bump LinearSampling_jll to v1.0.0, FASTX to v2.x.y

Author: marcom

Project.toml

@@ -13,10 +13,10 @@ SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 
 [compat]
-FASTX = "1.3"
+FASTX = "2"
 LinearFold_jll = "= 1.0.0"
 LinearPartition_jll = "= 1.0.0"
-LinearSampling_jll = "= 0.0.1"
+LinearSampling_jll = "= 1.0.0"
 LinearTurboFold_jll = "= 0.0.1"
 Unitful = "1.11"
 julia = "1.7"

src/LinearFold.jl

@@ -130,8 +130,10 @@ function cmd_linearsampling(; beamsize::Int=100,
             bin = LinearSampling_jll.linearsampling_lazysaving()
         end
     end
+    input_file = ""
+    shape_file_path = ""
     cmd = `$bin $beamsize $(Int(is_sharpturn)) $(Int(verbose))
-               $sample_number $read_forest $(Int(is_fasta))`
+               $sample_number $read_forest $(Int(is_fasta)) $input_file $shape_file_path`
     return cmd
 end