Expand description
§bedpull
CIGAR-aware sequence extraction from BAM and PAF alignment files using BED coordinates.
Standard coordinate-lifting tools (liftOver, samtools faidx) work purely in reference
space: an inserted sequence has no reference coordinate, so it is silently dropped when
you lift a BED interval. bedpull avoids this by walking the CIGAR string of each
alignment, tracking both the reference position and the read position simultaneously.
Insertions that fall inside — or immediately adjacent to — a BED region are captured
automatically.
§Extraction modes
| Mode | Required flags | Description |
|---|---|---|
| BAM | --bam | Query an indexed BAM for reads overlapping each BED region. |
| PAF | --paf --query_ref | Build/load a byte-offset index of a PAF file, find overlapping alignments, extract from the query FASTA. |
§Library usage
use bedpull::{BamConfig, PafIndex, get_read_cuts};See the individual module docs for full API details.
Re-exports§
pub use cigar::CigarOp;pub use cigar::CigarOps;pub use cigar::ToCigarOps;pub use paf::PafIndex;pub use paf::PafIndexEntry;pub use paf::PafRecord;pub use paf::read_paf_record_at_offset;pub use paf::read_paf_record_from_reader;pub use reads::BamConfig;pub use reads::BamRead;pub use reads::PafRead;pub use reads::StitchConfig;pub use reads::get_bam_reads;pub use reads::get_cram_reads;pub use reads::get_paf_reads;pub use utils::ReadCuts;pub use utils::calculate_qscore;pub use utils::extract_from_fasta_coords;pub use utils::extract_from_fasta_coords_reader;pub use utils::get_read_cuts;pub use utils::read_bed;pub use utils::revcomp;pub use utils::write_fasta_record;pub use utils::write_fastq_record;