add genome reader

src/Reference/Genome/Genome.jl

@@ -1,5 +1,7 @@
 export genome_dir,
-    download_genome
+    download_genome,
+    load_genome
 
 include("config.jl")
-include("downloader.jl")
+include("downloader.jl")
+include("reader.jl")

src/Reference/Genome/reader.jl

@@ -0,0 +1,22 @@
+function load_genome(assembly)
+    if !haskey(human_genomes, assembly)
+        error("$assembly is not supported, please use hg19/hg38")
+    end
+
+    # check if the assembly already exists
+    folder = joinpath(genome_dir(), assembly)
+    if isdir(folder) || !verify_human_genome_folder(folder)
+        if !download_genome(assembly)
+            error("Cannot download assembly $assembly")
+        end
+    end
+
+    chr_folder = joinpath(folder, "chroms")
+    chroms = readdir(chr_folder)
+    genome = Dict{ASCIIString, FastaRead}()
+    for chr in chroms
+        chrname = replace(chr, ".fa", "")
+        genome[chrname] = fasta_read(fasta_open(joinpath(chr_folder, chr)))
+    end
+    return genome
+end