pandora_lib_promethion/src/io/mod.rs

//! File I/O for all genomic formats used by Pandora.
//!
//! # Coordinate convention
//!
//! All types and functions in this module use **0-based, half-open `[start, end)`**
//! coordinates unless explicitly documented otherwise. This matches the BED format,
//! Rust's `Range<u32>`, and the internal [`GenomeRange`](crate::positions::GenomeRange)
//! representation. Conversions to/from 1-based formats (GFF3, VCF POS, SAM POS,
//! Tabix positions) are handled internally and noted in each function's documentation.
//!
//! # BGZF vs standard gzip
//!
//! All `.gz` files are treated as **BGZF** (block gzip), not standard gzip.
//! BGZF is produced by `bgzip` and used by BAM, VCF.gz, BED.gz, etc.
//! Plain `gzip` output will not decompress correctly. See [`readers`] for details.
//!
//! # Submodules
//!
//! | Module | Purpose |
//! |--------|---------|
//! | [`bam`] | BAM/CRAM reading, SA-tag parsing, fold-back inversion detection |
//! | [`bed`] | BED file I/O, overlap queries, gene annotation, tabix compression |
//! | [`vcf`] | VCF file I/O with BGZF + Tabix index |
//! | [`fasta`] | Indexed FASTA access, contig splitting |
//! | [`gff`] | GFF3 feature range extraction |
//! | [`modkit`] | Modkit bedMethyl pileup parsing, epigenetic activity computation |
//! | [`straglr`] | Straglr STR genotyper TSV parsing |
//! | [`liftover`] | UCSC chain file parsing and coordinate liftover |
//! | [`readers`] | Generic BGZF/plain readers, Tabix region fetch (`fetch_tabix_lines_with`) |
//! | [`writers`] | BGZF writers, `BgzTabixWriter` for combined BGZF + Tabix output |
//! | [`tsv`] | `TsvLine` — reusable delimiter-agnostic line buffer (replaces `csv::ByteRecord`) |
//! | [`dict`] | Sequence dictionary (`.dict`) reader |
//! | [`fastq`] | FASTQ writer from BAM records |
//! | [`pod5_infos`] | POD5 run metadata extraction via Arrow IPC + flatbuffers |
//! | [`pod5_footer_generated`] | Auto-generated flatbuffers types for the POD5 footer |

pub mod bam;
pub mod bed;
pub mod dict;
pub mod fasta;
pub mod fastq;
pub mod gff;
pub mod liftover;
pub mod modkit;
pub mod pod5_footer_generated;
pub mod pod5_infos;
pub mod readers;
pub mod straglr;
pub mod tsv;
pub mod vcf;
pub mod writers;