package bistro

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package bistro
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class type index = object ... end
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 -> fasta Bistro.pworkflow -> index Bistro.pworkflow
val 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:'a Fastq.format -> index Bistro.pworkflow -> [ `single_end of 'a Bistro.pworkflow list | `paired_end of 'a Bistro.pworkflow list * 'a Bistro.pworkflow list ] -> sam Bistro.pworkflow