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
weisburd 3c022e4b0c Improved command-line-arg validation at startup. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3374 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-18 02:46:17 +00:00
weisburd 35b4bba35e Refactored so it could be used for knownGene and CCDS as well as refGene 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3372 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-18 02:44:10 +00:00
weisburd bb86c0e03a Improved error message 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3371 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-18 02:43:13 +00:00
weisburd 68719615be For multiple matches, shifted counter to be 1-based 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3370 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-18 02:41:50 +00:00
hanna 73e2e32837 Fix typo. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3369 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-17 21:04:00 +00:00
chartl ebd0fabf86 First pass updates to annotations to work with indels. HomopolymerRun indel behavior is currently turned off by a global boolean until it's ready to go live. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3368 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-17 21:02:13 +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
kiran 4235164359 Removed the confusionMatrix column (of *course* this is a confusion matrix... what else would it be?!). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3365 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-14 21:55:37 +00:00
kiran 95b29f608b Specify default values. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3364 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-14 21:42:53 +00:00
rpoplin 6efd05831b Encapsulating annotation decoding function in order to use same fixed random seed in both VariantOptimizer and ApplyVariantClusters 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3363 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-14 20:03:38 +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
depristo 1538dc0144 optimizer now uses -an arguments instead of exclude and force for clarity. command-line length reduced by 50% 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3361 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-14 15:41:44 +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
hanna 3e9ad4bbd0 Porting SAM pileup ROD to Tribble as a case study. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3356 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-13 00:22:59 +00:00
aaron 6839c194cb although holding on to memories can be fun, it's bound to hurt performance. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3355 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-12 19:26:58 +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
depristo 3f07611187 Added support for -nSamples to varianteval (and getNSamplesForEval function). Allows you to calculate AC based metrics for files without genotypes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3350 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-12 13:36:31 +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
hanna 6868ce988f Fix hanging bug reported by Susanne Pfeifer (tiffy @ get satisfaction) where, if the last read(s) in a shard all have an 
indel in roughly the same location and that indel isn't covered by any other reads, LocusIteratorByState goes into an infinite
loop.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3348 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-11 17:31:19 +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
rpoplin b09e7231d1 A quick implementation of the experimental covariates for the TGen folks to work with. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3344 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-11 01:08:52 +00:00
kiran aec5f7b630 Can now threshold results based on minimum base and/or mapping quality. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3343 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-10 19:58:07 +00:00
kiran 13fd182b7c For dealing with slightly malformatted BAMs - mark every alignment as primary, or in the case of some BAM files from UWash, supply the sample information for each read group. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3340 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-10 15:17:05 +00:00
kiran 4a7902bb8e Bases 'A' and 'a' (etc.) no longer considered different. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3339 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-10 14:53:38 +00:00
kiran ec543b7b62 The Complete Genomics confusion matrix rates. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3338 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-10 14:52:10 +00:00
kiran b223b04331 Don't list '.' as an alternate allele, dummy! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3337 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-10 14:51:18 +00:00
kiran 98718d0faa Computes the error rate per cycle 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3336 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-10 14:50:22 +00:00
kiran 7527f950d1 Computes the quality score distribution per readgroup (one column per readgroup) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3335 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-10 14:49:38 +00:00
kiran c111c15072 Computes the distribution of insert size per library (for now, one output file per library) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3334 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-10 14:48:35 +00:00
ebanks a51bd57566 First version of the smart batch merging tool. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3333 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-10 02:18:48 +00:00
rpoplin 33a9549896 Variant Optimizer accepts a dbSNP rod arugment to use in determining known/novel status as opposed to using the rsID in the vcf record. VO generates plots of annotation values used in clustering broken out by knowns and novels. Useful for showing which annotations are approximately Gaussian. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3332 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-09 16:48:07 +00:00
hanna 76efa757f0 Switched over to reviewed version of Picard patch. In process, did some optimization to the IntervalSharder 
which improved startup time 5-10x when dynamically merging many BAMs.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3331 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-08 14:12:22 +00:00
depristo 504103bd15 Misc. additions to correct utilities 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3329 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-07 21:34:18 +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
