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Grammar fixes and headings #94

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Jun 10, 2019
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Grammar fixes and headings #94

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25b1c7d
Fixed some typos and style
Jun 10, 2019
1c8131b
Modified headings in design decisions section
Jun 10, 2019
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3 changes: 2 additions & 1 deletion docs/source/appendices/design_decisions.rst
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Expand Up @@ -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
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13 changes: 7 additions & 6 deletions docs/source/specification/computed_identifiers/normalization.rst
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion docs/source/specification/terms_and_model/interval.rst
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Expand Up @@ -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:

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2 changes: 1 addition & 1 deletion docs/source/specification/terms_and_model/location.rst
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Expand Up @@ -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.
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