bigdatagenomics/bdg-formats

Issues

• Update avro dependency version to 1.12.0

  #221 opened 5 months ago by heuermh
  0

• Documentation comment vs multiline comment warnings

  #219 opened a year ago by heuermh
  1

• Migrate CI from Travis to Github Actions

  #216 opened 2 years ago by heuermh
  0

• Fix avro-maven-plugin version 1.11.1 warnings

  #214 opened 2 years ago by heuermh
  1

• Update Avro dependency version to 1.11.1

  #213 opened 2 years ago by heuermh
  0

• Update pom.xml url to Github repository

  #211 opened 3 years ago by heuermh
  0

• Add proteinId field to Feature

  #208 opened 3 years ago by heuermh
  0

• Flatten VariantAnnotation and GenotypeAnnotation

  #156 opened 3 years ago by heuermh
  1

• Add sample to Sequence, Slice, and Read

  #205 opened 4 years ago by heuermh
  0

• Migrate bdg-formats to new adam-formats module

  #151 opened 4 years ago by heuermh
  1

• Add impact, strand, ref/alt protein sequence, ref/alt coding sequence to TranscriptEffect

  #202 opened 4 years ago by heuermh
  0

• Add record definition for VariantContext

  #183 opened 4 years ago by heuermh
  1

• Update release script to update changelog

  #197 opened 4 years ago by heuermh
  0

• Changelog is missing versions 0.14.0 and 0.15.0

  #196 opened 4 years ago by heuermh
  0

• Add record definition for VCF header

  #191 opened 4 years ago by heuermh
  1

• Jenkins build status icon link is broken

  #192 opened 4 years ago by heuermh
  1

• Migrate CI build to Travis or Github Actions

  #194 opened 4 years ago by heuermh
  0

• Rename AlignmentRecord --> Alignment or similar

  #164 opened 5 years ago by heuermh
  0

• Add barcodes field to ReadGroup

  #182 opened 5 years ago by heuermh
  3

• Alignment record quality vs Read qualityScores

  #181 opened 5 years ago by heuermh
  0

• Snapshot version should be 0.14.0-SNAPSHOT

  #184 opened 5 years ago by heuermh
  0

• ADAM Extension to precision medecine

  #158 opened 6 years ago by fbelghait
  1

• Replace NucleotideContigFragment with Sequence and Slice

  #142 opened 6 years ago by heuermh
  0

• Release version 0.12.0

  #178 opened 6 years ago by heuermh
  1

• Javadoc errors in generated code cause release to fail

  #179 opened 6 years ago by heuermh
  0

• All "original" fields should have the same prefix

  #130 opened 6 years ago by fnothaft
  2

• Update AlignmentRecord field docs with mappings to SAM spec where appropriate

  #155 opened 6 years ago by heuermh
  1

• Lengthen "abbreviated" field names

  #126 opened 6 years ago by fnothaft
  6

• Remove quality score variant

  #173 opened 6 years ago by heuermh
  0

• Release version 0.11.4

  #169 opened 6 years ago by heuermh
  1

• Clean up fields in Fragment

  #159 opened 6 years ago by fnothaft
  2

• Add sampleId for Feature record

  #170 opened 6 years ago by heuermh
  1

• jdk 9 compilation fails

  #165 opened 6 years ago by sreev
  2

• AlignmentRecord.attributes should be map<string>

  #161 opened 7 years ago by heuermh
  1

• Add API documentation link and badge

  #160 opened 7 years ago by heuermh
  0

• Release version 0.11.3

  #152 opened 7 years ago by heuermh
  1

• Add splitFromMultiallelic to Variant

  #149 opened 7 years ago by fnothaft
  0

• Release version 0.11.2

  #148 opened 7 years ago by heuermh
  3

• Add quality field to variant

  #146 opened 7 years ago by fnothaft
  5

• Floats for genotype likelihoods can underflow

  #144 opened 8 years ago by fnothaft
  0

• Add totalLength, index, and slices to Slice

  #141 opened 8 years ago by heuermh
  1

• Rename start/end fields in NucleotideContigFragment

  #138 opened 8 years ago by fnothaft
  7

• Rename RecordGroupMetadata --> RecordGroup

  #137 opened 8 years ago by heuermh
  1

• Add back contig length to NucleotideContigFragment

  #135 opened 8 years ago by fnothaft
  1

• Add program record equivalent

  #133 opened 8 years ago by fnothaft
  1

• NucleotideContigFragment uses `contig` instead of `contigName`

  #127 opened 8 years ago by fnothaft
  2

• Variant should store whether it has a non-ref model

  #124 opened 8 years ago by fnothaft
  1

• Default Strand uses wrong case

  #128 opened 8 years ago by heuermh
  0

• Add attributes map field to Sequence, Slice, Read records

  #122 opened 8 years ago by heuermh
  0

• Reference allele value for Number=R VCF INFO attributes

  #118 opened 8 years ago by heuermh
  6