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bdg-formats Changelog

Version 1.0.2

Closed issues:

Merged and closed pull requests:

Version 1.0.1

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)

Version 1.0

Closed issues:

  • Update pom.xml url to Github repository #211

Merged and closed pull requests:

  • Update pom.xml url to Github repository #212 (heuermh)

Version 0.17.0

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)

Version 0.16.0

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)

Version 0.15.0

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)

Version 0.14.0

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)

Version 0.13.0

Closed issues:

  • Replace NucleotideContigFragment with Sequence and Slice #142

Merged and closed pull requests:

  • [FORMATS-142] Replace NucleotideContigFragment with Sequence and Slice #153 (heuermh)

Version 0.12.0

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)

Version 0.11.4

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:

Version 0.11.3

Closed issues:

  • Release version 0.11.3 #152
  • Add splitFromMultiallelic to Variant #149

Merged and closed pull requests:

  • [FORMATS-149] Add splitFromMultiallelic to Variant. #150 (fnothaft)

Version 0.11.2

Closed issues:

  • Release version 0.11.2 #148
  • Add quality field to variant #146

Merged and closed pull requests:

Version 0.11.1

Closed issues:

  • Floats for genotype likelihoods can underflow #144

Merged and closed pull requests:

  • [FORMATS-144] Move genotype likelihood fields to doubles. #145 (fnothaft)

Version 0.11.0

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 of contigName #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)

Version 0.10.0

  • 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

Version 0.9.0

  • 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

Version 0.8.0

  • 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

Version 0.7.1

  • ISSUE 72: Replaced Contig with ContigName in AlignmentRecord

Version 0.7.0

  • ISSUE 70: Move record group metadata out from AlignmentRecord.
  • ISSUE 69: Move to avro 1.7.7.
  • ISSUE 66: Clean up fragment

Version 0.6.1

  • ISSUE 63: add optional referenceIndex field to Contigs

Version 0.6.0

  • 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

Version 0.5.0

  • ISSUE 39: [bdg-formats-38] Add prior/posterior fields, somatic status, and attribute map

Version 0.4.0

  • ISSUE 36: [BDG-FORMATS-35] Change Avro strings to Java String

Version 0.3.2

  • ISSUE 34: Added the oldPosition and oldCigar fields to the bdg.avdl schema.

Version 0.3.1

  • ISSUE 30: [BDG-FORMATS-29] Re-organize the Feature schema

Version 0.3.0

  • 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.

Version 0.2.0

  • 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

Version 0.1.1

  • ISSUE 8: Removes unused record group ID field.
  • ISSUE 7: Move the namespace from 'bdg_formats' to simply 'formats'
  • ISSUE 6: Adds contribution file and updates the license header on the AVDL file.

Version 0.1.0

  • ISSUE 5: Updating to prepare for schema move.
  • ISSUE 1: Moving over the adam.avdl file from adam-format.
  • ISSUE 2: Adding top-level files