type index = [ `bowtie2_index ] Bistro.Std.directoryval 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 ->
Defs.fasta Bistro.Std.workflow ->
index Bistro.Std.workflowval 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.Std.workflow ->
[ `single_end of 'a Defs.fastq Bistro.Std.workflow list
| `paired_end of
'a Defs.fastq Bistro.Std.workflow list
* 'a Defs.fastq Bistro.Std.workflow list ] ->
Defs.sam Bistro.Std.workflow