bigdatagenomics/adam issues and pull requests

#2198 - Add missing VariantContextDataset.save method

Issue - State: open - Opened by heuermh over 5 years ago

#2198 - Add missing VariantContextDataset.save method

Issue - State: open - Opened by heuermh over 5 years ago

#2195 - Bump htsjdk dependency version to 2.20.3

Pull Request - State: open - Opened by heuermh over 5 years ago - 8 comments

#2195 - Bump htsjdk dependency version to 2.20.3

Pull Request - State: open - Opened by heuermh over 5 years ago - 8 comments

#2187 - InMemoryFileIndex$SerializableFileStatus is not registered

Issue - State: closed - Opened by heuermh over 5 years ago - 2 comments

#2187 - InMemoryFileIndex$SerializableFileStatus is not registered

Issue - State: closed - Opened by heuermh over 5 years ago - 2 comments

#2185 - Investigate registrator performance re classForName

Issue - State: closed - Opened by heuermh over 5 years ago

#2185 - Investigate registrator performance re classForName

Issue - State: closed - Opened by heuermh over 5 years ago

#2170 - [ADAM-2168] Add command line option re: creating references from FASTA sources

Pull Request - State: closed - Opened by heuermh over 5 years ago - 2 comments

#2170 - [ADAM-2168] Add command line option re: creating references from FASTA sources

Pull Request - State: closed - Opened by heuermh over 5 years ago - 2 comments

#2166 - Keep dataset transformations on datasets where appropriate

Issue - State: closed - Opened by heuermh over 5 years ago - 1 comment

#2166 - Keep dataset transformations on datasets where appropriate

Issue - State: closed - Opened by heuermh over 5 years ago - 1 comment

#2150 - Ensembl Variant Effect Predictor annotations support

Issue - State: open - Opened by znikasz almost 6 years ago - 3 comments

#2150 - Ensembl Variant Effect Predictor annotations support

Issue - State: open - Opened by znikasz almost 6 years ago - 3 comments

#2111 - Replace dependency on Hadoop-BAM with Disq

Issue - State: closed - Opened by heuermh about 6 years ago - 1 comment
Labels: discussion

#2111 - Replace dependency on Hadoop-BAM with Disq

Issue - State: closed - Opened by heuermh about 6 years ago - 1 comment
Labels: discussion

#2071 - Support for Elastic Search

Issue - State: closed - Opened by jasonbrelsford over 6 years ago - 1 comment

#2071 - Support for Elastic Search

Issue - State: closed - Opened by jasonbrelsford over 6 years ago - 1 comment

#2071 - Support for Elastic Search

Issue - State: closed - Opened by jasonbrelsford over 6 years ago - 1 comment

#2071 - Support for Elastic Search

Issue - State: closed - Opened by jasonbrelsford over 6 years ago - 1 comment

#2057 - loadIndexedBam pulls entire bam file on http files, even when predicate is specified

Issue - State: closed - Opened by akmorrow13 over 6 years ago - 2 comments

#2018 - Indel realignment discards all unmapped reads

Issue - State: closed - Opened by pauldwolfe over 6 years ago - 3 comments

#2018 - Indel realignment discards all unmapped reads

Issue - State: closed - Opened by pauldwolfe over 6 years ago - 3 comments

#2018 - Indel realignment discards all unmapped reads

Issue - State: closed - Opened by pauldwolfe over 6 years ago - 3 comments

#2018 - Indel realignment discards all unmapped reads

Issue - State: closed - Opened by pauldwolfe over 6 years ago - 3 comments

#1993 - NullPointerException at htsjdk CramNormalizer.getByteOrDefault

Issue - State: closed - Opened by heuermh over 6 years ago - 5 comments

#1993 - NullPointerException at htsjdk CramNormalizer.getByteOrDefault

Issue - State: closed - Opened by heuermh over 6 years ago - 5 comments

#1990 - Add support for left semi, left anti region join

Issue - State: closed - Opened by fnothaft over 6 years ago - 1 comment
Labels: enhancement

#1990 - Add support for left semi, left anti region join

Issue - State: closed - Opened by fnothaft over 6 years ago - 1 comment
Labels: enhancement

#1990 - Add support for left semi, left anti region join

Issue - State: closed - Opened by fnothaft over 6 years ago - 1 comment
Labels: enhancement

#1987 - Alternate allele depth is incorrect for gVCF reference models

Issue - State: closed - Opened by fnothaft almost 7 years ago - 1 comment
Labels: bug

#1987 - Alternate allele depth is incorrect for gVCF reference models

Issue - State: closed - Opened by fnothaft almost 7 years ago - 1 comment
Labels: bug

