Skip to content

Commit

Permalink
moved bioinfo types to bistro
Browse files Browse the repository at this point in the history
  • Loading branch information
@pveber
pveber committed Nov 2, 2019
1 parent 2e5026d commit 1a55082
Show file tree
Hide file tree
Showing 4 changed files with 194 additions and 194 deletions.
97 changes: 0 additions & 97 deletions lib/bioinfo/bistro_bioinfo.ml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,103 +5,6 @@ open Bistro
open Bistro.Shell_dsl
open Stdio

class type bam = object
inherit binary_file
method format : [`bam]
end

class type bed3 = object
inherit tsv
method header : [`no]
method f1 : string
method f2 : int
method f3 : int
end

class type bed4 = object
inherit bed3
method f4 : string
end

class type bed5 = object
inherit bed4
method f5 : int
end

class type bed6 = object
inherit bed5
method f6 : [ `Plus | `Minus | `Unknown ]
end

class type fasta = object
inherit text_file
method format : [`fasta]
end

class type indexed_fasta = object
inherit directory
method contents : [`indexed_fasta]
end

class type fastq = object
inherit text_file
method format : [`fastq]
end

class type sanger_fastq = object
inherit fastq
method phred_encoding : [`sanger]
end

class type solexa_fastq = object
inherit fastq
method phred_encoding : [`solexa]
end

class type phred64_fastq = object
inherit fastq
method phred_encoding : [`phred64]
end

class type gff = object
inherit tsv
method header : [`no]
method f1 : string
method f2 : string
method f3 : string
method f4 : int
method f5 : int
method f6 : float
method f7 : [`Plus | `Minus]
method f8 : [`frame0 | `frame1 | `frame2]
method f9 : string
end

class type gff2 = object
inherit gff
method version : [`v2]
end

class type gff3 = object
inherit gff
method version : [`v3]
end

class type indexed_bam = object
inherit directory
method contents : [`indexed_bam]
end

class type sam = object
inherit text_file
method format : [`sam]
end

class type sra = object
inherit binary_file
method format : [`sra]
end

module Bed = struct
let keep ~n bed =
if n < 1 then raise (Invalid_argument "Bed.keep") ;
Expand Down
97 changes: 0 additions & 97 deletions lib/bioinfo/bistro_bioinfo.mli
View file
Original file line number Diff line number Diff line change
@@ -1,102 +1,5 @@
open Bistro

class type bam = object
inherit binary_file
method format : [`bam]
end

class type bed3 = object
inherit tsv
method header : [`no]
method f1 : string
method f2 : int
method f3 : int
end

class type bed4 = object
inherit bed3
method f4 : string
end

class type bed5 = object
inherit bed4
method f5 : int
end

class type bed6 = object
inherit bed5
method f6 : [ `Plus | `Minus | `Unknown ]
end

class type fasta = object
inherit text_file
method format : [`fasta]
end

class type indexed_fasta = object
inherit directory
method contents : [`indexed_fasta]
end

class type fastq = object
inherit text_file
method format : [`fastq]
end

class type sanger_fastq = object
inherit fastq
method phred_encoding : [`sanger]
end

class type solexa_fastq = object
inherit fastq
method phred_encoding : [`solexa]
end

class type phred64_fastq = object
inherit fastq
method phred_encoding : [`phred64]
end

class type gff = object
inherit tsv
method header : [`no]
method f1 : string
method f2 : string
method f3 : string
method f4 : int
method f5 : int
method f6 : float
method f7 : [`Plus | `Minus]
method f8 : [`frame0 | `frame1 | `frame2]
method f9 : string
end

class type gff2 = object
inherit gff
method version : [`v2]
end

class type gff3 = object
inherit gff
method version : [`v3]
end

class type indexed_bam = object
inherit directory
method contents : [`indexed_bam]
end

class type sam = object
inherit text_file
method format : [`sam]
end

class type sra = object
inherit binary_file
method format : [`sra]
end

module SE_or_PE : sig
type 'a t =
| Single_end of 'a
Expand Down
97 changes: 97 additions & 0 deletions lib/bistro.ml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -103,6 +103,103 @@ class type ['a] tar = object
method content_format : 'a
end

class type bam = object
inherit binary_file
method format : [`bam]
end

class type bed3 = object
inherit tsv
method header : [`no]
method f1 : string
method f2 : int
method f3 : int
end

class type bed4 = object
inherit bed3
method f4 : string
end

class type bed5 = object
inherit bed4
method f5 : int
end

class type bed6 = object
inherit bed5
method f6 : [ `Plus | `Minus | `Unknown ]
end

class type fasta = object
inherit text_file
method format : [`fasta]
end

class type indexed_fasta = object
inherit directory
method contents : [`indexed_fasta]
end

class type fastq = object
inherit text_file
method format : [`fastq]
end

class type sanger_fastq = object
inherit fastq
method phred_encoding : [`sanger]
end

class type solexa_fastq = object
inherit fastq
method phred_encoding : [`solexa]
end

class type phred64_fastq = object
inherit fastq
method phred_encoding : [`phred64]
end

class type gff = object
inherit tsv
method header : [`no]
method f1 : string
method f2 : string
method f3 : string
method f4 : int
method f5 : int
method f6 : float
method f7 : [`Plus | `Minus]
method f8 : [`frame0 | `frame1 | `frame2]
method f9 : string
end

class type gff2 = object
inherit gff
method version : [`v2]
end

class type gff3 = object
inherit gff
method version : [`v3]
end

class type indexed_bam = object
inherit directory
method contents : [`indexed_bam]
end

class type sam = object
inherit text_file
method format : [`sam]
end

class type sra = object
inherit binary_file
method format : [`sra]
end

module Template_dsl = struct
type template = Workflow.token Template.t

Expand Down

0 comments on commit 1a55082

Please sign in to comment.