package bistro

You can search for identifiers within the package.

in-package search v0.2.0

bistro
- Bistro
  - EDSL
  - EDSL'
  - Path
  - Std
    
    Unix_tools
    
    file
    
    tabular
    
    tsv
  - Template
  - Workflow
  - file
  - value
bistro.bioinfo
- Bistro_bioinfo
  - Bed
  - Bedtools
    
    Cmd
  - Bowtie
  - Bowtie2
  - ChIPQC
  - Deeptools
    
    compressed_numpy_array
  - Defs
    
    bed3
    
    bed4
    
    bed5
    
    bed6
    
    gff
  - Deseq2
    
    table
  - Ensembl
  - FastQC
  - Fastq
  - Fastq_screen
  - Htseq
    
    count_tsv
  - Jaspar
  - Macs
    
    narrow_peaks
    
    peak_summits
    
    peaks_xls
  - Macs2
    
    narrow_peaks
    
    peak_summits
    
    peaks_xls
  - Meme_suite
  - Misc
    
    Infix
  - Prokka
  - Samtools
  - Spades
  - Sra
  - Sra_toolkit
  - Srst2
  - Std
    
    bed3
    
    bed4
    
    bed5
    
    bed6
    
    gff
  - Tophat
  - Ucsc_gb
    
    bedGraph
    
    chrom_sizes
bistro.engine
- Bistro_engine
  - Allocator
  - Db
  - Scheduler
    
    DAG
    
    logger
    
    logger
  - Task
bistro.tdag
- Bistro_tdag
  - Tdag
    
    Make
    
    D
    
    Allocator
    
    Task
    
    Thread
    
    logger
  - Tdag_sig
    
    Domain
    
    Allocator
    
    Task
    
    Thread
    
    S
    
    logger
bistro.utils
- Bistro_utils

Legend:
Library
Module
Module type
Parameter
Class
Class type

val run_gen_cmd : 
  ?mlst_db:Defs.fasta Bistro.Std.workflow ->
  ?mlst_delimiter:string ->
  ?mlst_definitions:Defs.fasta Bistro.Std.workflow ->
  ?mlst_max_mismatch:int ->
  ?gene_db:Defs.fasta Bistro.Std.workflow 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.Template.t list ->
  Bistro.command

val run_se : 
  ?mlst_db:Defs.fasta Bistro.Std.workflow ->
  ?mlst_delimiter:string ->
  ?mlst_definitions:Defs.fasta Bistro.Std.workflow ->
  ?mlst_max_mismatch:int ->
  ?gene_db:Defs.fasta Bistro.Std.workflow 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 ->
  'a Defs.fastq Bistro.Std.workflow list ->
  [ `srst2 ] Bistro.Std.directory Bistro.Std.workflow

val run_pe : 
  ?mlst_db:Defs.fasta Bistro.Std.workflow ->
  ?mlst_delimiter:string ->
  ?mlst_definitions:Defs.fasta Bistro.Std.workflow ->
  ?mlst_max_mismatch:int ->
  ?gene_db:Defs.fasta Bistro.Std.workflow 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 ->
  'a Defs.fastq Bistro.Std.workflow list ->
  [ `srst2 ] Bistro.Std.directory Bistro.Std.workflow