depristo d070554329 A walker that calculates read lengths, number and size of clipping events 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3327 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-07 21:32:51 +00:00
chartl 1749a49042 Mapping and base quality thresholds for DoC default to none 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3326 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-07 18:08:13 +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
ebanks 44de92e09d Checking in the liftover script. I am including a post-processing walker to filter out bad records written in under 10 minutes as per my agreement with Mark. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3321 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-07 12:31:56 +00:00
ebanks 18f1d31a22 Moving to and organizing in core. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3320 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-07 04:05:36 +00:00
aaron 06ea65e60b again for JIRA GSA-320 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3319 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-07 03:47:58 +00:00
aaron ac9b32db88 a bug fix for Kiran; putting JIRA in for better type determination system for the new Tribble tracks so this doesn't happen again. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3318 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-07 03:31:43 +00:00
hanna 4e0019b04f Repair code that sorts and merges intervals. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3317 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-06 22:37:25 +00:00
aaron 72e030a670 require that snps be biallelic before we pass them to the TiTv calculation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3316 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-06 22:33:00 +00:00
rpoplin 7cecec7d00 Removing zero no-calls restriction in AC stats 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3314 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-06 18:55:07 +00:00
ebanks 0e58fb7cc0 Moved over to be a walker inside the GATK 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3313 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-06 18:28:03 +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
ebanks bacc507a48 Don't worry about sorting anymore in the liftover tool. That will come later. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3311 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-06 15:00:30 +00:00
ebanks 5df0361bd2 trivial removal of unnecessary comments 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3309 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-06 03:51:14 +00:00
ebanks 2975e3a4e8 picard Intervals don't sort right - switching to GenomeLocs 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3308 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-06 03:50:28 +00:00
ebanks 1a99fb9318 First pass at liftover tool. Passing buck over to Aaron... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3306 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-05 20:38:19 +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 6bbcc47b5d removing some out-of-date RODs and some unused genotype writer formats 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3304 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-05 19:07:13 +00:00
aaron c998c48a23 adding code to detect out-of-date index files, which we now remove and regenerate if the target file is newer than the index file. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3303 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-05 17:55:36 +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
asivache 0338345bee Fixing the issue with reads having insertion immediately followed by a S/H cigar element causing out of window error. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3300 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-05 15:42:27 +00:00
ebanks 64640d6b17 Complete the switch statement to deal with all possible cigar operators for Kris. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3299 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-05 13:41:05 +00:00
aaron f75e54e3f7 fixes for new package names in tribble 74 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3298 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-05 05:47:04 +00:00
chartl 617542853f Walker that can be used with refGene and a TCGA bed file to annotate intervals in an interval list with the genes and exons they overlap. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3296 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-05 02:55:01 +00:00
chartl 354262eabe New convenience methods to rodRefSeq for dealing with intervals that may be a superset of multiple exons. Needed for next commit. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3295 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-05 02:54:18 +00:00
ebanks 03bea70f3a Fixed edge case bug in cleaner: when no -L argument is used and a target interval abuts the end of the reference genome, we'll NullPointer at the first unmapped read. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3293 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-04 16:49:21 +00:00
kiran 510b3efcc2 Fixed an issue where asking for the alternate alleles at hom-ref sites would result in an array out-of-bounds exception. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3292 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-03 18:46:33 +00:00
sjia 94b51de401 HLA caller updated to examine class II loci, updated pointers to dictionary, allele frequencies. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3290 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-03 14:54:52 +00:00
rpoplin 97fdd92e7b Clean up the code to have a unified approach to calculating p(true) for both with and without ti/tv models 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3289 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-03 13:30:20 +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
rpoplin 9d01670f62 Major update to the Variant Optimizer. It now performs clustering for both the titv and titv-less models simultaneously, outputting the cluster files at every iteration. It makes use of the Jama matrix library to do full inverse and determinant calculation for the covariance matrix where before it was using only approximations. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3286 348d0f76-0448-11de-a6fe-93d51630548a
 2010-05-02 19:21:23 +00:00
weisburd a318b1871d Removed unused column 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3285 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-30 21:29:34 +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 0e10359a5e Okay, finished up the ability to cap a base's qual by its read's mapping quality. 
