From 93a6b60d26e2b0c70ea8755d5b0913c1df7bb88d Mon Sep 17 00:00:00 2001
From: Jonathan Bieler <jonathan.bieler@alumni.epfl.ch>
Date: Thu, 13 Oct 2022 15:06:39 +0200
Subject: [PATCH 1/2] added method for handling different bam index types

---
 src/bam/reader.jl | 12 ++++++------
 test/test_bam.jl  | 15 +++++++++++++++
 2 files changed, 21 insertions(+), 6 deletions(-)

diff --git a/src/bam/reader.jl b/src/bam/reader.jl
index 43e228e..d1e71ec 100644
--- a/src/bam/reader.jl
+++ b/src/bam/reader.jl
@@ -28,13 +28,8 @@ function BioGenerics.IO.stream(reader::Reader)
 end
 
 function Reader(input::IO; index=nothing)
-    if isa(index, AbstractString)
-        index = BAI(index)
-    elseif index != nothing
-        error("unrecognizable index argument")
-    end
     reader = init_bam_reader(input)
-    reader.index = index
+    reader.index = init_bam_index(index)
     return reader
 end
 
@@ -125,6 +120,11 @@ function init_bam_reader(input::IO)
     return init_bam_reader(BGZFStreams.BGZFStream(input))
 end
 
+init_bam_index(index::AbstractString) = BAI(index)
+init_bam_index(index::BAI) = index
+init_bam_index(index::Nothing) = nothing
+init_bam_index(index) = error("unrecognizable index argument")
+    
 function _read!(reader::Reader, record)
     unsafe_read(
         reader.stream,
diff --git a/test/test_bam.jl b/test/test_bam.jl
index beb6d03..0a504b1 100644
--- a/test/test_bam.jl
+++ b/test/test_bam.jl
@@ -241,6 +241,21 @@
 
     end
 
+    @testset "BAI" begin
+
+        filepath = joinpath(bamdir, "GSE25840_GSM424320_GM06985_gencode_spliced.head.bam")
+
+        index = BAM.BAI(filepath * ".bai")
+        reader = open(BAM.Reader, filepath, index=index)
+        
+        @test isa(eachoverlap(reader, "chr1", 1:100), BAM.OverlapIterator)
+
+        close(reader)
+
+        @test_throws ErrorException open(BAM.Reader, filepath, index=1234) 
+
+    end
+
     @testset "Random access" begin
         filepath = joinpath(bamdir, "GSE25840_GSM424320_GM06985_gencode_spliced.head.bam")
         reader = open(BAM.Reader, filepath, index=filepath * ".bai")

From 286e271e9135b4379996e69deb0c6726eb4c5a01 Mon Sep 17 00:00:00 2001
From: Jonathan Bieler <jonathan.bieler@alumni.epfl.ch>
Date: Thu, 13 Oct 2022 15:17:20 +0200
Subject: [PATCH 2/2] update docstring

---
 src/bam/reader.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/bam/reader.jl b/src/bam/reader.jl
index d1e71ec..3dd2f7f 100644
--- a/src/bam/reader.jl
+++ b/src/bam/reader.jl
@@ -8,7 +8,7 @@ Create a data reader of the BAM file format.
 
 # Arguments
 * `input`: data source
-* `index=nothing`: filepath to a random access index (currently *bai* is supported)
+* `index=nothing`: filepath to a random access index (currently *bai* is supported) or BAI object 
 """
 mutable struct Reader{T} <: BioGenerics.IO.AbstractReader
     stream::BGZFStreams.BGZFStream{T}