Typing utilities

methylphase typing <subcommand> provides subcommands used in phase-variants. These can be used to fit models, impute missing values, convert Floria haplosets, and split FASTQ files by assigned classes. These command are mostly for internal use but may be helpful for users.

fit

Fit a latent class model with a fixed number of classes.

methylphase typing fit \
  --data dataset.tsv \
  --config categories.toml \
  --classes 4 \
  --alpha-pi 1.0 \
  --alpha-phi 1.0 \
  --output-model fits/model_c4.json

Outputs a model JSON and (optionally) responsibilities.

select-best-c

Score multiple class counts and pick the best according to a criterion.

methylphase typing select-best-c \
  --data dataset.tsv \
  --config categories.toml \
  --classes 1..10 \
  --criterion icl \
  --penalty-multiplier 2.0 \
  --output-dir fits

Emits per-class fits in fits/, best_model.json, and best_responsibilities.tsv.

impute

Impute missing categorical/methylation values given a fitted model.

methylphase typing impute \
  --data dataset.tsv \
  --config categories.toml \
  --model best_model.json \
  --responsibilities best_responsibilities.tsv \
  --output imputed.tsv \
  --output-labels imputed_labels.tsv

convert-floria

Convert a Floria haploset to the dataset/config format used by typing.

methylphase typing convert-floria \
  --haploset haplotypes.hapset \
  --output-data dataset.tsv \
  --output-config categories.toml

Optionally merge methylation features if provided.

split-fastq

Split FASTQ files using assignments/responsibilities.

methylphase typing split-fastq \
  --fastq reads.fastq.gz \
  --responsibilities best_responsibilities.tsv \
  --output-dir fastq_by_class