From 2cad552f6308b28cd7a99aa3584da98716019bc4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ciar=C3=A1n=20O=27Mara?= <Ciaran.OMara@utas.edu.au>
Date: Sun, 2 Feb 2020 22:51:19 +1100
Subject: [PATCH] Quick fix for BioCore.RecordHelper: unsafe_parse_decimal

---
 src/sam/sam.jl | 33 ++++++++++++++++++++++++++++++++-
 1 file changed, 32 insertions(+), 1 deletion(-)

diff --git a/src/sam/sam.jl b/src/sam/sam.jl
index d0f006b..f7b6c92 100644
--- a/src/sam/sam.jl
+++ b/src/sam/sam.jl
@@ -9,12 +9,43 @@ import Automa
 import Automa.RegExp: @re_str
 import BioAlignments
 import BioGenerics.Exceptions: missingerror
-import BioGenerics.RecordHelper: unsafe_parse_decimal
 import BioGenerics: isfilled, header
 import BioSequences
 import BufferedStreams
 using Printf: @sprintf
 
+
+#TODO: update import BioCore.RecordHelper: unsafe_parse_decimal
+# r"[0-9]+" must match `data[range]`.
+function unsafe_parse_decimal(::Type{T}, data::Vector{UInt8}, range::UnitRange{Int}) where {T<:Unsigned}
+    x = zero(T)
+    @inbounds for i in range
+        x = Base.Checked.checked_mul(x, 10 % T)
+        x = Base.Checked.checked_add(x, (data[i] - UInt8('0')) % T)
+    end
+    return x
+end
+
+# r"[-+]?[0-9]+" must match `data[range]`.
+function unsafe_parse_decimal(::Type{T}, data::Vector{UInt8}, range::UnitRange{Int}) where {T<:Signed}
+    lo = first(range)
+    if data[lo] == UInt8('-')
+        sign = T(-1)
+        lo += 1
+    elseif data[lo] == UInt8('+')
+        sign = T(+1)
+        lo += 1
+    else
+        sign = T(+1)
+    end
+    x = zero(T)
+    @inbounds for i in lo:last(range)
+        x = Base.Checked.checked_mul(x, 10 % T)
+        x = Base.Checked.checked_add(x, (data[i] - UInt8('0')) % T)
+    end
+    return sign * x
+end
+
 include("flags.jl")
 include("metainfo.jl")
 include("record.jl")