let gatk_indel_realigner_joint
?(configuration = Tools.Gatk.Configuration.default_indel_realigner)
bam_pair =
let bam1 = (AF.get_file bam_pair) |> pair_fst |> get_bam in
let bam2 = (AF.get_file bam_pair) |> pair_snd |> get_bam in
let bam_list_node =
indel_realigner_function (KEDSL.Bam_workflow_list [bam1; bam2])
~configuration in
begin match KEDSL.explode_bam_list_node bam_list_node with
| [realigned_normal; realigned_tumor] ->
Pair (Bam realigned_normal, Bam realigned_tumor)
|> indel_realigner_provenance ~configuration
["bam-pair", AF.get_provenance bam_pair]
| other ->
failf "Gatk.indel_realigner did not return the correct list of length 2 (tumor, normal): it gave %d bams"
(List.length other)
end