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::convert::TryFrom;
use std::str::FromStr;
use read_structure::{
    ReadStructure,
    SegmentType,
};
let read_sequence = b"\
    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGGGGCCCCCCCCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT"
.to_vec();
let kind_of_interest = SegmentType::Template;
let rs = ReadStructure::from_str("76T8B8B76T").unwrap();

let mut sections = vec![];
for segment in rs.segments_by_type(kind_of_interest) {
    sections.push(segment.extract_bases(read_sequence.as_slice()).unwrap())
}
assert_eq!(sections, vec![
    b"AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA",
    b"TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT"
]);

Structs

ErrorMessageParts

Helper struct for isolating the erroneous portion of a string.

ReadSegment

The read segment describing a given kind (SegmentType), optional length, and offset of the bases within a crate::read_structure::ReadStructure.

ReadStructure

The read structure composed of one or more ReadSegments.

SegmentTypeIter

An iterator over the variants of Self

Enums

ReadStructureError

SegmentType

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

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”.