This is experimental - I have not tested its performance on SNP calling, or even played around with it.  If you want to test it out, go nuts.  But don't come running to me if your results are not good.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3282 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-30 16:58:30 +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
weisburd 8b2ce128b5 Optimized the join(..) method. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3280 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-30 15:55:07 +00:00
hanna 8bb15ef812 Checking in the reference implementation of the downsampler for back comparison. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3278 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-30 15:41:13 +00:00
ebanks 1714c322c2 Reorg of UG args; checking in first before upcoming changes that will break integration tests. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3274 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-30 14:48:46 +00:00
weisburd ba78d146ec Finished implementing 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3273 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-30 14:14:31 +00:00
weisburd 5d5c7f9d34 Changed short code of stop codon to 'stop' 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3272 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-30 13:55:52 +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
chartl 82818a417b Allow header fields to come in any order... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3269 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-29 18:33:10 +00:00
hanna 4617abf1ff Fix bug in the interval sharder in cases where contigs specified in intervals are not present in any supplied BAM file. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3268 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-28 20:42:04 +00:00
chartl e2ff4167af Added "#Family ID" as a possible header value for PlinkRod ... since that's in the new sequenom headers for pilot 3 validation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3266 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-28 18:38:33 +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
aaron 64c5f287c5 fixes for edge-cases when using reflections to find classes outside of the main jar. Will push as a patch to reflections 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3264 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-27 17:46:46 +00:00
aaron c647153b10 Adding Jama for Ryan. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3262 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-27 14:30:36 +00:00
aaron f6468f9143 a fix for a bug we've worked around in the reflections package: previously it didn't find classes that weren't in the main jar. Fixed in this version. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3261 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-27 04:49:49 +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
aaron 68bdac254b a utility walker for validating changes made to the underlying ROD system in the transistion to Tribble. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3258 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-26 05:21:24 +00:00
ebanks d9bf441391 Have UG emit calls at sites from one or more 'trigger' tracks when provided 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3257 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-26 05:04:43 +00:00
ebanks 8f2bfac7a6 Bug fix for NullPointerException 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3256 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-26 05:02:09 +00:00
ebanks f5a3b128c8 Fixing bug that's not caught by integration tests: 
If the first eval seen has one or more no-calls, then that's the 2N chromosome count that gets set as the max for the metrics.  Instead, just check that any eval's no-call count is 0.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3255 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-26 02:40:34 +00:00
depristo 29ab59a7b3 Bug fix for Kiran; insertions now get a null reference allele even if the ref input object is null 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3254 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-24 21:31:03 +00:00
aaron c8d09a29ed some quick changes to the VE output system - more to come. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3253 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-23 21:55:08 +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
ebanks 42bcca1010 Pulling out the left-alignment code for indels so that other walkers can use it. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3251 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-23 16:12:34 +00:00
weisburd 9e28e4eb42 git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3250 348d0f76-0448-11de-a6fe-93d51630548a 2010-04-23 15:50:09 +00:00
weisburd 10bcd72593 1st attempt to implement extra columns 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3249 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-23 15:49:37 +00:00
weisburd a72a5a7b1a Data object for representing a single amino acid 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3248 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-23 15:49:06 +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
ebanks e0b51d0df0 Trigger cleaning of duplicate reads. Also beeter debug output. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3246 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-23 15:12:28 +00:00
ebanks 3adf7fbf64 bug fix for known-indels used as consenses 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3245 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-23 13:52:51 +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
depristo 3d2c836db6 Bug fix for case sensitivity 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3242 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-23 03:08:58 +00:00
ebanks 8c94df6f00 Bug fix for Chris: deal with sites that have "semi-deletions" 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3241 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-22 18:34:41 +00:00
chartl 121163dd49 interim commit 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3240 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-22 13:44:45 +00:00
weisburd f0fe2ea530 A simple codon -> AA lookup table 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3239 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-22 12:18:00 +00:00
weisburd e643a9e7a5 Takes a refGene table ( -B arg must be: -B refgene,AnnotatorInfoTable,/path/to/refgene_file.txt) and generates the big table of nucleotides containing annotations for each possible variant at each transcript position (eg. 4 variants for each position). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3238 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-22 12:11:19 +00:00
weisburd 653e08c0b6 Takes a refGene table ( -B arg must be: -B refgene,AnnotatorInfoTable,/path/to/refgene_file.txt) and generates the big table of nucleotides containing annotations for each possible variant at each transcript position (eg. 4 variants for each position). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3237 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-22 12:11:03 +00:00
weisburd 20379c3f82 Added location-caching optimization, temporary attributes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3236 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-22 11:35:45 +00:00
ebanks 84ebceb9a6 Fix for Chris: need to use the appropriate conversion method. Added a warning to the adaptor. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3235 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-22 02:05:10 +00:00
chartl e7334ec11f Checkin for Eric (IndelDBRateWalker is a prelude to a VariantEval module for comparisons for indels) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3234 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-22 00:40:27 +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
asivache ef6d900eb8 for now, set log error to -1 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3231 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-21 19:21:06 +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
asivache 1373fee278 Because of the ugly VCF format, generic addCall() method of GenotypeWriter interface acquired an additional parameter, explicitly specified reference base (in VCF it's the base immediately *before* the event in case of indels, so we got to pass it). All implementing classes are modified to accomodate the change. 
