val bowtie2_build :
?large_index:bool ->
?noauto:bool ->
?packed:bool ->
?bmax:int ->
?bmaxdivn:int ->
?dcv:int ->
?nodc:bool ->
?noref:bool ->
?justref:bool ->
?offrate:int ->
?ftabchars:int ->
?seed:int ->
?cutoff:int ->
Formats.fasta Bistro.file ->
[ `bowtie2_index ] Bistro.directoryval bowtie2 :
?skip:int ->
?qupto:int ->
?trim5:int ->
?trim3:int ->
?preset:[ `very_fast | `fast | `sensitive | `very_sensitive ] ->
?_N:int ->
?_L:int ->
?ignore_quals:bool ->
?mode:[ `end_to_end | `local ] ->
?a:bool ->
?k:int ->
?_D:int ->
?_R:int ->
?minins:int ->
?maxins:int ->
?orientation:[ `fr | `ff | `rf ] ->
?no_mixed:bool ->
?no_discordant:bool ->
?dovetail:bool ->
?no_contain:bool ->
?no_overlap:bool ->
?no_unal:bool ->
?seed:int ->
?fastq_format:Fastq.format ->
?additional_samples:Fastq_sample.t list ->
[ `bowtie2_index ] Bistro.directory ->
Fastq_sample.t ->
Formats.sam Bistro.file