Module read_naming 

Read naming schemes for simulated reads.

Supports two modes: encoded names that embed truth coordinates (contig, position, strand, haplotype, fragment length, error count) for downstream evaluation, and simple names that are just sequential identifiers.

Fields are separated by :: (double colon). Contig names may legally contain single : characters (e.g. HLA contigs like HLA-A*01:01:01:01); using :: as the separator keeps parsing unambiguous without requiring right-to-left tricks.

Structs

TruthAlignment

Truth alignment data for a single read, used to encode position information into the read name.

Functions

encoded_pe_name

Format a read name in encoded mode for a paired-end read.

encoded_se_name

Format a read name in encoded mode for a single-end read.

parse_encoded_pe_name

Parse an encoded paired-end read name back into truth alignments.

parse_encoded_se_name

Parse an encoded single-end read name back into a truth alignment.

simple_name

Format a simple read name with no truth information.