VCFGenotypeWriterAdapter now explicitly uses the passed reference base instead of deriving it from VatriantContext (in SNP mode as well!), other writers simply ignore that additional argument. 

SimpleIndelCalculationModel now WORKS (or rather, it does produce calls :) )

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3228 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-21 18:19:03 +00:00
hanna ab34397d2e Continuing to stamp out the non-ASCII copyright virus. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3227 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-21 14:50:45 +00:00
chartl 84f1ccd6ac Two dumb oneoff walkers written to fix & annotate the Baylor indel calls (which came in sans reference, and without coding/intron annotations). 
ERIC -- does the IndelAnnotator (the RefSeq lookup code I stole from IndelGentoyperV2) want to be its own Annotation inside VariantAnnotator? Is Andrey already doing this as part of adding indel calling to UG?



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3226 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-21 14:04:10 +00:00
depristo 2fdc1cf490 Bed ROD track support 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3225 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-21 13:22:42 +00:00
depristo 51b3998082 deleting unused code from VariationFiltration 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3224 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-21 13:22:19 +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 114819d980 Allow user to set min confidence score for comp tracks too 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3222 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-21 05:09:09 +00:00
ebanks 3db73e0791 Renaming for consistency 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3221 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-21 03:00:43 +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
asivache 6fda78f93f Always return deleted bases in upper case 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3218 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 19:17:40 +00:00
asivache 52a570637d Always keep event bases in upper case 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3217 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 19:16:39 +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
asivache 7d952a34ae Fixing copyright note 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3215 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 18:28:57 +00:00
asivache cdc175f7e3 Synchronizing version to make sure everything compiles; this model is not operational yet 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3214 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 17:41:52 +00:00
asivache 4437456bb5 Pass array of ref bases to callExtendedLocus() 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3213 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 17:41:13 +00:00
asivache 5d2fab93f4 Method signature changed: for extended events, pass array of reference bases (to ensure we cover the full length of the indel event), not just reference base. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3212 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 17:40:30 +00:00
asivache 01e6492ba9 Updated to work correctly with extended pileups. Clogged and uses some dirty tricks; pileups/extended pileups need to be redesigned someday 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3211 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 17:38:09 +00:00
asivache 4723cad1be New method: getBasesAtLocus(int n); for the windowed reference context, this method extracts n bases starting at the current locus (NOT at the window start, so this method is an extension of getBase()) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3210 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 17:35:09 +00:00
asivache cac125b35c Fixed incorrect symbol printed into the output file (tag had 'R', should have had 'T') 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3209 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 16:37:28 +00:00
rpoplin f4977965b6 Removing debug statements 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3208 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 16:22:40 +00:00
rpoplin 124b7a2a58 Moved ApplyVariantClusters over to VariationContext 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3207 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 16:20:25 +00:00
asivache 200d3e2c47 added copyright note 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3205 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 15:44:26 +00:00
asivache 546dfb629e A draft (working) version of a tool that computes per-cycle base qualities averaged across the reads; the computed base qual profiles are stratifeid by lane/read end and separately by library.Come and shoot me if we already have such a tool somewhere in the repository :) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3204 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 15:38:16 +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 818a95ea6e Test of new copyright message without unicode characters. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3200 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 14:14:54 +00:00
rpoplin 00feb3eee0 Moving over to VariationContext in CountCovariates. Removed references to class Variation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3199 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-20 13:26:22 +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 131703d9db more clean-up: moving AlleleBalanceInspector to archive. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3192 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-16 20:53:33 +00:00
ebanks 534f24177a Move to VariantContext and improve performance (and ease of use) by transitioning to be a RODWalker. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3191 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-16 20:09:48 +00:00
ebanks 8c32bb8f0a Complete the move over to VariantContext so that we can remove dependence on Variation (in the VCF code) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3190 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-16 19:41:42 +00:00
aaron 821e8b1c5f more cleanup. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3189 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-16 19:16:16 +00:00
