solve bug - now work also when the reads does not have mate
Rev htsjdk to version 1.132 and picard to version 1.131, and switch to using the versions in maven central
…o using the versions in maven central -We now pull htsjdk and picard from maven central. -Updated the GATK codebase as necessary to adapt to changes in the Feature interface. -Since VCFHeader now requires that all header lines have unique keys, uniquified the keys of GVCFBlock header lines by including the min/max GQ in the key. Updated MD5s accordingly. -Other MD5s changed as a result of an htsjdk fix to eliminate "-0" in VCF output.
Added --invert_selection flag for variant selection queries
Fixed a small feature/bug that I introduced with the spanning deletions genotyping
…ns genotyping. In the case where there's a low quality SNP under a spanning deletion in the gvcfs: if the SNP is not genotyped by GenotypeGVCFs (because it's just noise) we were still emitting a record with just the symbolic DEL allele (because that allele is high quality). We no longer do that.
reads with no mate will be counted as valid reads
Correct errant array element swap in FAM file output.
…_in_genotyping Added a fix for genotyping positions over spanning deletions.
dad and mom are swapped; paternal first, then maternal updated MD5 chksums for test files remove commented lines
Previously, if a SNP occurred in sample A at a position that was in the middle of a deletion for sample B, sample B would be genotyped as homozygous reference there (but it's NOT reference - there's a deletion). Now, sample B is genotyped as having a symbolic DEL allele. Minor cleanup added. Note that I also removed Laura's previous fix for this problem. Existing integration tests change because I've added a new header line to the VCF being output. I also added several tests for the new functionality showing: 1. genotyping from separate and already combined gvcfs give the same output 2. genotyping over multiple spanning deletions works 3. combining works too Existing unit tests also cover this case.
Jw deprecate mergeVariantsViaLD argument
…#966 Un-exclude SD and TRA from HC annotators
Exclude MQ0BySample Move SD and TRA to new StandardUGAnnotation interface There is now annotation interface (StandardUGAnnotation) holding annots that are standard in UG but should't be used as they are now with HC. This allows us to not have to exclude these annotations explicitly in HC, but still be able to use them for development purposes.
Fairly minor if plentiful fixes to various gatkdocs. Merging this without formal review since all tests pass, the gatkdocs build, and no one really wants to review corrections to grammar, typos and layout for 120+ documents. Review will be done by users in production ;-)
Clamp the HMM window starting coordinate to 1 instead of 0
More allele trimming for VariantAnnotator
Queue: add -qsub-broad argument
Fix implementation of allowNonUniqueKmersInRef so that it applies to all...
…all kmer sizes
Bypass edge alignment reads while making pileup
Fix the scala wrapper for Picard MarkDuplicates
CatVariants now allows different input / output file types.
Escaping the CatVariantsIntegrationTest classpaths for possible spaces in the directory names.
… was broken. here's the fix. it would be good to have tests for all the scala picard-wrappers, but that is out of scope for this commit.