CHANGELOG.md

@@ -7,12 +7,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
-## [0.2.1] - 2023-01-11
-
 ### Added
 
 - `translate` functionality for `Haplotype`s ([#31](https://github.com/BioJulia/SequenceVariation.jl/pull/31))
-- More informative errors when constructing invalid `Haplotype`s ([#34](https://github.com/BioJulia/SequenceVariation.jl/pull/34))
 
 ## [0.2.0] - 2023-01-10
 
@@ -70,8 +67,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - `Variant` constructor to automatically detect mutations from a `BioAlignments.PairwiseAlignment`
 - Methods to get reference and alternate bases from a `Variation`
 
-[unreleased]: https://github.com/BioJulia/SequenceVariation.jl/compare/v0.2.1...HEAD
+[unreleased]: https://github.com/BioJulia/SequenceVariation.jl/compare/v0.2.0...HEAD
-[0.2.1]: https://github.com/BioJulia/SequenceVariation.jl/compare/v0.2.0...v0.2.1
 [0.2.0]: https://github.com/BioJulia/SequenceVariation.jl/compare/v0.1.4...v0.2.0
 [0.1.4]: https://github.com/BioJulia/SequenceVariation.jl/compare/v0.1.3...v0.1.4
 [0.1.3]: https://github.com/BioJulia/SequenceVariation.jl/compare/v0.1.2...v0.1.3

Project.toml

@@ -1,7 +1,7 @@
 name = "SequenceVariation"
 uuid = "eef6e190-9969-4f06-a38f-35a110a8fdc8"
 authors = ["Jakob Nybo Nissen <jakobnybonissen@gmail.com>", "Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>"]
-version = "0.2.1"
+version = "0.2.0"
 
 [deps]
 BioAlignments = "00701ae9-d1dc-5365-b64a-a3a3ebf5695e"

src/Haplotype.jl

@@ -29,8 +29,7 @@ function Haplotype{S,T}(
 ) where {S<:BioSequence,T<:BioSymbol}
     sort!(edits; by=x -> x.pos)
     result = Haplotype{S,T}(ref, edits, Unsafe())
-    valid, message = _is_valid(result)
+    _is_valid(result) || error("TODO") # report what kind of error message?
-    valid || error(message)
     return result
 end
 
@@ -63,12 +62,11 @@ function _is_valid(h::Haplotype)
         op = edit.x
         # Sanity check: for this to be a valid variant, it must be comprised of valid
         # variations
-        _is_valid(Variation(h.ref, edit)) || return (false, "Invalid Variation")
+        _is_valid(Variation(h.ref, edit)) || return false
 
         # For substitutions we simply do not allow another modification of the same base
         if op isa Substitution
-            pos in valid_positions ||
+            pos in valid_positions || return false
-                return (false, "Multiple modifications at same position")
             valid_positions = (first(valid_positions) + 1):last(valid_positions)
             last_was_insert = false
             # Insertions affect 0 reference bases, so it does not modify the valid positions
@@ -77,18 +75,18 @@ function _is_valid(h::Haplotype)
         elseif op isa Insertion
             pos in
             ((first(valid_positions) - 1 + last_was_insert):(last(valid_positions) + 1)) ||
-                return (false, "Multiple insertions at same position")
+                return false
             last_was_insert = true
             # Deletions obviously invalidate the reference bases that are deleted.
         elseif op isa Deletion
             len = length(op)
             pos in (first(valid_positions):(last(valid_positions) - len + 1)) ||
-                return (false, "Deletion out of range")
+                return false
             valid_positions = (first(valid_positions) + len):last(valid_positions)
             last_was_insert = false
         end
     end
-    return (true, "")
+    return true
 end
 
 function Haplotype(