Merge pull request #94 from cyenyxe/master

Grammar fixes and headings
ga4gh · Jun 10, 2019 · c8969d0 · c8969d0
2 parents ed591e4 + 1c8131b
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diff --git 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
@@ -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
@@ -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
@@ -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.