Crate read_structure 

Read structures is a library for working with strings that describe how the bases in a sequencing run should be allocated into logical reads.

Each read structure is made up of one or more read segments which are in turn a segment type.

For more details see here

Example

Parsing a complex read structure.

use std::str::FromStr;
use read_structure::ReadStructure;

let rs = ReadStructure::from_str("76T8B8B76T").unwrap();
let templates: String = rs.templates().map(|s| s.to_string()).collect();
assert_eq!(templates, "76T76T");

Extracting segments from an actual read based on the read structure:

use std::str::FromStr;
use read_structure::{ReadStructure, SegmentType, SkipHandling};

let bases = b"\
    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGCCCCCCCCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT";
let quals = &[b'I'; 168][..];
let rs = ReadStructure::from_str("76T8B8B76T").unwrap();

let templates: Vec<&[u8]> = rs.extract(bases, quals, SkipHandling::Exclude)
    .unwrap()
    .filter(|(seg, _, _)| seg.kind == SegmentType::Template)
    .map(|(_, bases, _)| bases)
    .collect();

assert_eq!(templates, vec![
    &b"AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"[..],
    &b"TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT"[..],
]);

Structs

ErrorMessageParts

Helper struct for isolating the erroneous portion of a string.

ExtractedSegments

Iterator returned by ReadStructure::extract.

ReadSegment

A single segment of a read structure: a segment type and an optional fixed length.

ReadStructure

A read structure made up of one or more ReadSegments.

SegmentTypeIter

An iterator over the variants of SegmentType

Enums

ReadStructureError

SegmentType

The SegmentType type. See the module level documentation for more.

SkipHandling

Controls whether SegmentType::Skip segments are emitted by ReadStructure::extract.

Constants

ANY_LENGTH_BYTE

A character that can be put in place of a number in a read structure to mean “1 or more bases”.

ANY_LENGTH_BYTE_SLICE

Defined for efficiency, same as ANY_LENGTH_BYTE.

ANY_LENGTH_STR

A string that can be put in place of a number in a read structure to mean “1 or more bases”.