b) Bug fixes and update to how we represent indels and other complex events in a VariantContext object. Convention is now that all events are left aligned, with the first variant context location marking the common base before an event occurs. However, alleles in a VC don't have the common base in all VC's. Two new functions are now part of VariantContextUtils: CreateVariantContextWithPaddedAlleles and CreateVariantContextWithTrimmedAlleles. Both take a VC as an input and create a VC as an output.
Main flow is that a VCF reader would create a VC with trimmed alleles, all walkers would ideally work with these trimmed alleles, and then the VCF writer would pad back the alleles before writing. However, there are special cases where we need to pad alleles like for example when merging/combining VC's.
Pending issues:
- PED and DBSNP RODs have to be updated to create VC's for indels following the convention above. Changes will go in after Tribble location is moved and things are tested.
- Need to verify Indel genotyper and other modules that create VC's with indels.- Wiki page describing convention above and how walkers should interpret indel VC's still needs updating/detailing.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3850 348d0f76-0448-11de-a6fe-93d51630548a
2) Keep track of whether vcf records are unfiltered vs. pass filters in the variant context so we can regenerate the records on output.
3) No more "ID" hard-coded all over the code to set the VariantContext ID. Use a static variable instead.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3840 348d0f76-0448-11de-a6fe-93d51630548a
2. Moved Jared's VCFTool code into archive so that everything would compile.
3. Added the vcf reference base (needed for indels) as an attribute to the VariantContext from the reader.
4. TribbleRMDTrackBuilderUnitTest was complaining that a validation file didn'r exist, so I commented it out.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3835 348d0f76-0448-11de-a6fe-93d51630548a
- changed to a better method for getting headers from Codecs
- some removal of old commented out code in the GATKAgrumentCollection
- changes for the rename of FeatureReader to FeatureSource
- removed the old Beagle ROD
- cleaned up some of the code in SampleUtils
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3826 348d0f76-0448-11de-a6fe-93d51630548a
a) VCF track name can work again with 3.3 or 4.0 VCF's when specifying -B name,VCF,file. Code will read header and parse automatically the version.
b) Old VCF codec is deprecated. Reader goes now direct from parsing VCF lines into producing VariantContext objects, with no intermediate VCF records. If anyone can't resist the urge to still input files using the old method, a new VCF3Codec is in place with the old code, but it will be eventually deleted.
c) VCF headers and VCF info fields no longer keep track of the version. They are parsed into an internal representation and will be output only in VCF4.0 format.
d) As a consequence, the existing GATK bug where files are produced with VCF4 body but VCF3.3 headers is solved.
e) Several VCF 4.0 writer bugs are now solved.
f) Integration test MD5's are changed, mostly because of corrected VCF4.0 headers and because validation data mostly uses now VCF4.0.
g) Several VCF files in the ValidationData/ directory have been converted to VCF 4.0 format. I kept the old versions, and the new versions have a .vcf4 extension.
Pending issues:
a) We are still not dealing with indels consistently or correctly when representing them. This will be a second part of the changes.
b) The VCF writer doesn't use VCFRecord but it does still use a lot of leftovers like VCFGenotypeEncoding, VCFGenotypeRecord, etc. This needs to be simplified and cleaned.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3813 348d0f76-0448-11de-a6fe-93d51630548a
that the semantics for which reads are in an extended event pileup are not
clear at this point. Eric and I have planned a future clarification for this
and the two of us will discuss who will implement this clarification and when
it'll happen.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3809 348d0f76-0448-11de-a6fe-93d51630548a
FYI: creating an exclusive lock on a file that does not exist will create that file as an empty file, and will NOT delete that file after the program terminates. So watch out if it's possible that the file you're locking does not exist - could end up leaving extra files that confuse users.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3795 348d0f76-0448-11de-a6fe-93d51630548a
2. Updated liftover code (and scripts) to emit vcf 4.0 and no longer depend on VCFRecord.
3. Beagle walker now also emits vcf 4.0.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3767 348d0f76-0448-11de-a6fe-93d51630548a
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
- 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
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
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
(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
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
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
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
asivache
delangel
chartl
ebanks
aaron
depristo
rpoplin
hanna
bthomas