Test for append

Mmap needs 8x skip. Mine was 23. I added another reserved byte,
which caused some test errors.

Project.toml

@@ -1,7 +1,7 @@
 name = "GeneMatrix"
 uuid = "b017c6bb-e7c7-4437-8ee6-a27b72ea26ab"
 authors = ["Xijiang Yu <[email protected]> and contributors"]
-version = "0.1.3"
+version = "0.1.4"
 
 [deps]
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"

README.md

@@ -32,7 +32,7 @@ symmetric, then `mattp` is overruled as `S`.
 The package also provides two other I/O functions to input and output
 plink bed files.
 
-*To be added*
+- *To be added*
 
 ## Matrix construction
 
@@ -42,11 +42,13 @@ plink bed files.
 
 ## Pedigree
 
-## Compat genotype storage
+## Compact genotype storage and manipulation methods
 
 ## Todo
 
-- [ ] `xyappend` functions
-- [ ] `nrm`: numerical relationship matrix
-- [ ] `nrminv`: the inverse of nrm
-- [ ] `sortped`, recode pedigree to 1:nID.
+- `nrm`: numerical relationship matrix
+- `nrminv`: the inverse of nrm
+- `sortped`, recode pedigree to 1:nID.
+- `readmacs`, read simulation results from MaCS.
+- `bed2int8`, convert bed file formats to Int8
+- tests merging.

src/append.jl

@@ -3,7 +3,7 @@
 
 Append genotypes in `mat` to `file`.
 """
-function xyappend(file::AbstractString, mat::Matrix; trans='N')
+function xyappend(file::AbstractString, mat::AbstractMatrix; trans='N')
     isfile(file) || error("File $file doesn't exist")
     open(file, "r+") do io
         mt, _, et, nrow, ncol = readhdr(io)
@@ -21,7 +21,7 @@ function xyappend(file::AbstractString, mat::Matrix; trans='N')
             write(io, mat')
         end
 
-        seek(io, 15)
+        seek(io, 16)
         write(io, [ncol + ncl2])
     end
 end

src/io.jl

@@ -12,7 +12,6 @@ function readxy(file)
     mat = nothing               # to return if success
     open(file, "r") do io
         mt, id, et, nrow, ncol = readhdr(io)
-        @info id
         if et == Bool           # eltype
             mat = BitArray(undef, nrow, ncol)
             read!(io, mat)
@@ -114,5 +113,6 @@ function writebed(bed, mat)
     end
 end
 
-function bed2bytes(bed)
+function bed2int8(bed)
 end
+

test/runtests.jl

@@ -1,4 +1,4 @@
-using GeneArrays
+using GeneMatrix
 using Test
 
 @testset "I/O" begin
@@ -7,30 +7,30 @@ using Test
 
     nrow, ncol = 200, 100
     a = rand(nrow, ncol)
-    GeneArrays.writexy(file, a)
-    b = GeneArrays.readxy(file)
+    GeneMatrix.writexy(file, a)
+    b = GeneMatrix.readxy(file)
     @test a == b
 
     a = a'a
-    GeneArrays.writexy(file, a)
-    b = GeneArrays.readxy(file)
-    @test filesize(file) == ncol * (ncol + 1) * 4 + 23
+    GeneMatrix.writexy(file, a)
+    b = GeneMatrix.readxy(file)
+    @test filesize(file) == ncol * (ncol + 1) * 4 + 24
     @test a == b
 
     a = rand(nrow, 2ncol)
     b = view(a, :, 1:ncol)
     c = view(a, :, ncol+1:2ncol)
-    GeneArrays.writexy(file, b)
-    GeneArrays.xyappend(file, c)
-    d = GeneArrays.readxy(file)
+    GeneMatrix.writexy(file, b)
+    GeneMatrix.xyappend(file, c)
+    d = GeneMatrix.readxy(file)
     @test a == d
 
-    GeneArrays.writexy(file, b)
-    GeneArrays.writexy(f2, c)
-    GeneArrays.xyappend(file, f2)
-    d = GeneArrays.readxy(file)
+    GeneMatrix.writexy(file, b)
+    GeneMatrix.writexy(f2, c)
+    GeneMatrix.xyappend(file, f2)
+    d = GeneMatrix.readxy(file)
     @test a == d
-
+    
     rm(file)
     rm(f2)
 end