From 9fd6f01ad819f6ebb8a5818afaac66ec9c39894c Mon Sep 17 00:00:00 2001
From: Steven Weaver <sweaver@temple.edu>
Date: Tue, 26 Nov 2024 13:55:44 -0800
Subject: [PATCH] veg/datamonkey-js#752 -- adding new fel options

---
 app/fel/fel.js | 79 ++++++++++++++++++++++++++++----------------------
 app/fel/fel.sh | 11 +++----
 2 files changed, 50 insertions(+), 40 deletions(-)

diff --git a/app/fel/fel.js b/app/fel/fel.js
index 259a9d4..8681cfb 100644
--- a/app/fel/fel.js
+++ b/app/fel/fel.js
@@ -5,7 +5,7 @@ var config = require("../../config.json"),
   fs = require("fs"),
   path = require("path");
 
-var fel = function(socket, stream, params) {
+var fel = function (socket, stream, params) {
   var self = this;
   self.socket = socket;
   self.stream = stream;
@@ -13,6 +13,11 @@ var fel = function(socket, stream, params) {
 
   // object specific attributes
   self.type = "fel";
+
+  // New attributes for multiple hits and site multihit
+  self.multiple_hits = self.params.analysis.multiple_hits || "None"; // e.g., [Double, Double+Triple, None]
+  self.site_multihit = self.params.analysis.site_multihit || "Estimate"; // e.g., [Estimate, Global]
+
   self.qsub_script_name = "fel.sh";
   self.qsub_script = __dirname + "/" + self.qsub_script_name;
 
@@ -38,52 +43,56 @@ var fel = function(socket, stream, params) {
   self.tree_fn = self.fn + ".tre";
 
   self.qsub_params = [
-    "-l walltime=" + 
-    config.fel_walltime + 
-    ",nodes=1:ppn=" + 
+    "-l walltime=" +
+    config.fel_walltime +
+    ",nodes=1:ppn=" +
     config.fel_procs,
     "-q",
     config.qsub_queue,
     "-v",
     "fn=" +
-      self.fn +
-      ",tree_fn=" +
-      self.tree_fn +
-      ",sfn=" +
-      self.status_fn +
-      ",pfn=" +
-      self.progress_fn +
-      ",rfn=" +
-      self.results_short_fn +
-      ",treemode=" +
-      self.treemode +
-      ",bootstrap=" +
-      self.bootstrap +
-      ",resample=" +
-      self.resample+
-      ",genetic_code=" +
-      self.genetic_code +
-      ",analysis_type=" +
-      self.type +
-      ",rate_variation=" +
-      self.rate_variation +
-      ",ci=" +
-      self.ci +
-      ",cwd=" +
-      __dirname +
-      ",msaid=" +
-      self.msaid +
-      ",procs=" +
-      config.fel_procs,
+    self.fn +
+    ",tree_fn=" +
+    self.tree_fn +
+    ",sfn=" +
+    self.status_fn +
+    ",pfn=" +
+    self.progress_fn +
+    ",rfn=" +
+    self.results_short_fn +
+    ",treemode=" +
+    self.treemode +
+    ",bootstrap=" +
+    self.bootstrap +
+    ",resample=" +
+    self.resample +
+    ",genetic_code=" +
+    self.genetic_code +
+    ",analysis_type=" +
+    self.type +
+    ",rate_variation=" +
+    self.rate_variation +
+    ",ci=" +
+    self.ci +
+    ",cwd=" +
+    __dirname +
+    ",msaid=" +
+    self.msaid +
+    ",procs=" +
+    config.fel_procs +
+    ",multiple_hits=" +
+    self.multiple_hits +
+    ",site_multihit=" +
+    self.site_multihit,
     "-o",
     self.output_dir,
     "-e",
     self.output_dir,
-    self.qsub_script
+    self.qsub_script,
   ];
 
   // Write tree to a file
-  fs.writeFile(self.tree_fn, self.nwk_tree, function(err) {
+  fs.writeFile(self.tree_fn, self.nwk_tree, function (err) {
     if (err) throw err;
   });
 
diff --git a/app/fel/fel.sh b/app/fel/fel.sh
index c790260..1d6d139 100644
--- a/app/fel/fel.sh
+++ b/app/fel/fel.sh
@@ -17,6 +17,8 @@ RESAMPLE=$resample
 RESULTS_FN=$rfn
 GENETIC_CODE=$genetic_code
 RATE_VARIATION=$rate_variation
+MULTIPLE_HITS=$multiple_hits
+SITE_MULTIHIT=$site_multihit
 PROCS=$procs
 
 HYPHY=$CWD/../../.hyphy/HYPHYMPI
@@ -30,12 +32,11 @@ trap 'echo "Error" > $STATUS_FILE; exit 1' ERR
 
 if [ $BOOTSTRAP = "true" ]
 then
-  echo "mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH  $FEL --alignment $FN --tree $TREE_FN --code $GENETIC_CODE --branches FG --srv $RATE_VARIATION --output $RESULTS_FILE --resample $RESAMPLE --ci $CI >> $PROGRESS_FILE"
-  mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH ENV="TOLERATE_NUMERICAL_ERRORS=1;" $FEL --alignment $FN --tree $TREE_FN --code $GENETIC_CODE --branches FG --srv $RATE_VARIATION --output $RESULTS_FILE --resample $RESAMPLE --ci $CI >> $PROGRESS_FILE
+  echo "mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH  $FEL --alignment $FN --tree $TREE_FN --code $GENETIC_CODE --branches FG --srv $RATE_VARIATION --output $RESULTS_FILE --resample $RESAMPLE --ci $CI --multiple-hits $MULTIPLE_HITS --site-multihit $SITE_MULTIHIT >> $PROGRESS_FILE"
+  mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH ENV="TOLERATE_NUMERICAL_ERRORS=1;" $FEL --alignment $FN --tree $TREE_FN --code $GENETIC_CODE --branches FG --srv $RATE_VARIATION --output $RESULTS_FILE --resample $RESAMPLE --ci $CI --multiple-hits $MULTIPLE_HITS --site-multihit $SITE_MULTIHIT >> $PROGRESS_FILE
 else
-  echo "mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH  $FEL --alignment $FN --tree $TREE_FN --code $GENETIC_CODE --branches FG --srv $RATE_VARIATION --output $RESULTS_FILE --ci $CI >> $PROGRESS_FILE"
-  mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH ENV="TOLERATE_NUMERICAL_ERRORS=1;" $FEL --alignment $FN --tree $TREE_FN --code $GENETIC_CODE --branches FG --srv $RATE_VARIATION --output $RESULTS_FILE --ci $CI >> $PROGRESS_FILE
+  echo "mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH  $FEL --alignment $FN --tree $TREE_FN --code $GENETIC_CODE --branches FG --srv $RATE_VARIATION --output $RESULTS_FILE --ci $CI --multiple-hits $MULTIPLE_HITS --site-multihit $SITE_MULTIHIT >> $PROGRESS_FILE"
+  mpirun -np $PROCS $HYPHY LIBPATH=$HYPHY_PATH ENV="TOLERATE_NUMERICAL_ERRORS=1;" $FEL --alignment $FN --tree $TREE_FN --code $GENETIC_CODE --branches FG --srv $RATE_VARIATION --output $RESULTS_FILE --ci $CI --multiple-hits $MULTIPLE_HITS --site-multihit $SITE_MULTIHIT >> $PROGRESS_FILE
 fi
 
 echo "Completed" > $STATUS_FILE
-