# Changelog

## Score

- CAI 72 → 68 (-3.7)
- Rubric changed (rubric-2026.10.1 → rubric-2026.10.5) — scores are not directly comparable.

## Lenses

- Code Health 100 → 72 (-27.5)
- Architecture 88 → 91 (+3.8)
- Maturity 68 → 67 (-0.3)
- Readiness 67 → 63 (-3.7)
- Security 78 → 78 (+0.0)

## Resolved (4)

- Documentation: no installation or build instructions (docs/source/index.rst)
- Documentation: no usage examples (docs/source/index.rst)
- Orphaned files with no living knowledge
- Workflow holding a long-lived secret is unscoped

## New (130)

- BgenRecordWriter.getCompressedGenotypeProbabilityData (cognitive 20) (core/src/main/scala/io/projectglow/bgen/BgenRecordWriter.scala)
- CallSummaryStats.update (cognitive 40) (core/src/main/scala/io/projectglow/sql/expressions/SampleCallSummaryStats.scala)
- CallSummaryStats.update (cyclomatic 20) (core/src/main/scala/io/projectglow/sql/expressions/SampleCallSummaryStats.scala)
- Concentrated knowledge decay
- Documentation: no usage examples (docs/source/customizing/index.rst)
- Duplicated block (10 lines × 2) (python/glow/gwas/lin_reg.py)
- Duplicated block (21 lines × 2) (python/glow/wgr/logistic_ridge_regression.py)
- Duplicated block (26 lines × 3) (core/src/main/shim/3.4/SparkShim.scala)
- Duplicated block (27–30 lines × 2) (python/glow/wgr/logistic_ridge_regression.py)
- Duplicated block (5 lines × 2) (python/glow/wgr/ridge_reduction.py)
- Duplicated block (6 lines × 2) (core/src/main/scala/org/apache/spark/sql/catalyst/expressions/QuinaryOptionalExpression.scala)
- Duplicated block (8 lines × 2) (core/src/main/scala/io/projectglow/vcf/TabixIndexHelper.scala)
- Duplicated block (9 lines × 2) (core/src/main/scala/io/projectglow/sql/LeftOverlapJoin.scala)
- HardCalls.getHardCalls (cognitive 23) (core/src/main/scala/io/projectglow/sql/expressions/VariantUtilExprs.scala)
- InternalRowToBgenRowConverter.makeGenotypeConverter (cognitive 35) (core/src/main/scala/io/projectglow/bgen/InternalRowToBgenRowConverter.scala)
- InternalRowToBgenRowConverter.makeGenotypeConverter (cyclomatic 23) (core/src/main/scala/io/projectglow/bgen/InternalRowToBgenRowConverter.scala)
- InternalRowToVariantContextConverter.createAnnotationArray (cognitive 18) (core/src/main/scala/io/projectglow/vcf/InternalRowToVariantContextConverter.scala)
- InternalRowToVariantContextConverter.makeGenotypeConverter (cyclomatic 16) (core/src/main/scala/io/projectglow/vcf/InternalRowToVariantContextConverter.scala)
- Low cohesion: InternalRowToVariantContextConverter (LCOM4 9) (core/src/main/scala/io/projectglow/vcf/InternalRowToVariantContextConverter.scala)
- Low cohesion: VariantContextToInternalRowConverter (LCOM4 8) (core/src/main/scala/io/projectglow/vcf/VariantContextToInternalRowConverter.scala)
- …and 110 more

## Architecture

- 0 containers · 2 bounded contexts · 0 dependency edges (baseline)