#1987 - Alternate allele depth is incorrect for gVCF reference models

Issue - State: closed - Opened by fnothaft almost 7 years ago - 1 comment
Labels: bug

#1987 - Alternate allele depth is incorrect for gVCF reference models

Issue - State: closed - Opened by fnothaft almost 7 years ago - 1 comment
Labels: bug

#1973 - Startup scripts still don't resolve correctly when symlinks

Issue - State: open - Opened by heuermh almost 7 years ago

#1962 - Add examples to all functions supported across languages

Issue - State: closed - Opened by fnothaft almost 7 years ago - 1 comment

#1962 - Add examples to all functions supported across languages

Issue - State: closed - Opened by fnothaft almost 7 years ago - 1 comment

#1962 - Add examples to all functions supported across languages

Issue - State: closed - Opened by fnothaft almost 7 years ago - 1 comment

#1956 - Inconsistent counts for shuffleRegionJoin without Sequence Dictionaries

Issue - State: open - Opened by heuermh almost 7 years ago - 3 comments

#1956 - Inconsistent counts for shuffleRegionJoin without Sequence Dictionaries

Issue - State: open - Opened by heuermh almost 7 years ago - 3 comments

#1956 - Inconsistent counts for shuffleRegionJoin without Sequence Dictionaries

Issue - State: open - Opened by heuermh almost 7 years ago - 3 comments

#1956 - Inconsistent counts for shuffleRegionJoin without Sequence Dictionaries

Issue - State: open - Opened by heuermh almost 7 years ago - 3 comments

#1950 - Log validation errors back to driver

Issue - State: closed - Opened by fnothaft almost 7 years ago - 1 comment
Labels: enhancement

#1950 - Log validation errors back to driver

Issue - State: closed - Opened by fnothaft almost 7 years ago - 1 comment
Labels: enhancement

#1950 - Log validation errors back to driver

Issue - State: closed - Opened by fnothaft almost 7 years ago - 1 comment
Labels: enhancement

#1950 - Log validation errors back to driver

Issue - State: closed - Opened by fnothaft almost 7 years ago - 1 comment
Labels: enhancement

#1947 - Support loadIndexedBam from R

Issue - State: open - Opened by fnothaft almost 7 years ago
Labels: enhancement

#1947 - Support loadIndexedBam from R

Issue - State: open - Opened by fnothaft almost 7 years ago
Labels: enhancement

#1945 - Surface VariantContextRDD loaders in Python and R

Issue - State: open - Opened by fnothaft almost 7 years ago
Labels: enhancement

#1945 - Surface VariantContextRDD loaders in Python and R

Issue - State: open - Opened by fnothaft almost 7 years ago
Labels: enhancement

#1902 - Parallelize loading metadata

Issue - State: closed - Opened by fnothaft about 7 years ago - 1 comment
Labels: enhancement

#1902 - Parallelize loading metadata

Issue - State: closed - Opened by fnothaft about 7 years ago - 1 comment
Labels: enhancement

#1902 - Parallelize loading metadata

Issue - State: closed - Opened by fnothaft about 7 years ago - 1 comment
Labels: enhancement

#1872 - suffix arrays implementation

Issue - State: closed - Opened by antonkulaga about 7 years ago - 3 comments

#1872 - suffix arrays implementation

Issue - State: closed - Opened by antonkulaga about 7 years ago - 3 comments

#1863 - Allow users to configure partitioning for pipe APIs

Issue - State: closed - Opened by fnothaft about 7 years ago - 2 comments
Labels: enhancement

#1863 - Allow users to configure partitioning for pipe APIs

Issue - State: closed - Opened by fnothaft about 7 years ago - 2 comments
Labels: enhancement

#1863 - Allow users to configure partitioning for pipe APIs

Issue - State: closed - Opened by fnothaft about 7 years ago - 2 comments
Labels: enhancement

#1863 - Allow users to configure partitioning for pipe APIs

Issue - State: closed - Opened by fnothaft about 7 years ago - 2 comments
Labels: enhancement

#1850 - optimize SmithWaterman alignment

Issue - State: closed - Opened by eyalfa about 7 years ago - 8 comments

#1850 - optimize SmithWaterman alignment

Issue - State: closed - Opened by eyalfa about 7 years ago - 8 comments

#1850 - optimize SmithWaterman alignment

Issue - State: closed - Opened by eyalfa about 7 years ago - 8 comments

#1850 - optimize SmithWaterman alignment

Issue - State: closed - Opened by eyalfa about 7 years ago - 8 comments

#1833 - Support pushing down range queries to CRAM index

Issue - State: closed - Opened by fnothaft about 7 years ago - 1 comment

#1833 - Support pushing down range queries to CRAM index

Issue - State: closed - Opened by fnothaft about 7 years ago - 1 comment