bed_utils::bed

Trait BEDLike

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pub trait BEDLike {

Show 16 methods    // Required methods
    fn chrom(&self) -> &str;
    fn set_chrom(&mut self, chrom: &str) -> &mut Self;
    fn start(&self) -> u64;
    fn set_start(&mut self, start: u64) -> &mut Self;
    fn end(&self) -> u64;
    fn set_end(&mut self, end: u64) -> &mut Self;

    // Provided methods
    fn name(&self) -> Option<&str> { ... }
    fn score(&self) -> Option<Score> { ... }
    fn strand(&self) -> Option<Strand> { ... }
    fn len(&self) -> u64 { ... }
    fn compare(&self, other: &Self) -> Ordering { ... }
    fn overlap<B: BEDLike>(&self, other: &B) -> Option<GenomicRange> { ... }
    fn n_overlap<B: BEDLike>(&self, other: &B) -> u64 { ... }
    fn to_genomic_range(&self) -> GenomicRange { ... }
    fn split_by_len(&self, bin_size: u64) -> impl Iterator<Item = GenomicRange> { ... }
    fn rsplit_by_len(&self, bin_size: u64) -> impl Iterator<Item = GenomicRange> { ... }

}
Expand description

Common BED fields

Required Methods§

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fn chrom(&self) -> &str

Return the chromosome name of the record

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fn set_chrom(&mut self, chrom: &str) -> &mut Self

Change the chromosome name of the record

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fn start(&self) -> u64

Return the 0-based start position of the record

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fn set_start(&mut self, start: u64) -> &mut Self

Change the 0-based start position of the record

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fn end(&self) -> u64

Return the end position (non-inclusive) of the record

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fn set_end(&mut self, end: u64) -> &mut Self

Change the end position (non-inclusive) of the record

Provided Methods§

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fn name(&self) -> Option<&str>

Return the name of the record

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fn score(&self) -> Option<Score>

Return the score of the record

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fn strand(&self) -> Option<Strand>

Return the strand of the record

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fn len(&self) -> u64

Return the length of the record. Return 0 if the end position is smaller than the start position.

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fn compare(&self, other: &Self) -> Ordering

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fn overlap<B: BEDLike>(&self, other: &B) -> Option<GenomicRange>

Return the overlap

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fn n_overlap<B: BEDLike>(&self, other: &B) -> u64

Return the size of overlap between two records

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fn to_genomic_range(&self) -> GenomicRange

Convert the record to a GenomicRange

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fn split_by_len(&self, bin_size: u64) -> impl Iterator<Item = GenomicRange>

Split into consecutive records with the specified length. The length of the last record may be shorter.

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fn rsplit_by_len(&self, bin_size: u64) -> impl Iterator<Item = GenomicRange>

Split into consecutive records with the specified length starting from the end. The result is in reverse order compared to split_by_len. The length of the last record may be shorter.

Dyn Compatibility§

This trait is not dyn compatible.

In older versions of Rust, dyn compatibility was called "object safety", so this trait is not object safe.

Implementors§