JLinAlg v0.3.5

JLinAlg 0.3.5

Executable mediation and fine-mapping workflows

• The executable JAR now exposes Gaussian mediation workflows for ordinary,
  grouped-REML, and pedigree-REML models, with common complete-case alignment
  and explicit component-model convergence output.
• New susie and coloc commands run summary-statistic fine mapping from
  labeled LD matrices and multi-signal colocalization from the resulting
  effect tables.
• Progressive CLI tutorials now cover association, Mendelian randomization,
  mediation, SuSiE, and colocalization from input files through interpretation.

Association preflight and option validation

• --max-maf and --max-mac complement the existing lower-bound variant
  filters and are applied after sample alignment.
• Phenotype-only --dry-run and --explain now compile and validate the
  selected route before fitting. Genotype transforms, unsupported family/link
  combinations, and the common --explains typo fail with specific guidance.

Pedigree identity and hierarchy

• Family columns now disambiguate duplicate member IDs without partitioning
  the ancestry graph. Globally unique raw observation and parent IDs resolve
  automatically across family labels, while exact family:individual IDs
  remain accepted and ambiguous raw IDs fail with a qualification request.
• Parent-child links recursively define the full pedigree hierarchy, including
  shared ancestors and consanguineous matings. A direct R pedigreemm 0.3.5
  fixture now verifies the additive relationship matrix, inbreeding
  coefficients, and Henderson sparse inverse through a cousin-mating example.
• Runs with zero aligned source-pedigree matches now fail rather than silently
  constructing an all-singleton model. Logs and manifests distinguish matched
  source observations, automatically resolved aliases, and true singletons.

Release downloads: jlinalg-0.3.5.jar is the self-contained executable;
JLinAlg-0.3.5-library.jar is the thin library. Sources and Javadoc JARs and
SHA256SUMS.txt are also included.