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定稿版本，在论文投出之前不改了

This commit is contained in:
zzh 2025-03-05 10:24:52 +08:00
parent 62708dda77
commit ee45166765
3 changed files with 25 additions and 22 deletions
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6
src/markdup/markdup.cpp
View File

@ -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;
}

38
src/util/profiling.cpp
View File

@ -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

3
src/util/profiling.h
View File

@ -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 };