diff --git a/docs/source/appendices/design_decisions.rst b/docs/source/appendices/design_decisions.rst index 6477cb24..627f52f9 100644 --- a/docs/source/appendices/design_decisions.rst +++ b/docs/source/appendices/design_decisions.rst @@ -6,8 +6,9 @@ specification. As these trade-offs may not be apparent to outside readers, this section highlights the most significant ones and the rationale for our design decisions, including: +* Use “Variation” rather than “Variant” * Use “Allele” rather than “Variant” -* Alleles must be right normalized +* Alleles are fully justified * Sequence ranges use an interbase coordinate system * Modelling Language * Serialization Options diff --git a/docs/source/specification/computed_identifiers/normalization.rst b/docs/source/specification/computed_identifiers/normalization.rst index 7efa39d6..d0626a9f 100644 --- a/docs/source/specification/computed_identifiers/normalization.rst +++ b/docs/source/specification/computed_identifiers/normalization.rst @@ -3,15 +3,16 @@ Normalization !!!!!!!!!!!!! -The VR-Spec RECOMMENDS that Alleles at precise locations be normalized -to an fully-justified ("expanded") form. Implementations MUST use -fully justified variation when generating :ref:`computed-identifiers`. +VR Spec implementations MUST normalize Alleles to a fully justified +("expanded") form when generating :ref:`computed-identifiers`. The VR +Spec RECOMMENDS that Alleles at precise locations are also normalized +to a fully justified form. Conceptually, fully justified variation is expanded to the outer -bounds of left- and right- shuffling. As a result, fully justified -variation describes the unambiguous state of the resulting sequence. +bounds of left- and right- shuffling. As a result, it describes the +unambiguous state of the resulting sequence. -The process for fully justifying a two alleles (reference sequence and +The process for fully justifying two alleles (reference sequence and alternate sequence) at an interval is: * Trim common suffixes, if any, common to both allele sequences. Adjust the diff --git a/docs/source/specification/terms_and_model/interval.rst b/docs/source/specification/terms_and_model/interval.rst index 2b552357..5e9010ca 100644 --- a/docs/source/specification/terms_and_model/interval.rst +++ b/docs/source/specification/terms_and_model/interval.rst @@ -9,7 +9,7 @@ None. **Computational definition** -The *Interval* abstract class defines a range on a :ref:`sequence`, possibly with length zero, and specified using interbase coordinates. An Interval may be a :ref:`SimpleInterval` with a single start and end coordinate. Additional :ref:`planned-intervals` may also be nested or complex intervals, for use in describing fuzzy endpoint and more complex ranges. Any of these may be used as the Interval for Location. +The *Interval* abstract class defines a range on a :ref:`sequence`, possibly with length zero, and specified using :ref:`interbase coordinates`. An Interval may be a :ref:`SimpleInterval` with a single start and end coordinate. Additional :ref:`planned-intervals` may also be nested or complex intervals, for use in describing fuzzy endpoint and more complex ranges. Any of these may be used as the Interval for Location. .. _SimpleInterval: diff --git a/docs/source/specification/terms_and_model/location.rst b/docs/source/specification/terms_and_model/location.rst index b5ddf253..7463a211 100644 --- a/docs/source/specification/terms_and_model/location.rst +++ b/docs/source/specification/terms_and_model/location.rst @@ -42,7 +42,7 @@ A Location subclass for describing a defined :ref:`Interval` over a named :ref:` * 0 ≤ *interval.start* ≤ *interval.end* ≤ *n* * interbase coordinate 0 refers to the point before the start of the Sequence * interbase coordinate n refers to the point after the end of the Sequence. -* Coordinates MUST refer to valid Sequence. VR does not +* Coordinates MUST refer to a valid Sequence. VR does not support referring to intronic positions within a transcript sequence, extrapolations beyond the ends of sequences, or other implied sequence.