Module fragment 

Fragment extraction and read base generation.

Handles extracting genomic fragments from haplotypes, reverse-complement operations, adapter sequence appending for short fragments, and R1/R2 base extraction from fragments.

Lowercase-as-marker convention

crate::fasta::Fasta::load_contig stores bases resolved from IUPAC ambiguity codes (including N) in lowercase, while real A/C/G/T bases remain uppercase. Reads that carry those synthesized bases through from the reference can be detected by counting lowercase bytes via lowercase_fraction, and the buffers are upper-cased in place with uppercase_in_place before being emitted.

Structs

Fragment

A simulated fragment extracted from a haplotype.

Functions

extract_fragment

Extract a fragment from a haplotype at a given position and strand.

extract_read_bases

Extract read bases from a fragment, handling adapter sequences for short fragments.

lowercase_fraction

Fraction of lowercase ASCII bytes in bases.

reverse_complement

Reverse-complement a DNA sequence in place.

uppercase_in_place

Upper-case every ASCII letter in bases in place.