From ee45166765cd9eb50e92bd941645d02de87ef5f8 Mon Sep 17 00:00:00 2001
From: zzh <zzhofhust@gmail.com>
Date: Wed, 5 Mar 2025 10:24:52 +0800
Subject: [PATCH] =?UTF-8?q?=E5=AE=9A=E7=A8=BF=E7=89=88=E6=9C=AC=EF=BC=8C?=
 =?UTF-8?q?=E5=9C=A8=E8=AE=BA=E6=96=87=E6=8A=95=E5=87=BA=E4=B9=8B=E5=89=8D?=
 =?UTF-8?q?=E4=B8=8D=E6=94=B9=E4=BA=86?=
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---
 src/markdup/markdup.cpp |  6 +++---
 src/util/profiling.cpp  | 38 ++++++++++++++++++++------------------
 src/util/profiling.h    |  3 ++-
 3 files changed, 25 insertions(+), 22 deletions(-)

diff --git a/src/markdup/markdup.cpp b/src/markdup/markdup.cpp
index 432b617..e844315 100644
--- a/src/markdup/markdup.cpp
+++ b/src/markdup/markdup.cpp
@@ -57,7 +57,7 @@ static string getFileExtension(const string &filename) {
 
 // entrance of mark duplicates
 int MarkDuplicates() {
-
+    PROF_START(whole_process);
     /* 初始化一些参数和变量*/
     nsgv::gNameParsers.resize(nsgv::gMdArg.NUM_THREADS);
     for (auto &parser : nsgv::gNameParsers)
@@ -154,8 +154,6 @@ int MarkDuplicates() {
     spdlog::info("{} optical reads found", opticalIdxQue.Size());
     // spdlog::info("{} represent reads found", repIdxQue.Size());
 
-    // return 0;
-
     uint64_t bamIdx = 0;
     DupInfo dupIdx = dupIdxQue.Pop();
     DupInfo repIdx = repIdxQue.Pop();
@@ -366,5 +364,7 @@ int MarkDuplicates() {
     sam_close(nsgv::gOutBamFp);
     sam_close(nsgv::gInBamFp);
 
+    PROF_END(gprof[GP_whole_process], whole_process);
+
     return 0;
 }
\ No newline at end of file
diff --git a/src/util/profiling.cpp b/src/util/profiling.cpp
index 7173483..17833a2 100644
--- a/src/util/profiling.cpp
+++ b/src/util/profiling.cpp
@@ -49,32 +49,34 @@ int DisplayProfiling(int nthread) {
 
 #ifdef SHOW_PERF
     fprintf(stderr, "\n");
-    PRINT_GP(read_wait);
-    PRINT_GP(gen_wait);
-    PRINT_GP(sort_wait);
-    PRINT_GP(markdup_wait);
-    PRINT_GP(intersect_wait);
+    // PRINT_GP(read_wait);
+    // PRINT_GP(gen_wait);
+    // PRINT_GP(sort_wait);
+    // PRINT_GP(markdup_wait);
+    // PRINT_GP(intersect_wait);
     PRINT_GP(read);
     PRINT_GP(gen);
     PRINT_GP(sort);
     PRINT_GP(markdup);
     PRINT_GP(intersect);
-    PRINT_GP(merge_result);
-    PRINT_GP(sort_pair);
-    PRINT_GP(sort_frag);
-    PRINT_GP(markdup_pair);
-    PRINT_GP(markdup_frag);
-    PRINT_GP(merge_match);
-    PRINT_GP(merge_markdup);
-    PRINT_GP(merge_update);
-    PRINT_GP(merge_add);
+    // PRINT_GP(merge_result);
+    // PRINT_GP(sort_pair);
+    // PRINT_GP(sort_frag);
+    // PRINT_GP(markdup_pair);
+    // PRINT_GP(markdup_frag);
+    // PRINT_GP(merge_match);
+    // PRINT_GP(merge_markdup);
+    // PRINT_GP(merge_update);
+    // PRINT_GP(merge_add);
     PRINT_GP(markdup_all);
-    PRINT_GP(final_read);
+    // PRINT_GP(final_read);
     PRINT_GP(write);
+    PRINT_GP(whole_process);
+    
+    // PRINT_TP(gen, nthread);
+    // PRINT_TP(sort_frag, nthread);
+    // PRINT_TP(sort_pair, nthread);
 
-    PRINT_TP(gen, nthread);
-    PRINT_TP(sort_frag, nthread);
-    PRINT_TP(sort_pair, nthread);
     fprintf(stderr, "\n");
 #endif
 
diff --git a/src/util/profiling.h b/src/util/profiling.h
index d4bddd6..8986d32 100644
--- a/src/util/profiling.h
+++ b/src/util/profiling.h
@@ -60,7 +60,8 @@ enum {
     GP_merge_add,
     GP_markdup_all,
     GP_final_read,
-    GP_write
+    GP_write,
+    GP_whole_process
 };
 // THREAD
 enum { TP_0 = 0, TP_1, TP_2, TP_3, TP_4, TP_5, TP_6, TP_7, TP_8, TP_9, TP_10 };