let bwa_mem_opt
?(configuration = Tools.Bwa.Configuration.Mem.default)
~reference_build
input =
match input with
| `Fastq f ->
aligner "bwa-mem-opt-fq" (Tools.Bwa.Configuration.Mem.name configuration)
~reference_build f
| `Fastq_gz f ->
aligner "bwa-mem-opt-fqz" (Tools.Bwa.Configuration.Mem.name configuration)
~reference_build f
| `Bam (f, _) ->
aligner "bwa-mem-opt-bam" (Tools.Bwa.Configuration.Mem.name configuration)
~reference_build f