Module output 

Output writers for simulated reads and ground truth files.

Provides FASTQ output (always) and optional golden BAM output for benchmarking alignment pipelines. Supports single-threaded and multi-threaded BGZF compression via pooled-writer.

Modules

cpg_truth

Coverage-weighted per-CpG truth tally written as a MethylDackel-format bedGraph from simulated reads. Per-CpG ground-truth methylation tally and bedGraph writer.

fastq

FASTQ output for simulated reads.

golden_bam

Golden BAM output for ground-truth alignments.

methylation_bedgraph

Closed-form per-CpG population-fraction bedGraph writer derived from a per-haplotype methylation bitmap; no simulated reads required. Population-fraction methylation bedGraph in MethylDackel extract format.