aaron e11ca74eb5 removing some outdated ROD classes (PooledEMSNPROD and SangerSNPROD), removing an out-of-date interface (VariantBackedByBenotype), and moving AnalyzeAnnotationWalker over to VariationContext. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3188 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-16 18:59:29 +00:00
ebanks d5e5589b8f No longer used 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3187 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-16 17:57:39 +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
aaron 4d75b26b7a Removing the code that made the ROD system case insensitive. Anyone using specific ROD names in their classes should take care in naming required tracks; All lowercase is the best practice. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3184 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-16 06:17:31 +00:00
asivache 6dc1275cfb Utility method added: getQualsInCycleOrder(read) - examines the read and returns its quals in the order the machine read them (i.e. always from cycle 1 to cycle N). Simply inverts quals if the read happens to be rc-aligned :) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3183 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-16 00:15:57 +00:00
ebanks f4673efd2f Moving to archive as it's no longer supported 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3182 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-15 22:10:42 +00:00
ebanks 02a6f4c401 Moving over to VariantContext 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3181 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-15 22:07:28 +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 3330e254a9 Standardize the dbsnp track name in preparation for case-sensitivity 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3176 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-15 19:41:57 +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
aaron b54031fc86 adding an experimental format to VariantEval2, which when you source() from R, imports all VE2 output as individual tables with appropriate row and column names. More testing and feedback needed. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3172 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-15 06:09:27 +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
ebanks f1189bac5a Bug fix: final map call wasn't being triggered (because we returned when ref==null before applying update0) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3168 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-14 16:58:55 +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
weisburd c0f4695902 Improved handling of haplotypeReference and haplotypeAlternate columns. Added haplotypeStrand column. Improved handling of empty fields in data files. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3166 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-14 14:42:19 +00:00
weisburd 74ec72d1ac Added AnnotatorROD - the TabularROD format specific to GenomicAnnotator 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3164 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-14 14:39:50 +00:00
weisburd 77a6608784 Changed a variable name 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3163 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-14 14:38:18 +00:00
weisburd 7b8056099c Fixed 'N' reference-base handling, changed some comments, var names 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3162 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-14 14:37:25 +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
ebanks 0b575596f8 Fix for concordance: samples found only in truth no longer kill it. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3160 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-13 21:33:49 +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
weisburd d0123956bc Modified comments. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3158 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-13 15:41:59 +00:00
chartl 7b05091c04 DoC now does not require a -o argument. (Change for Matt) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3157 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-13 13:58:17 +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
hanna 14b8101d45 Error message fail. Failed to supply one of the valid interval file types. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3153 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-12 01:19:01 +00:00
hanna 60d54e69f3 Hackish fix to present a better error message if the file does not have the proper extension. Will work with Brett to come up with a better solution. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3152 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-12 01:11:27 +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 3434a61146 Don't trigger when ref=N (which can happen when a dbsnp track is provided) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3150 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-11 02:59:11 +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
ebanks 0cc6d0fbbb One more quick memory improvement: reuse Alleles in a given context instead of creating new ones for each sample (duh). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3147 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-09 18:48:36 +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 e73e6a4fb0 Significant memory improvements to plink code 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3144 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-09 16:12:38 +00:00
rpoplin f1b1e70612 Bug fix for multisample calls in ApplyVariantClusterWalker 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3142 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-09 12:01:15 +00:00
ebanks 3f2455e346 Better error message as suggested by James P 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3141 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-09 05:52:53 +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
ebanks e286623f6f Use byte[] instead of String in an attempt to cut down on memory usage 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3139 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-09 05:32:54 +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 e148a3ac61 added the ability to create interval lists directly from a ROD, using the command line arg '-BTI' (long name '--rodToIntervalTrackName'). The parameter to this arg is the name of the ROD track, which must be a track name specified in the -B option. 
Using this feature, sites covered by the target ROD will be iterated over.  This list of intevals generated is merged with any intervals from the -L and -XL args, and the Walker is run over the resulting merged list.

