added in house LMM in pipeline

app/lmm_benchmark.ml

@@ -4,11 +4,12 @@ let benchmark d =
   let open Simulation_dataset in
   Utils.recall_precision_curve
     ~oracle:(oracle d)
-    ~labels:[|"topological";"multinomial";"gemma_score";"tdg09"|]
+    ~labels:[|"topological";"multinomial";"gemma_score";"inhouse";"tdg09"|]
     ~results:[
       topological d ;
       multinomial_asymptotic_lrt d ;
       gemma ~lmm_test:`Score ~relatedness_mode:`Standardized d ;
+      inhouse_lmm d ;
       tdg09 d ;
     ]
 

lib/detection_pipeline.ml

@@ -54,6 +54,8 @@ module type S = sig
     relatedness_mode:[ `Centered | `Standardized ] ->
     text file
 
+  val inhouse_lmm : query -> text file
+
   val diffsel : query -> text file
 
   val diffseldsparse :
@@ -173,6 +175,11 @@ module Make (Q : Query) = struct
       ~relatedness_matrix
     |> Gemma.result_table_of_output alignment
 
+  let inhouse_lmm q =
+    let alignment = amino_acid_alignment q in
+    let tree = tree ~branch_length_unit:`Amino_acid q in
+    Inhouse_lmm.test alignment tree
+
   let diffseltree d =
     Tree_dataset.prepare_diffsel_tree
       (tree ~branch_length_unit:`Amino_acid d)

lib/detection_pipeline.mli

@@ -54,6 +54,8 @@ module type S = sig
     relatedness_mode:[ `Centered | `Standardized ] ->
     text file
 
+  val inhouse_lmm : query -> text file
+
   val diffsel : query -> text file
 
   val diffseldsparse :

lib/inhouse_lmm.ml

+open Phylogenetics
+open Codepitk
+
+let%pworkflow[@version 2] test alignment tree =
+  let alignment =
+    Alignment.from_fasta [%path alignment]
+    |> Rresult.R.get_ok
+  in
+  let tree = Convergence_tree.from_file [%path tree] in
+  Inhouse_lmm.test ~alignment ~tree
+  |> Inhouse_lmm.result_table_of_test
+  |> Result_table.to_file ~output:[%dest]

lib/inhouse_lmm.mli

+open Bistro
+open File_formats
+
+val test :
+  aminoacid_fasta file ->
+  nhx file ->
+  text file