Closed issues:
Merged and closed pull requests:
- Bump org.apache.avro:avro from 1.11.3 to 1.11.4 #222 (dependabot[bot])
Closed issues:
Merged and closed pull requests:
- Bump org.apache.avro:avro from 1.11.1 to 1.11.3 #218 (dependabot[bot])
Closed issues:
- Migrate CI from Travis to Github Actions #216
- Fix avro-maven-plugin version 1.11.1 warnings #214
- Update Avro dependency version to 1.11.1 #213
Merged and closed pull requests:
- Migrate CI from Travis to Github Actions #217 (heuermh)
- Update Avro dependency version to 1.11.1 #215 (heuermh)
Closed issues:
- Update pom.xml url to Github repository #211
Merged and closed pull requests:
Closed issues:
- Add proteinId field to Feature #208
- Flatten VariantAnnotation and GenotypeAnnotation #156
- Improve gVCF support #106
- Reconsider StructuralVariant and StructuralVariantType #104
Merged and closed pull requests:
- Update github-changes-maven-plugin version to 1.2 #210 (heuermh)
- [FORMATS-208] Add proteinId field to Feature #209 (heuermh)
- Update avro dependency version to 1.10.2 #207 (heuermh)
- [FORMATS-106] Refactor Genotype and GenotypeAnnotation. #176 (heuermh)
Closed issues:
- Add sample to Sequence, Slice, and Read #205
- Add impact, strand, ref/alt protein sequence, ref/alt coding sequence to TranscriptEffect #202
- Update release script to update changelog #197
- Changelog is missing versions 0.14.0 and 0.15.0 #196
- Migrate CI build to Travis or Github Actions #194
- Jenkins build status icon link is broken #192
- Add record definition for VCF header #191
- Add record definition for VariantContext #183
- Migrate bdg-formats to new adam-formats module #151
Merged and closed pull requests:
- [FORMATS-205] Add sample to Sequence, Slice, and Read #206 (heuermh)
- Update maven plugin dependency versions #204 (heuermh)
- [FORMATS-202] Add impact, strand, ref/alt coding sequence, ref/alt protein sequence to TranscriptEffect #203 (heuermh)
- Fix typo in contributing doc #201 (heuermh)
- Minor updates to readme #200 (heuermh)
- [FORMATS-197] Update release script to update changelog #199 (heuermh)
- [FORMATS-196] Update changelog for versions 0.14.0 and 0.15.0 #198 (heuermh)
- [FORMATS-194] Enable Travis for CI build #195 (heuermh)
- Add encoded sequence and sequence encoding. #189 (heuermh)
Closed issues:
- Rename AlignmentRecord --> Alignment or similar #164
Merged and closed pull requests:
- [FORMATS-192] Use direct Jenkins build status link. #193 (heuermh)
- Use private field visibility in generated source. #190 (heuermh)
- [FORMATS-164] Rename AlignmentRecord to Alignment. #188 (heuermh)
Closed issues:
- Snapshot version should be 0.14.0-SNAPSHOT #184
- Add barcodes field to ReadGroup #182
- Alignment record quality vs Read qualityScores #181
- ADAM Extension to precision medecine #158
- Document schema design philosophy #91
- Update Fragment type to support more general "read-bucketing" #54
- Publish C/C++ artifacts #22
Merged and closed pull requests:
- [FORMATS-182] Add barcodes field to ReadGroup #187 (heuermh)
- [FORMATS-181] Use qualityScores for base quality scores #186 (heuermh)
- [FORMATS-184] Snapshot version should be 0.14.0-SNAPSHOT #185 (heuermh)
- [BDG-FORMATS-54] Generalizing the Fragment type #56 (laserson)
- Platform-specific data #55 (ilveroluca)
Closed issues:
- Replace NucleotideContigFragment with Sequence and Slice #142
Merged and closed pull requests:
Closed issues:
- Javadoc errors in generated code cause release to fail #179
- Remove quality score variant #173
- Update AlignmentRecord field docs with mappings to SAM spec where appropriate #155
- All "original" fields should have the same prefix #130
- Lengthen "abbreviated" field names #126
- Rename Contig objects #43
Merged and closed pull requests:
- [FORMATS-179] Use additionalJOptions element instead of additionalparam. #180 (heuermh)
- Updating CHANGES.md #177 (heuermh)
- Refactor AlignmentRecord, RecordGroup, and ProcessingStep #175 (heuermh)
- [FORMATS-173] Remove quality score variant #174 (heuermh)
- Re-add reference.assembly field. #172 (heuermh)
- [FORMATS-43] Rename contig to reference. #154 (heuermh)
- Lengthen "abbreviated" field names #143 (Gasta88)
- Refactor Genotype and GenotypeAnnotation #108 (heuermh)
Closed issues:
- Add sampleId for Feature record #170
- Release version 0.11.4 #169
- jdk 9 compilation fails #165
- AlignmentRecord.attributes should be map #161
- Add API documentation link and badge #160
- Clean up fields in Fragment #159
Merged and closed pull requests:
- Update avro dependency version to 1.8.2. #171 (heuermh)
