bigdatagenomics bdg-formats issues

bigdatagenomics / bdg-formats

Open source formats for scalable genomic processing systems using Avro. Apache 2 licensed.

Apache License 2.0

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issues

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Add attributes map field to Sequence, Slice, Read records

#122 heuermh closed 7 years ago
0
Doc fixes to CHANGES.md and CONTRIBUTING.md

#121 heuermh closed 7 years ago
2
Use separate fields for Number=R VCF INFO attributes

#120 heuermh closed 7 years ago
5
Use [reference allele, alternate allele] arrays for Number=R VCF INFO attributes

#119 heuermh closed 7 years ago
2
Reference allele value for Number=R VCF INFO attributes

#118 heuermh closed 7 years ago
6
Add forward reference between Variant and VariantAnnotation

#117 heuermh closed 7 years ago
8
Forward reference between Variant and VariantAnnotation

#116 heuermh closed 7 years ago
0
Remove AlignmentRecord.mateAlignmentEnd

#115 ryan-williams closed 7 years ago
0
Add processing description schema

#114 fnothaft closed 7 years ago
0
[FORMATS-112] Harmonize filter representation between Variant and VariantCallingAnnotations

#113 fnothaft closed 8 years ago
2
Harmonize Variant/VariantCallingAnnotations filters

#112 fnothaft closed 8 years ago
0
Improve doc for VariantAnnotation

#111 heuermh closed 8 years ago
2
Add variant filters for VCF column 7 FILTER

#110 heuermh closed 8 years ago
2
Refactor Genotype and GenotypeAnnotation

#109 fnothaft closed 7 years ago
6
Refactor Genotype and GenotypeAnnotation

#108 heuermh closed 5 years ago
31
Upgrade some fields/documentation to improve gVCF support

#107 fnothaft closed 7 years ago
15
Improve gVCF support

#106 fnothaft closed 3 years ago
1
Merge VariantAnnotation and DatabaseVariantAnnotation records

#105 heuermh closed 8 years ago
19
Reconsider StructuralVariant and StructuralVariantType

#104 heuermh closed 3 years ago
3
Remove StructuralVariant and StructuralVariantType, add names field to Variant

#103 heuermh closed 8 years ago
7
Remove StructuralVariant and StructuralVariantType, add names field to Variant

#102 heuermh closed 8 years ago
0
Code style and doc fixes

#101 heuermh closed 8 years ago
5
Code style and doc fixes

#100 heuermh closed 8 years ago
0
Revert back to 0.9.0

#99 fnothaft closed 8 years ago
2
Revert back to 0.9.0

#98 fnothaft closed 8 years ago
0
Complete refactoring of variant and related annotation records

#97 heuermh closed 8 years ago
16
Add back dbSnp ID field

#96 fnothaft closed 8 years ago
4
Why was alternateAllele in TranscriptEffect removed?

#95 heuermh closed 8 years ago
2
[BDG-FORMATS-20] Add readme

#94 heuermh closed 8 years ago
2
Release bdg-formats 1.0.0

#93 fnothaft closed 2 years ago
1
Release bdg-formats 0.10.0

#92 fnothaft closed 7 years ago
1
Document schema design philosophy

#91 fnothaft closed 5 years ago
2
Refactor variant and genotype annotations

#90 heuermh closed 8 years ago
6
Streamline genotype/variant annotations

#89 fnothaft closed 8 years ago
0
Use separate filtersFailed and filtersPassed arrays for variant quality filters

#88 heuermh closed 8 years ago
4
Use separate filtersFailed and filtersPassed arrays for variant quality filters

#87 heuermh closed 8 years ago
0
Adding key signatures for artifact signers.

#86 fnothaft closed 8 years ago
2
Fix transcript effect protein length field

#85 heuermh closed 8 years ago
4
Add schema for sample

#84 heuermh closed 8 years ago
15
Add sequence, slice, and read schema

#83 heuermh closed 8 years ago
27
Update feature and related records to support GFF3

#82 heuermh closed 8 years ago
23
Update maven-javadoc-plugin configuration to not fail build on JDK8

#81 heuermh closed 8 years ago
2
Release fails under Java 8

#80 fnothaft closed 8 years ago
0
add fragmentEndPosition to NucleotideContigFragment

#79 erictu closed 8 years ago
4
Increase Avro dependency version to 1.8.0

#78 heuermh closed 8 years ago
5
Flatten Variant into Genotype

#77 erictu closed 8 years ago
17
Replace contig with contigName in Variant. Resolves #75.

#76 fnothaft closed 8 years ago
4
Migrate `Contig` out of `Variant`

#75 fnothaft closed 8 years ago
0
I can't find Pileup class file in org.bdgenomics.formats.avro package.

#74 xubo245 closed 8 years ago
3
Update Avro dependency version to 1.8.0

#73 heuermh closed 8 years ago
0

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