package bistro

You can search for identifiers within the package.

in-package search v0.2.0

bistro
- Bistro
  - Command
  - EDSL
  - Path
  - Std
    
    Unix_tools
    
    binary_file
    
    bz2
    
    directory
    
    file
    
    gz
    
    html
    
    marshalled_value
    
    pdf
    
    png
    
    sexp_value
    
    svg
    
    tar
    
    text_file
    
    tsv
    
    zip
  - Template
  - U
  - Workflow
  - directory
bistro.bioinfo
- Bistro_bioinfo
  - Bed
  - Bedtools
    
    Cmd
  - Bowtie
  - Bowtie2
  - ChIPQC
  - Deeptools
    
    compressed_numpy_array
    
    deeptools_matrix
  - Defs
    
    bam
    
    bed3
    
    bed4
    
    bed5
    
    bed6
    
    fasta
    
    fastq
    
    gff
    
    gff2
    
    gff3
    
    sam
    
    sra
  - Deseq2
    
    table
  - Ensembl
  - FastQC
  - Fastq
  - Fastq_screen
  - Htseq
    
    count_tsv
  - Jaspar
  - Macs
    
    narrow_peaks
    
    peak_summits
    
    peaks_xls
  - Macs2
    
    broad_peaks
    
    narrow_peaks
    
    peak_summits
    
    peaks_xls
  - Meme_suite
  - Misc
    
    Infix
  - Prokka
  - Samtools
  - Spades
  - Sra
  - Sra_toolkit
  - Srst2
  - Std
    
    bed3
    
    bed4
    
    bed5
    
    bed6
    
    fasta
    
    fastq
    
    gff
    
    sam
    
    sra
  - Tophat
  - Ucsc_gb
    
    Lift_over
    
    chain_file
    
    bedGraph
    
    bigBed
    
    bigWig
    
    chrom_sizes
    
    twobit
    
    wig
bistro.engine
- Bistro_engine
  - Allocator
  - Db
  - Lwt_utils
  - 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
  - Console_logger
  - Dot_output
  - Html_logger
  - Logger
  - Repo
  - Term
    
    Syntax
    
    Let_syntax

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Module
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Parameter
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Class type

type 'a format

val bam : Defs.bam format

val sam : Defs.sam format

val sort : 
  ?on:[ `name | `position ] ->
  Defs.bam Bistro.Std.workflow ->
  Defs.bam Bistro.Std.workflow

val indexed_bam_of_sam : 
  Defs.sam Bistro.Std.workflow ->
  Defs.indexed_bam Bistro.Std.workflow

val indexed_bam_of_bam : 
  Defs.bam Bistro.Std.workflow ->
  Defs.indexed_bam Bistro.Std.workflow

val indexed_bam_to_bam : ([ `indexed_bam ], Defs.bam) Bistro.Std.selector

val bam_of_sam : Defs.sam Bistro.Std.workflow -> Defs.bam Bistro.Std.workflow

val sam_of_bam : Defs.bam Bistro.Std.workflow -> Defs.sam Bistro.Std.workflow

val view : 
  output:'o format ->
  ?h:bool ->
  ?_H:bool ->
  ?q:int ->
  < kind : [ `file ] ; format : [< `bam | `sam ].. > Bistro.Std.workflow ->
  'o Bistro.Std.workflow