Crate seq_geom_parser

This is a crate for parsing and interpreting sequence fragment geometry specifications in the sequence fragment geometry description language (FGDL). The FGDL describes how sequenced fragments are laid out, and how different parts of the sequence correspond to technical tags or to biological sequence. It provides a standard and unified way to represent the sequence layouts used in many different sequencing protocols, and is currently developed with a focus on representing different single-cell sequencing chemistries.

This crate provides a library for parsing these descriptions, and a set of structures for representing them in memory, as well as some common traits for transforming and printing them.

Structs

FragGeomParser

FragmentGeomDesc

This structure holds our representation of the parsed fragment geometry description.

PiscemGeomDesc

This struct holds a piscem compatible description of the fragment geometry specification.

SalmonSeparateGeomDesc

This struct holds a salmon compatible description of the fragment geometry specification.

Enums

GeomLen

The types of lengths that a piece of geometry can have.

GeomPiece

The pieces of geometry (types) we currently support.

NucStr

Represents the sequence held by a fixed sequence anchor.

Rule

Traits

AppendToCmdArgs

This trait says that a given implementor is able to properly add itself to the command represented by cmd.

Functions

parse_segment

Parses any type of geometry segment. According to the grammer, this will be either a fixed_segment, fixed_seq_segment, ranged_segment, or unbounded_segment. This function is the top-level parser for individual “pieces” of geometry, and returns the corresponding GeomPiece.