Update documentation wording to reflect new type names

docs/src/compare.md

@@ -4,7 +4,7 @@ CurrentModule = SequenceVariation
 
 # Comparing variations in sequences
 
-## Checking for variations in a known variant
+## Checking for variations in a known haplotype
 
 Looking for a known [`Variation`](@ref) within a [`Haplotype`](@ref) is
 efficiently accomplished using the `in` operator.
@@ -21,27 +21,27 @@ bos_ovis_alignment =
 bos_human_alignment =
     PairwiseAlignment(AlignedSequence(human, Alignment("32M", 1, 1)), bovine);
 
-bos_ovis_variant = Haplotype(bos_ovis_alignment)
+bos_ovis_haplotype = Haplotype(bos_ovis_alignment)
-bos_human_variant = Haplotype(bos_human_alignment)
+bos_human_haplotype = Haplotype(bos_human_alignment)
 ```
 
 ```@example call_variants
 println("\tOvis aires\tHomo sapiens")
-for v in vcat(variations(bos_ovis_variant), variations(bos_human_variant))
+for v in vcat(variations(bos_ovis_haplotype), variations(bos_human_haplotype))
-    is_sheep = v in bos_ovis_variant
+    is_sheep = v in bos_ovis_haplotype
-    is_human = v in bos_human_variant
+    is_human = v in bos_human_haplotype
     println("$v\t$is_sheep\t\t$is_human")
 end
 ```
 
-## Constructing new variants based on other variations
+## Constructing new haplotypes based on other variations
 
-New variants can be constructed using variations. This might be useful to pool
+New haplotypes can be constructed using variations. This might be useful to pool
-variations found on different reads or to filter variations from a variant
+variations found on different reads or to filter variations from a haplotype
-that aren't validated by another variant.
+that aren't validated by another haplotype.
 
 ```@repl call_variants
-sheeple = vcat(variations(bos_ovis_variant), variations(bos_human_variant));
+sheeple = vcat(variations(bos_ovis_haplotype), variations(bos_human_haplotype));
 Haplotype(bovine, sheeple)
 reconstruct!(bovine, ans)
 ```

docs/src/haplotypes.md

@@ -2,13 +2,14 @@
 CurrentModule = SequenceVariation
 ```
 
-# Working with variants
+# Working with haplotypes
 
 ## Calling variants
 
 The first step in working with sequence variation is to identify (call)
-variations. SequenceVariation can directly call variants using the
+variations between two sequences. SequenceVariation can directly call variants
-`Haplotype(::PairwiseAlignment)` constructor of the [`Haplotype`](@ref) type.
+using the `Haplotype(::PairwiseAlignment)` constructor of the
+[`Haplotype`](@ref) type.
 
 ```@repl call_variants
 using SequenceVariation, BioAlignments, BioSequences
@@ -22,19 +23,19 @@ bos_ovis_alignment =
 bos_human_alignment =
     PairwiseAlignment(AlignedSequence(human, Alignment("32M", 1, 1)), bovine);
 
-bos_ovis_variant = Haplotype(bos_ovis_alignment)
+bos_ovis_haplotype = Haplotype(bos_ovis_alignment)
-bos_human_variant = Haplotype(bos_human_alignment)
+bos_human_haplotype = Haplotype(bos_human_alignment)
 ```
 
 ## Sequence reconstruction
 
-If the alternate sequence of a variant is no longer available (as is often the
+If the alternate sequence of a haplotype is no longer available (as is often the
 case when calling variants from alignment files), then the sequence can be
 retrieved using the [`reconstruct!`](@ref) function.
 
 ```@repl call_variants
 human2 = copy(bovine);
-reconstruct!(human2, bos_human_variant)
+reconstruct!(human2, bos_human_haplotype)
 human2 == bovine
 human2 == human
 ```

docs/src/variations.md

@@ -42,13 +42,13 @@ bos_ovis_alignment =
 bos_human_alignment =
     PairwiseAlignment(AlignedSequence(human, Alignment("32M", 1, 1)), bovine);
 
-bos_ovis_variant = Haplotype(bos_ovis_alignment)
+bos_ovis_haplotype = Haplotype(bos_ovis_alignment)
-bos_human_variant = Haplotype(bos_human_alignment)
+bos_human_haplotype = Haplotype(bos_human_alignment)
 ```
 
 ```@repl call_variants
-variations(bos_ovis_variant)
+variations(bos_ovis_haplotype)
-variations(bos_human_variant)
+variations(bos_human_haplotype)
 ```
 
 ## Reference switching
@@ -59,8 +59,8 @@ alignment between the new and old references using the [`translate`](@ref).
 ```@repl call_variants
 ovis_human_alignment =
     PairwiseAlignment(AlignedSequence(human, Alignment("32M", 1, 1)), ovine)
-human_variation = first(variations(bos_ovis_variant))
+human_variation = first(variations(bos_ovis_haplotype))
 reference(ans) == bovine
-SequenceVariation.translate(human_variation, ovis_human_alignment)
+SequenceVariation.translate(human_variation, ovis_human_haplotype)
 reference(ans) == bovine
 ```

src/Haplotype.jl

@@ -2,7 +2,7 @@
     Haplotype{S<:BioSequence,T<:BioSymbol}
 
 A set of variations within a given sequence that are all found together. Depending on the
-field, it might also be referred to as a "genotype," "haplotype," or "strain."
+field, it might also be referred to as a "genotype" or "strain."
 
 # Constructors