WARNING: for very large ROD's this can be costly.  Consider this experimental for now.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3134 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-08 05:14:41 +00:00
aaron 20cc2a85a4 removed the hashmap from Genotype Concordance, moved it into a table 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3133 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-07 21:24:48 +00:00
aaron e55f27b3b1 forgot a file 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3132 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-07 20:51:13 +00:00
aaron 9ca8e345fc by-by old junk. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3131 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-07 20:41:48 +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
ebanks e7dad728df Trivial output changes for consistency 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3128 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-07 14:47:43 +00:00
depristo 058e7d3d12 Bug fix for Gregory 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3127 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-07 00:21:35 +00:00
rpoplin 7b44e6bd55 ApplyVariantClusters now outputs interesting threshold points based on hitting the target novel TiTv 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3126 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-06 19:47:29 +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
asivache 3530ef5a41 Explicit type cast fixed in order to work with new ROD implementation 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3124 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-06 15:02:56 +00:00
rpoplin 2d002c56c3 Added histogram of variant quality scores broken out by true positive and false positive calls to the GenotypeConcordance module of VariantEval2 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3123 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-06 13:48:31 +00:00
aaron 12e4f88ca7 a little bit more clean-up 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3122 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-05 20:49:06 +00:00
aaron df7e7921ce removing some unused code. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3121 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-05 19:30:08 +00:00
ebanks 56eb15f91f Error checking for bad input (thanks, Aaron). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3120 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-04 03:17:01 +00:00
weisburd 705b28e90d First attempt at implement record filtering based on special 'hap_ref', 'hap_alt' columns in the input files 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3118 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-02 21:52:26 +00:00
weisburd d78e7f6c0a Added documentation. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3117 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-02 21:51:28 +00:00
aaron 8017fb123f changed the depth of coverage walkers class name, and added a dependency in the packaging system so that RODs will all get imported. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3116 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-02 20:55:19 +00:00
weisburd 6b7b07f178 First checkin of GenomicAnnotator which annotates an input VCF file by pulling data in a generic way from an arbitrary set of TabularRODs. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3114 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-02 17:49:42 +00:00
rpoplin 642c969896 reverting optimizer changes 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3112 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-02 16:59:13 +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
hanna d00bde22db Reverting one of Brett's changes that should not have been committed. Will 
address with Brett separately.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3107 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-01 16:10:46 +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 c3c6e632d1 support for two new VCF header info field value-types, Flag (for fields that are just boolean truths), and Character (for single charatcer info fields). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3105 348d0f76-0448-11de-a6fe-93d51630548a
 2010-04-01 03:11:32 +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
hanna 4fcee248f9 For Kristian: functions which, given a read, can uniquely identify the BAM file storing that read. 
Introducing this into the pile of code which peeks under the covers of the SAMDataSource in the hopes
that this function can help to replace the others and provide a single path for crosstalk.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3103 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-31 20:46:44 +00:00
rpoplin d58fe70708 Correctly ignore filtered calls and indel calls in the truth sets 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3101 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-31 14:33:01 +00:00
hanna b60197ae10 Another round of cleanup and simplification in Picard -- Picard's unit tests 
are now passing for my branch.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3100 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-31 01:02:59 +00:00
depristo 40f8e7644c Better, multi-haplotype aware haplotype scores. Looking very good now, seems to be vastly better at dealing with incorrect calls in deep and low pass data. Almost ready for use 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3099 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-30 23:57:36 +00:00
depristo f992f51a3b Deleting incorrect sampling genotype likelihoods from the codebase 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3098 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-30 23:56:35 +00:00
kiran b9d3fc3fbb Now checks if the i-th element of the FiltrationContext[] is null before trying to access it. This seems to happen occassionally at the very end of a VCF file... the array will be 6 elements long, but the last element will actually be null. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3097 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-30 22:40:17 +00:00
hanna 400684542c Revisions to take into account finalization of Picard patch: naming changes, better definition 
of public interfaces.  This won't be the last Picard patch, but it should be the last big one.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3096 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-30 19:28:14 +00:00
aaron b00d2bf2bc fixing an annotation that was breaking the error log output system. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3095 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-30 15:34:04 +00:00
aaron a6e8687d71 implementing a clean way to import the template files into the GATK jar (they should not always get bundled). All further resources should be added to the gatk.resources path id in the build script. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3094 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-30 04:20:19 +00:00
ebanks babb9fb825 snp cluster filter should ignore ref calls when determining the clusters 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3093 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-29 17:57:33 +00:00
chartl 24461a2503 Let's *not* import classes that no longer exist. How my own ant test compiled is beyond me. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3091 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-29 13:59:01 +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
ebanks 1e8b3ca6ba Fare thee well, oh LocusWindowTraversal. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3089 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-29 13:17:26 +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
hanna 85037ab13f Fix for Kiran's sharding issue (Invalid GZIP header). General cleanup of 
Picard patch, including move of some of the Picard private classes we use to Picard public.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3087 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-29 03:21:27 +00:00
depristo a45ac220aa Removing unnecessary printing routines 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3086 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-28 22:34:54 +00:00
depristo b8ab74a6dc Minor useful changes to BaseUtils and MathUtils to support a new haplotype score annotation that determines to the two most likely haplotypes over an interval and scores variants by their consistency with a diploid model. Appears to be useful. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3085 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-28 21:45:22 +00:00
kshakir e9e53f68ab Filter lists can now end with .list or .txt. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3084 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-27 17:41:24 +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
kiran 85f4f66180 Updated to use VariantContext. Output has been reformatted: variant and genotype concordance are emitted for every coverage level per variant. If the requested sampling level is higher than what's available, the maximum available coverage at that locus is used. This makes it much easier to make plots indicating the percentage of comparison callset recovered at a certain sampling depth. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3082 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-26 21:02:43 +00:00
kiran 391e5843e4 If the annotation engine has not been supplied, don't try to annotate anything. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3081 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-26 20:52:21 +00:00
kiran 8048b709a0 Selects a single sample on which to operate. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3080 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-26 20:50:58 +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
hanna 78af6d5a40 New sharding system is going live again for on-the-fly merging. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3076 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-25 18:39:04 +00:00
hanna 46c14ec63f New, much less memory intensive implementation of BAM file sharding. Streams indices together with the expectation 
that bins will be present in the bin sparse array, which avoids the problem of having to hold the sparse bin array
stored in every BAM file index in memory at the same time.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3075 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-25 17:41:22 +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
ebanks 2373a4618f bug caused by a misprint: context != contexts 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3073 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-25 03:08:24 +00:00
ebanks 3176715c74 1. Alignability mask returns null when not available. 
