Module read 

Simulated read pair generation.

Combines fragment extraction, error model application, and read naming into complete ReadPair objects ready for FASTQ output. Computes proper CIGARs from the haplotype-to-reference coordinate mapping for golden BAM output.

Structs

ReadPair

A simulated read pair (or single read for SE mode).

SimulatedRead

A single simulated read with bases, quality scores, and metadata.

Functions

cigar_from_ref_positions

Compute a CIGAR from a slice of ascending reference positions, plus optional adapter soft-clipping.

cigar_to_string

Format a CIGAR as a human-readable string (e.g. “50M3I20M2S”).

generate_read_pair

Generate a simulated read pair from a fragment.