Expand description
Multi-sequence extractor for FASTA files using FAI indexing.
Re-exports§
pub use extract::apply_alt_substitution;pub use extract::extract_region;pub use extract::reverse_complement;pub use fai::FaiRecord;pub use fai::build_fai;pub use fai::read_fai;pub use gff::parse_regions_gff;pub use intervals::intersect_regions;pub use intervals::subtract_regions;pub use mask::MaskIndex;pub use mask::MaskMode;pub use output::wrap_fasta;pub use region::AltInfo;pub use region::Region;pub use region::deduplicate_regions;pub use region::merge_regions;pub use region::parse_region_str;pub use region::parse_regions_bed;pub use region::resolve_flanks;pub use region::sort_regions;pub use region::tile_regions;pub use stats::RegionStats;pub use stats::compute_stats;pub use template::expand_template;pub use transform::TransformConfig;pub use validate::is_gzip;pub use validate::resolve_bgzip;pub use vcf::VcfRecord;pub use vcf::expand_vcf_alt_seq;pub use vcf::parse_regions_vcf;
Modules§
- extract
- fai
- gff
- Minimal GFF3/GTF parser for extracting regions from annotation files.
- intervals
- Interval operations on genomic regions.
- mask
- Sequence masking using BED intervals.
- noindex
- Sequential scan mode for FASTA extraction without an FAI index.
- output
- region
- stats
- Statistics mode: compute per-region summary statistics instead of extracting sequences.
- table
- template
- Name template expansion for FASTA/FASTQ headers.
- transform
- Sequence transforms applied after extraction and reverse complement, before output.
- validate
- vcf
- Minimal VCF parser for extracting regions from VCF files.