2. --list now prints out the available classes/groups too.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3072 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-24 20:49:07 +00:00
rpoplin 06a212e612 Adding VariantConcordanceROCCurveWalker to create ROC curves comparing concordance between optimized call sets and validation truth sets in VCF format in order to evaluate performance of variant optimizer independently of achieving a particular novel ti/tv ratio. Added option to ignore only the specified filters in the input call sets via --ignore_filter <String>. Added option to provide a prior estimate of error for known snps via --known_prior <qual>. The het and hom calls are clustered independently. Infrastructure in place to use titv of known snps to inform p(true) of novel snps. Tweaked protection against overfitting based on suggestions from several people. Minor edits to AnalyzeAnnotations. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3071 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-24 19:43:10 +00:00
ebanks 47e30aba92 Rods for reads hooked up into the cleaner 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3070 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-24 18:17:56 +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
ebanks 49117819f5 For the cleaner to clean, it must beat the entropy produced by the aligner (and not just the raw reads). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3068 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-24 15:21:58 +00:00
aaron 60dfba997b added some sample annotations to VariantEval2 analysis modules, and some changes to the report system. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3067 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-24 05:40:10 +00:00
hanna 1f451e17e5 Changing preloaded index to only "preload" reference sequences on demand. 
Results in drastic lowering of startup cost when multiple BAM files are 
merged.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3066 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-23 22:02:28 +00:00
hanna 884a577013 Phase 2 of Picard patch refactoring: kill off SAMFileReader2/BAMFileReader2, merging the changes back into the base classes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3065 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-23 16:48:11 +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
hanna 3767adb0bb Processing intervals as they stream in means much lower memory usage and 
quicker runtime.  Making change as minimal as possible to avoid conflicts
with BT's incoming patch.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3061 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-22 22:04:45 +00:00
ebanks 0097106938 VariantFiltration can now filter specific samples. 
This is *NOT* an ideal implementation.  One day when we have lots of free time (or a greater desire), we will implement this correctly and sophisticatedly using all the power of JEXL.  For now, though, this will have to do.
Docs coming tonight.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3060 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-22 20:45:11 +00:00
asivache 543aefc3d7 Fixing the bug introduced with the earlier commit. When trimming locus to the current bases, we need to take into account expanded boundaries (for windowed reference traversals) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3059 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-22 19:20:34 +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
asivache d2944461ef We also have to allow the window to be (partially) outside the bounds and trimming to the contig size is not enough (thanks to shards). Now we trim to the current bounds too (i.e. if the interval is not completely within current bounds, we create reference context that contains only bases from the overlap between the interval and the bounds). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3057 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-22 17:36:29 +00:00
asivache 9053406798 LocusReferenceView: If the locus a view is requested for spans beyond the reference contig ends, create the actual window bounded by contig ends (so that the locus will not be fully contained in the window!!). 
ReferenceContext: constructor does not throw an excepion anymore when locus is not fully contained inside the window. So now we can have a reference context associated with a locus such that the window/actual bases do not cover the whole locus. Scary. I am not sure I like this...

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3056 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-22 15:59:15 +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
depristo 076d21d394 Minor bug workaround in GenotypeConcordance module (see todo). General platform read filter. You can say -rl Platform illumina to remove all SLX reads 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3054 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-22 02:47:09 +00:00
hanna 6cd97b78ab An additional safety check to ensure that we only walk over coordinate-sorted 
data when doing locus traversals.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3053 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-21 23:31:45 +00:00
hanna b4b4e8d672 For Sarah Calvo: initial implementation of read pair traversal, for BAM files 
sorted by read name.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3052 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-21 23:22:25 +00:00
hanna c0eb5c27ea Lower memory support for merged sharding. Merged sharding is still not available. 
