From 8c8248d6903591a1937a8c7aff38007e9b720fcf Mon Sep 17 00:00:00 2001
From: Qiang Zhang <45829450+qzhang503@users.noreply.github.com>
Date: Mon, 1 May 2023 11:13:22 -0500
Subject: [PATCH] v1.2.4.1

Speed optimzation
---
 R/msmsmatches.R | 5 -----
 R/scores.R      | 5 +++++
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/R/msmsmatches.R b/R/msmsmatches.R
index cecf892..6af969e 100644
--- a/R/msmsmatches.R
+++ b/R/msmsmatches.R
@@ -1354,11 +1354,6 @@ matchMS <- function (out_path = "~/mzion/outs",
                    add_ms2moverzs = add_ms2moverzs, 
                    add_ms2ints = add_ms2ints,
                    digits = digits)
-    
-    hadd_primatches(out_path = out_path, 
-                    add_ms2theos = add_ms2theos, add_ms2theos2 = add_ms2theos2, 
-                    add_ms2moverzs = add_ms2moverzs, add_ms2ints = add_ms2ints, 
-                    index_mgf_ms2 = index_mgf_ms2)
   }
   
   ## Peptide FDR 
diff --git a/R/scores.R b/R/scores.R
index 52610d3..0b2027f 100644
--- a/R/scores.R
+++ b/R/scores.R
@@ -713,6 +713,11 @@ calc_pepscores <- function (topn_ms2ions = 100L, type_ms2ions = "by",
               n_cores = detect_cores(16L), 
               digits = digits)
     
+  hadd_primatches(out_path = out_path, 
+                  add_ms2theos = add_ms2theos, add_ms2theos2 = add_ms2theos2, 
+                  add_ms2moverzs = add_ms2moverzs, add_ms2ints = add_ms2ints, 
+                  index_mgf_ms2 = index_mgf_ms2)
+  
   .savecall <- TRUE
   
   invisible(NULL)