bio: fixed warnings

pveber · Nov 13, 2021 · fb285b2 · fb285b2
1 parent 94c54b8
commit fb285b2
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Showing 3 changed files with 6 additions and 6 deletions.
diff --git a/lib/bio/bedtools.ml b/lib/bio/bedtools.ml
@@ -13,7 +13,7 @@ let bed = Bed
 let gff = Gff
 
 module Cmd = struct
-  let slop_args ?strand ?header ~mode = [
+  let slop_args ?strand ?header mode = [
     option (flag string "-s") strand ;
     option (flag string "-header") header ;
     seq (
@@ -29,7 +29,7 @@ module Cmd = struct
 
   let slop ?strand ?header ~mode input chrom_size =
     bedtools "slop" ~stdout:dest [
-      seq (slop_args ?strand ?header ~mode) ;
+      seq (slop_args ?strand ?header mode) ;
       opt "-i" dep input ;
       opt "-g" dep chrom_size ;
     ]

diff --git a/lib/bio/ensembl.ml b/lib/bio/ensembl.ml
@@ -38,7 +38,7 @@ let ucsc_chr_names_gtf gff =
     ]
   ]
 
-let gff ?(chr_name = `ensembl) ~release ~species =
+let gff ?(chr_name = `ensembl) ~release species =
   let url =
     sprintf "ftp://ftp.ensembl.org/pub/release-%d/gff3/%s/%s.%s.%d.gff3.gz"
       release (string_of_species species)
@@ -51,7 +51,7 @@ let gff ?(chr_name = `ensembl) ~release ~species =
   | `ucsc -> ucsc_chr_names_gtf gff
 
 
-let gtf ?(chr_name = `ensembl) ~release ~species =
+let gtf ?(chr_name = `ensembl) ~release species =
   let url =
     sprintf "ftp://ftp.ensembl.org/pub/release-%d/gtf/%s/%s.%s.%d.gtf.gz"
       release (string_of_species species)

diff --git a/lib/bio/ensembl.mli b/lib/bio/ensembl.mli
@@ -8,8 +8,8 @@ type species = [
 
 val ucsc_reference_genome : release:int -> species:species -> Ucsc_gb.genome
 
-val gff : ?chr_name : [`ensembl | `ucsc] -> release:int -> species:species -> gff file
-val gtf : ?chr_name : [`ensembl | `ucsc] -> release:int -> species:species -> gff file
+val gff : ?chr_name : [`ensembl | `ucsc] -> release:int -> species -> gff file
+val gtf : ?chr_name : [`ensembl | `ucsc] -> release:int -> species -> gff file
 
 val cdna : release:int -> species:species -> fasta gz file