From 959a2ef8369368b4ca532e39835e27e81294dbfd Mon Sep 17 00:00:00 2001
From: Jakob Nybo Nissen <jakobnybonissen@gmail.com>
Date: Thu, 23 Oct 2025 13:46:27 +0200
Subject: [PATCH] Allow creating a BAMCIGAR from existing memory.

---
 Project.toml          |  2 +-
 docs/src/index.md     |  1 +
 docs/src/reference.md |  1 +
 src/CIGARStrings.jl   |  2 +-
 src/bamcigar.jl       | 38 +++++++++++++++++++++++++++++++++++---
 5 files changed, 39 insertions(+), 5 deletions(-)

diff --git a/Project.toml b/Project.toml
index 33f8d61..ce26838 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,6 +1,6 @@
 name = "CIGARStrings"
 uuid = "e5b51f81-6ffd-4e20-bbec-f118e37ea906"
-version = "0.1.4"
+version = "0.1.5"
 authors = ["Jakob Nybo Nissen <jakobnybonissen@gmail.com>"]
 
 [deps]
diff --git a/docs/src/index.md b/docs/src/index.md
index f209435..ba56fe1 100644
--- a/docs/src/index.md
+++ b/docs/src/index.md
@@ -236,6 +236,7 @@ However, in order to make zero-copy CIGARs possible, the `BAMCIGAR` type is back
 
 ```@docs
 CIGARStrings.BAMCIGAR
+CIGARStrings.BAMCIGAR(::MutableMemoryView{UInt8}, ::CIGAR)
 ```
 
 A `BAMCIGAR` can be constructed from its binary representation, using any type which implements `MemoryViews.MemoryView`:
diff --git a/docs/src/reference.md b/docs/src/reference.md
index 53383df..e786a32 100644
--- a/docs/src/reference.md
+++ b/docs/src/reference.md
@@ -10,6 +10,7 @@ end
 
 ```@docs; canonical = false
 CIGAR
+BAMCIGAR
 CIGARElement
 CIGAROp
 Translation
diff --git a/src/CIGARStrings.jl b/src/CIGARStrings.jl
index b20e62f..ab19844 100644
--- a/src/CIGARStrings.jl
+++ b/src/CIGARStrings.jl
@@ -11,7 +11,7 @@ export CIGAR,
 public CIGARError, CIGARErrorType, Errors, try_parse, outside, pos, gap,
     TranslationKind, PositionMapper
 
-using MemoryViews: MemoryViews, ImmutableMemoryView, MemoryView
+using MemoryViews: MemoryViews, ImmutableMemoryView, MemoryView, MutableMemoryView
 
 struct Unsafe end
 const unsafe = Unsafe()
diff --git a/src/bamcigar.jl b/src/bamcigar.jl
index e62781f..86c38ae 100644
--- a/src/bamcigar.jl
+++ b/src/bamcigar.jl
@@ -14,7 +14,8 @@ stored compactly in 32-bit integers.
 Semantically, a BAMCIGAR behaves much similar to a CIGAR.
 
 Construct a BAMCIGAR either from a CIGAR, taking an optional `Vector{UInt8}`
-to use as backing storage, or using [`CIGARStrings.try_parse`](@ref).
+to use as backing storage, or using [`CIGARStrings.try_parse`](@ref),
+or [`BAMCIGAR(::MutableMemoryView{UInt8}, ::CIGAR)`](@ref)
 
 # Examples
 ```jldoctest
@@ -135,20 +136,51 @@ function cigar_view!(v::Vector{UInt8}, x::BAMCIGAR)
 end
 
 BAMCIGAR(x::CIGAR) = BAMCIGAR(x, UInt8[])
+
 function BAMCIGAR(x::CIGAR, v::Vector{UInt8})
     resize!(v, 4 * length(x))
+    return @inbounds BAMCIGAR(MemoryView(v), x)
+end
+
+"""
+    BAMCIGAR(mem::MutableMemoryView{UInt8}, x::CIGAR)::BAMCIGAR
+
+Construct a `BAMCIGAR` equal to `x`, using the memory `mem`.
+After calling this, `mem` may not be mutated, and is considered
+owned by the resulting `BAMCIGAR`.
+
+Throw a `BoundsError` if `length(mem) < 4 * length(x)`.
+
+# Examples
+```jldoctest
+julia> x = CIGAR("150M3D9S");
+
+julia> mem = MemoryView(zeros(UInt8, 15));
+
+julia> cigar = BAMCIGAR(mem, x)
+BAMCIGAR(CIGAR("150M3D9S"))
+
+julia> parent(MemoryView(cigar)) === parent(mem)
+true
+```
+"""
+function BAMCIGAR(mem::MutableMemoryView{UInt8}, x::CIGAR)
+    @boundscheck if length(mem) < 4 * length(x)
+        throw(BoundsError(mem, 4 * length(x)))
+    end
+    mem = @inbounds mem[1:(4 * length(x))]
     i = 1
     for element in x
         u = getfield(element, :x)
         for _ in 1:4
-            @inbounds v[i] = u % UInt8
+            @inbounds mem[i] = u % UInt8
             i += 1
             u >>= 8
         end
     end
     return BAMCIGAR(
         unsafe,
-        ImmutableMemoryView(v),
+        ImmutableMemoryView(mem),
         x.aln_len,
         x.ref_len,
         x.query_len