JLinAlg v0.3.3

JLinAlg 0.3.3

Complete-case sample handling

• Phenotype rows with missing values in any model column are omitted by
  default, and the corresponding samples are removed from streamed omics
  inputs before fitting.
• Console, log, and manifest output distinguish aligned samples from the final
  analysis sample count and report how many incomplete phenotype rows were
  omitted.

Exact streamed mixed-model scans

• Numeric Gaussian omics scans now refit variance components by REML for every
  feature through the lmer-like pathway instead of using P3D or EMMAX.
• Non-Gaussian numeric omics scans now refit a first-order Laplace GLMM for
  every feature through the glmer-like pathway instead of PQL.
• Pedigree-enabled scans use direct sparse Henderson relationship precision
  with ancestry-graph inbreeding, matching the intended pedigreemm model
  structure without materializing a dense relationship matrix.
• The selected mixed-fit strategy is recorded in the console preflight, run
  log, and manifest. Genotype LMM scans retain their documented null-model
  P3D pathway.

Delimited output and compact schemas

• A .csv output path now produces correctly quoted comma-separated output;
  .tsv and other existing outputs remain tab-separated.
• Generic numeric omics results omit genotype-only allele, frequency, call,
  imputation, Hardy-Weinberg, and filter columns.
• Per-row error fields are consolidated as failure_reason. Invariant
  omics_type, statistic_type, df_method, partial_r2_method, and
  output_format metadata now live in the run log and manifest instead of
  being repeated in every result row.

Release downloads: jlinalg-0.3.3.jar is the self-contained executable;
JLinAlg-0.3.3-library.jar is the thin library. Sources and Javadoc JARs and
SHA256SUMS.txt are also included.