let bwa_mem_opt_inputs_exn inp =
let open Input in
let is_gz r =
Filename.check_suffix r ".gz" || Filename.check_suffix r ".fqz" in
let inputs =
match inp with
| Bam _ -> failwith "Can't pass Input.t Bam to bwa_mem_opt_inputs"
| Fastq {fastq_sample_name; files} ->
let sample_name = fastq_sample_name in
List.map files ~f:(fun (fragment_id, source) ->
match source with
| PE (r1, r2) when is_gz r1 && is_gz r2 ->
`Fastq_gz Bfx.(
let r1 = input_url r1 in
let r2 = input_url r2 in
Bfx.fastq_gz ~sample_name ?fragment_id ~r1 ~r2 ()
)
| PE (r1, r2) when not (is_gz r1 || is_gz r2) ->
`Fastq Bfx.(
let r1 = input_url r1 in
let r2 = input_url r2 in
Bfx.fastq ~sample_name ?fragment_id ~r1 ~r2 ()
)
| PE _ ->
failwithf "Heterogeneous gzipped / non-gzipped input paired-end FASTQs not implemented"
| SE r when is_gz r ->
`Fastq_gz Bfx.(
let r1 = input_url r in
Bfx.fastq_gz ~sample_name ?fragment_id ~r1 ()
)
| SE r ->
`Fastq_gz Bfx.(
let r1 = input_url r in
Bfx.fastq_gz ~sample_name ?fragment_id ~r1 ()
)
| Of_bam (how, sorting, reference_build, path) ->
let f = Bfx.input_url path in
let bam = Bfx.bam ~sample_name ?sorting ~reference_build f in
`Bam (bam, how)
)
in
inputs