WARNING: If you update frequently, you might have to rm -rf ~/.ant/cache -- this is an unfortunate side effect of the way we
	 distribute picard-private.jar.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3050 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 22:03:47 +00:00
ebanks 4d4db7fe63 Renaming for consistency 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3049 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 18:45:01 +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
rpoplin cdec84aa8f Bug fix for variant optimizer. Remember to close the PrintStreams it uses to output the cluster files. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3046 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 15:07:32 +00:00
depristo d8ff552311 Support for EXPERIMENT sampling-based genotype likelihoods 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3044 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 13:19:40 +00:00
depristo 7b17bcd0af Refactoring a few useful routines for detecting mendelian violations 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3043 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 13:19:01 +00:00
depristo 56092a0fc2 Slight cleanup for mathutils 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3042 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 13:18:08 +00:00
depristo b221ce94ce Still being tested trio-aware genotyper that calculates P(de novo) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3041 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 13:11:39 +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 e757f6f078 Missing value for arbitrary format entries is empty string (need to revisit at some point, but it will require updating the VCF spec). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3038 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 03:56:27 +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
hanna 9b61d95d9c Khalid found an out-of-memory condition with the new sharding system when 
merging lots of BAMs, and the fix is taking longer than I thought.  Disable
experimental sharding when merging until the fix is ready.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3036 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-19 02:43:46 +00:00
ebanks b8e8852b4f Better interface for the Annotator in how it interacts with VariantContext. 
Also, added a proof of concept genotype-level annotation (not working yet, almost there).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3035 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-18 20:41:57 +00:00
hanna 96662d8d1b Moving from GATK dependencies on isolated classes checked into the GATK 
codebase to a dependency on a jar file compiled from my private picard branch.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3034 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-18 17:43:42 +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
rpoplin c78fc23ec5 Minor updates to output of variant optimizer. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3031 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-18 12:46:47 +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
rpoplin 58a31bab6a Variant optimizer now outputs VCF files via ApplyVariantClustersWalker. Documentation to be added to the wiki. It is ready to be used by other people but only with great caution. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3028 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 20:41:42 +00:00
hanna d9398dc347 Remove some of the restrictions on getStart() and getStop(); getStart() and getStop() 
now do the minimum validation rather than the more rigorous only-within-the-contig-bounds 
header validation.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3027 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 19:39:30 +00:00
aaron 182f1061ff Bamboo isn't picking up commits for some reason; updating a copyright to see if it'll get this commit. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3025 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 17:56:48 +00:00
ebanks 5e29d0c219 Be smarter about dealing with infinite quals for ref calls 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3024 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 17:35:23 +00:00
rpoplin 1bb4394aa9 Adding a skeleton for the second step of the variant optimization process. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3023 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 17:03:40 +00:00
ebanks ded4ba8966 Let's make artificial reads that actually adhere to the specs... 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3022 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 16:51:42 +00:00
bthomas 5b34bb9ab0 Adding three minor new features: 
+ -L all now walks over all intervals

+ if a -L argument is passed with a .list extension, and file does not exist, returns a \
File Not Found error instead of "bad interval" error. We plan to soon revisit interval \
lists and generate a concrete list of filenames, so this is likely temporary.

+ Error is thrown if the start position on an interval is higher number than the end position.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3021 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 16:24:10 +00:00
ebanks 4340601c26 -Pushed base quals back down into SAMRecord; if -OQ is used, the SAMRecord quals get updated automatically 
-Better integration test


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3020 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 16:00:10 +00:00
ebanks 76d14d17dc oops, need to update class names too 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3019 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 14:01:31 +00:00
ebanks 85a030069d renaming for consistency 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3018 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 14:00:28 +00:00
ebanks af5fd99444 Added filter for bad cigars (based on consecutive indels) - and cleaned up bad mates filter. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3017 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 13:53:42 +00:00
hanna 2cc040aa1c New sharding system is live. Disable with -ds. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3016 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 03:32:45 +00:00
ebanks 1fd909cdaf Fix for Kiran: -1 is a valid value for genotype qualities in VCF, so VariantContext shouldn't die. Cleaned up the relevant VCF code while I was in there. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3015 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-17 00:20:15 +00:00
hanna 849bd1f451 Set the eagerDecode flag in such a way that the binary data block in the BAM will always be considered dirty. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3014 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-16 22:01:23 +00:00
rpoplin 933823c8bc Removed the StingException when mkdir fails for Sendu in AnalyzeCovariates. Incremental updates to VariantOptimizer. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3013 348d0f76-0448-11de-a6fe-93d51630548a
 2010-03-16 19:45:02 +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