Module parsing 

Parsers for extracting sequence dictionaries from various file formats.

This module provides parsers for:

• SAM/BAM/CRAM files: Extract @SQ lines from alignment file headers
• Picard .dict files: Parse sequence dictionary files
• FASTA index (.fai) files: Parse FASTA index files
• NCBI assembly reports: Parse NCBI assembly reports with multiple naming conventions
• VCF headers: Extract ##contig lines from VCF files
• TSV/CSV files: Parse tabular contig definitions

Example

use ref_solver::parsing::sam::{parse_file, parse_header_text};
use std::path::Path;

// Parse from a BAM file
let query = parse_file(Path::new("sample.bam")).unwrap();

// Or parse from raw header text
let header = "@SQ\tSN:chr1\tLN:248_956_422\tM5:6aef897c3d6ff0c78aff06ac189178dd\n";
let query = parse_header_text(header).unwrap();

Supported Tags

From SAM @SQ lines, the following tags are extracted:

Tag	Description	Required
SN	Sequence name	Yes
LN	Sequence length	Yes
M5	MD5 checksum	No
AS	Assembly identifier	No
UR	URI for sequence	No
SP	Species	No
AN	Alternate names (aliases)	No

Modules

dict

fai

Parser for FASTA index (.fai) files using noodles.

fasta

Parser for FASTA files using noodles.

ncbi_report

Parser for NCBI assembly report files.

sam

tsv

vcf

Parser for VCF header contig lines.