- [FORMATS-165] Support JDKs 9 and above. #168 (heuermh)
- [FORMATS-170] Add sampleId to Feature record #167 (akmorrow13)
- compilation fails on jdk 9 [https://github.com/bigdatagenomics/bdg-fo… #166 (sreev)
- [FORMATS-160] Adding API documentation link and badge. #163 (heuermh)
- [FORMATS-159] Clean up fields and doc in fragment. #162 (heuermh)
- Adding code of contact adapted from the Contributor Convenant, version 1.4. #157 (heuermh)
Closed issues:
Merged and closed pull requests:
Closed issues:
Merged and closed pull requests:
Closed issues:
- Floats for genotype likelihoods can underflow #144
Merged and closed pull requests:
Closed issues:
- Add totalLength, index, and slices to Slice #141
- Rename start/end fields in NucleotideContigFragment #138
- Add back contig length to NucleotideContigFragment #135
- NucleotideContigFragment uses
contig
instead ofcontigName
#127 - Remove AlignmentRecord.mateAlignmentEnd #115
- Add processing description schema #114
Merged and closed pull requests:
- [FORMATS-141] Add totalLength, index, and slices to Slice. #140 (heuermh)
- [FORMATS-138] Rename NucleotideContigFragment start/end fields. #139 (fnothaft)
- [FORMATS-135] Store the total contig length with a nucleotide contig … #136 (fnothaft)
- [FORMATS-114] Add processing description record. #134 (fnothaft)
- [FORMATS-127] Use contigName instead of contig #132 (heuermh)
- [FORMATS-115] Remove AlignmentRecord.mateAlignmentEnd #131 (heuermh)
- Fix case for default Strand #129 (heuermh)
- [FORMATS-124] Add field for generic non-reference allele. #125 (fnothaft)
- Add attributes map field to Sequence, Slice, Read records #123 (heuermh)
- Doc fixes to CHANGES.md and CONTRIBUTING.md #121 (heuermh)
- ISSUE 118: Use separate fields for Number=R VCF INFO attributes
- ISSUE 116: Add forward reference between Variant and VariantAnnotation
- ISSUE 113: Harmonize filter representation between Variant and VariantCallingAnnotations
- ISSUE 111: Improve doc for VariantAnnotation
- ISSUE 110: Add variant filters for VCF column 7 FILTER
- ISSUE 105: Merge VariantAnnotation and DatabaseVariantAnnotation records
- ISSUE 103: Remove StructuralVariant and StructuralVariantType, add names field to Variant
- ISSUE 101: Code style and doc fixes
- ISSUE 99: Revert back to 0.9.0
- ISSUE 97: Complete refactoring of variant and related annotation records
- ISSUE 94: Add readme
- ISSUE 90: Refactor variant and genotype annotations
- ISSUE 88: Use separate filtersFailed and filtersPassed arrays for variant quality filters
- ISSUE 84: Add schema for sample
- ISSUE 86: Adding key signatures for artifact signers.
- ISSUE 85: Fix transcript effect protein length field
- ISSUE 82: Update feature and related records to support GFF3
- ISSUE 81: Update maven-javadoc-plugin configuration to not fail build on JDK8
- ISSUE 67: Adding schema for variant annotations
- ISSUE 77: Flatten Variant into Genotype
- ISSUE 76: Replace contig with contigName in Variant.
- ISSUE 79: add fragmentEndPosition to NucleotideContigFragment
- ISSUE 78: Increase Avro dependency version to 1.8.0
- ISSUE 72: Replaced Contig with ContigName in AlignmentRecord
- ISSUE 70: Move record group metadata out from AlignmentRecord.
- ISSUE 69: Move to avro 1.7.7.
- ISSUE 66: Clean up fragment
- ISSUE 63: add optional referenceIndex field to Contigs
- ISSUE 51: Clean up VariantCallingAnnotations
- ISSUE 61: Added fragmentLength field to NucleotideContigFragment
- ISSUE 59: [FORMATS-58] Remove flat genotype.
- ISSUE 46: [bdg-formats-45] Removing pileup type.
- ISSUE 48: Generate UML diagrams from source (issue #47)
- ISSUE 42: fix artifact/schema publishing
- ISSUE 39: [bdg-formats-38] Add prior/posterior fields, somatic status, and attribute map
- ISSUE 36: [BDG-FORMATS-35] Change Avro strings to Java String
- ISSUE 34: Added the oldPosition and oldCigar fields to the bdg.avdl schema.
- ISSUE 30: [BDG-FORMATS-29] Re-organize the Feature schema
- ISSUE 32: [BDG-FORMATS-31] Added sampleId to Pileup
- ISSUE 26: [BDG-FORMATS-26] Removing bulky fields from the pileup record.
- ISSUE 27: [BDG-FORMATS-27] Add structural variant descriptor.
- ISSUE 21: Changing read to alignment record.
- ISSUE 23: Adding script to publish JSON/AVDL schemas to bigdatagenomics.github.io.
- ISSUE 24: Making modifications to array fields, and adding documentation.
- ISSUE 18: Adding two new fields, 'featureType' and 'source', to ADAMRecord.
- ISSUE 16: Adding IntelliJ files to the .gitignore
- ISSUE 15: Rename ADAMVariant variantAllele --> alternateAllele