package bistro-bio

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val run_gen_cmd : ?mlst_db:Formats.fasta Bistro.file -> ?mlst_delimiter:string -> ?mlst_definitions:Formats.fasta Bistro.file -> ?mlst_max_mismatch:int -> ?gene_db:Formats.fasta Bistro.file list -> ?no_gene_details:bool -> ?gene_max_mismatch:int -> ?min_coverage:int -> ?max_divergence:int -> ?min_depth:int -> ?min_edge_depth:int -> ?prob_err:float -> ?truncation_score_tolerance:int -> ?other:string -> ?max_unaligned_overlap:int -> ?mapq:int -> ?baseq:int -> ?samtools_args:string -> ?report_new_consensus:bool -> ?report_all_consensus:bool -> string -> Bistro.Shell_dsl.template list -> Bistro.Shell_dsl.command
val run_se : ?mlst_db:Formats.fasta Bistro.file -> ?mlst_delimiter:string -> ?mlst_definitions:Formats.fasta Bistro.file -> ?mlst_max_mismatch:int -> ?gene_db:Formats.fasta Bistro.file list -> ?no_gene_details:bool -> ?gene_max_mismatch:int -> ?min_coverage:int -> ?max_divergence:int -> ?min_depth:int -> ?min_edge_depth:int -> ?prob_err:float -> ?truncation_score_tolerance:int -> ?other:string -> ?max_unaligned_overlap:int -> ?mapq:int -> ?baseq:int -> ?samtools_args:string -> ?report_new_consensus:bool -> ?report_all_consensus:bool -> ?threads:int -> Formats.fastq Bistro.file list -> [ `srst2 ] Bistro.directory
val run_pe : ?mlst_db:Formats.fasta Bistro.file -> ?mlst_delimiter:string -> ?mlst_definitions:Formats.fasta Bistro.file -> ?mlst_max_mismatch:int -> ?gene_db:Formats.fasta Bistro.file list -> ?no_gene_details:bool -> ?gene_max_mismatch:int -> ?min_coverage:int -> ?max_divergence:int -> ?min_depth:int -> ?min_edge_depth:int -> ?prob_err:float -> ?truncation_score_tolerance:int -> ?other:string -> ?max_unaligned_overlap:int -> ?mapq:int -> ?baseq:int -> ?samtools_args:string -> ?report_new_consensus:bool -> ?report_all_consensus:bool -> ?threads:int -> Formats.fastq Bistro.file list -> [ `srst2 ] Bistro.directory
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