Module libradicl::rad_types

This module contains the relevant structures and traits for most of the core RAD types. This includes the integer, numeric and composite types, as well as other relevant types built from them (e.g. TagSections). It also contains the types and traits related to parsing and writing values of specific types.

Structs

• TagDesc
  A description for a type tag. This specifies the name that the tag should be given, and the type of value that it holds. At other points in the file, when this tag is used it will conform to this type description.
• TagMap
  This type represents a mapping from TagDescs to a corresponding set of values conforming to these descriptions (i.e. in terms of types). The TagMap allows you to fetch the value for a specific tag by name or index, or to add values to a corresponding set of descriptions.
• TagSection
  A TagSection consists of a series of TagDescs that are logically grouped together as tags for a specific unit
• TagViewMap
  This type represents a mapping from TagDescs to a corresponding set of values conforming to these descriptions (i.e. in terms of types). The TagMap allows you to fetch the value for a specific tag by name or index, or to add values to a corresponding set of descriptions. This type is much like a TagMap, except that it relies on a shared reference to the TagDescs, rather than an owned copy (usually a clone) of them.

Enums

• MappedFragmentOrientation
  Encodes the orientation of a mapped fragment. If the fragment is a single-end mapping (or orphan), then there are only 2 possible orientations, while for paired and mapped reads, there are 4 possible orientations. Finally, this enum can also represent an “Unknown” orientation.
• MappingType
  Represents the manner in which a fragment (read or read pair) may map to a target. This type does not encode orientation, but rather the mapping status.
• RadAtomicId
  This type represents any non-aggregate RadType, differentiating between an Int, Float, Bool and String types. Each Int and Float type contains a further description of the width of that type as a RadIntId.
• RadFloatId
• RadIntId
• RadType
  The top-level enum representing the different types that can be encoded in the tag system.
• TagSectionLabel
  A label of the type of a TagSection. The RAD format has file, read, and alignment-level tags, though the Unlabeled variant is reserved for potential other applications.
• TagValue
  This enum holds the different values that can be represented in a RAD tag. For the aggregate (i.e. array) types, the type of the element being stored in the array is encoded in the TagValue variant, but the length of the array is not.

Traits

• PrimitiveInteger

Functions

• decode_int_type_tag
  This function takes a u8 and returns the corresponding RadIntId. If the type_id represents a valid RadIntId then return Some(RadIntId), otherwise return None.
• encode_type_tag
  This function takes a RadType and returns the underlying id (i.e. u8 value) that defines the type in the RAD format.