Proto commits in opencb/biodata

These 71 commits are when the Protocol Buffers files have changed:

2026-01-20

test: update JUnit tests, #TASK-5564

The documentation is generated from this commit.

2025-11-12

models: Add missing fields to variant_annotation.proto #TASK-7555

2025-10-20

models: Update proto variant model and converter #TASK-7555

2020-11-06

models: Modify VariantType enum. #193 Deprecate SNP and MNP Rename CNV with COPY_NUMBER Add COPY_NUMBER_GAIN, COPY_NUMBER_LOSS, TANDEM_DUPLICATION Deprecate StructuralVariantType

2020-04-09

Revert wild renaming Revert almost all "genotypeCounters" to "genotypes"

models: Rename sampleCount, fileCount and qualityCount from VariantStats. #174

2020-04-08

models: Add samplesCount, filesCount and qualityValuesCount to VariantStats. #174

2020-03-24

models: Replace FileEntry.call with dedicated model #179

2020-03-20

models: Remove hgvs from Variant model. #179

models: Replace StudyEntry.samples map with list #179

models: Rename FileEntry.attributes to FileEntry.data

models: Rename StudyEntry.format to StudyEntry.sampleDataKeys #179

2020-03-18

models: Replace List<List<String>> samplesData with List<SampleEntry> samples. #179

2020-02-10

models: Add new VariantStats fields. #174

2018-12-10

Update code

2018-10-22

models: Add field description for VariantStats model. #154

2018-06-22

models: Clean VariantStats model. Remove unused fields. #154

2018-04-11

models: Synchronize BND in avro and proto model.

2018-01-25

models: Ensure avro and proto VariantType enums are synchronized.

2018-01-08

models: Parse and normalize Mated Breakend variants.

2017-09-20

feature-docm: new Drug field added to VariantAnnotation

2017-09-18

Merge branch 'develop' of github.com:opencb/biodata into develop

2017-09-15

models: Create VariantBuilder #153

2017-09-12

hotfix-1.2.x: VariantAnnotation.Cytoband object now contains a chromosome field

2017-07-20

feature-improveclinical: variant annotation proto file synchronyzed with the avro one

2017-07-06

Merge branch 'develop' into feature-improveclinical

develop: VariantAnnotation.exonOverlap is now an array of ExonOverlap objects

2017-05-26

Merge branch 'develop' into feature-improveclinical Conflicts: biodata-models/src/main/proto/protobuf/opencb/variant_annotation.proto

2017-05-15

feature-dgv: new field type added to StructuralVariation nested object which stores COPY_NUMBER_GAIN, COPY_NUMBER_LOSS, TANDEM, etc. Also, improvements made on setType/inferLength methods The commit message for your changes. Lines starting

2017-05-12

Merge branch 'feature-cytoband-annotation' of https://github.com/opencb/biodata into feature-cytoband-annotation Conflicts: biodata-models/src/main/proto/protobuf/opencb/variant_annotation.proto

2017-05-09

feature-cytoband-annotation: proto VariantAnnotation data model updated with cytobands

2017-05-05

feature-repeats: few Repeat fixes

feature-repeats: new Repeat data model and field added to VariantAnnotation

2017-03-22

feature-improveclinical: bug fixed at variant_annotation.proto and VariantContextToVariantProtoConverter

Merge branch 'develop' into feature-improveclinical Conflicts: biodata-models/src/main/proto/protobuf/opencb/variant_annotation.proto

2017-02-01

models: Synchronize variant proto and avro models

2016-09-22

feature-improveclinical: proto models fixed

feature-improveclinical: proto models need to be completed

2016-07-13

models: Change AdditionalAttributes to Map<String<Map<String, String>>

2016-05-25

models: Variant model change. Replace ids list with id+names. closes #98

2016-05-03

models: Move avro schemas to src/main/avro Generated files are now created in target/generated-sources

2016-03-10

tools: VariantMerger uses format key FT instead of FILTER

2016-03-01

models: protobuf Request message rename to BasicRequest, it is expectead each OpenCB project to have their own Request objects

models: major reorganization of proto files, we have flatten the folder structure and added opencb in the package name

2016-02-26

biodata-models: more updated and improvement in protobuf and gRPC, closes #94

2016-02-24

Merge branch 'develop' of github.com:opencb/biodata into develop Conflicts: biodata-models/pom.xml biodata-models/src/main/java/org/opencb/biodata/models/variant/protobuf/VariantProto.java biodata-models/src/main/java/org/opencb/biodata/models/variant/protobuf/VcfSliceProtos.java

biodata-models: several improvements in protobuf models, closes #93

2016-02-19

models: Add AlternateCoordinates to VcfRecord. Update converters.

2016-02-18

tools: Add list of GTs for VcfSlice compression

tools: Calculate default info keys for VcfSlice.Fields Remove END field from INFO. Already in VcfRecord Start and End are int32, not uint32, as they can be negative in some cases. Modified VariantType. First element (default for protobuf) is now NO_VARIATION (almost all the values on a gVCF file)

tools: Add common fields compression for VcfRecord in VcfSlice Some string fields on VcfRecord are now uint32 referring to the indexOf in the array of strings in VcfSlice.Fields object.

2016-02-16

models: Change VcfRecord.qual type from String to Float

2016-02-03

variant-merge: Update complex variant model and test cases

2016-02-02

protobuf: Add class to store Complex variants in the Analysis table

2015-12-15

models: protobuf folder structrure flatten

2015-11-19

models: VariantAnnoation expression and variantFunctionalScore renamed

2015-11-17

models: Added Type and Call to VcfRecord model. Removed old VcfMeta

2015-11-12

Merge branch 'develop' of github.com:opencb/biodata into develop

models: new protobuf 3 data models for Gene, Trasncript and Exon among others

2015-11-11

vcfrecord-proto: Allow for multi-allelic calls

2015-10-09

tools: a new converter from HTSJDK to Variant PB3 has been implemented, closes #78

2015-10-08

models: created Variant and VariantAnnotation data models for new Protocol Buffer 3, closes #77

2015-10-01

models: proto file moved into protobuf folder

2015-09-08

MODEL: update VCF Record proto file

2015-09-04

MODEL - VcfRecord: update ALT name #54

2015-09-03

MODEL - VcfRecord: first draft version #54

2014-08-18

Major changes: * formats, modles and tools modules and folders renamed to match maven style names, now all of them are prefixed with 'biodata' * Uniprot and Drugbank packages excluded from javadoc plugin to make it compatible with Java 8

2014-08-09

Maven configuration of the project to make it homogenous with the other projects in OpenCB, major changes include: * Prefix 'biodata-' added to modules and folders * Maven GroupId renamed from 'org.opencb' to 'org.opencb.biodata' because of Maven Central Repository requirement * Maven clean up and configuration added to pom.xml for deployment at OSS Central Repository * Version of the package upgraded to 0.2.0

2014-06-26

MAF allele and MGF genotype added to Protobuf representation of VariantStats

2014-05-20

Protocol Buffers specification for VariantStats objects

2014-05-15

Protocol Buffers specification for Variant objects