去掉了一些调试信息，把cout等输出都换成了spdlog，可以作为开源代码发布了，README还需要详细写一写
This commit is contained in:
parent
5d9a52e90b
commit
01d14d539f
|
|
@ -5,6 +5,5 @@ set(CMAKE_CXX_STANDARD_REQUIRED ON)
|
||||||
# set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread")
|
# set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread")
|
||||||
# set(CMAKE_BUILD_TYPE Debug)
|
# set(CMAKE_BUILD_TYPE Debug)
|
||||||
# set(CMAKE_BUILD_TYPE Release)
|
# set(CMAKE_BUILD_TYPE Release)
|
||||||
# add_definitions(-DSHOW_PERF)
|
|
||||||
add_definitions(-DSHOW_PERF=1)
|
add_definitions(-DSHOW_PERF=1)
|
||||||
add_subdirectory(src)
|
add_subdirectory(src)
|
||||||
11
README.md
11
README.md
|
|
@ -1,3 +1,10 @@
|
||||||
# markdups
|
# FastDup
|
||||||
|
|
||||||
mark duplicate，去除冗余
|
Identifies duplicate reads. This tool locates and tags duplicate reads in a coordinate ordered SAM or BAM file.
|
||||||
|
|
||||||
|
Use the same algorithm as picard MarkDuplicates and output identical results.
|
||||||
|
Use spdlog as log tool and the default level is 'info'.
|
||||||
|
|
||||||
|
### Features
|
||||||
|
|
||||||
|
* Fast -
|
||||||
|
|
@ -0,0 +1,111 @@
|
||||||
|
## StringHeader
|
||||||
|
# /home/zzh/work/ngs/FastDup/build/bin/fastdup --input /home/zzh/data/bam/normal_all.sam --output /home/zzh/data1/out.sam --metrics ./metrics.txt --num-threads 1 --create-index --index-format CSI --tag-duplicate-set-members
|
||||||
|
## StringHeader
|
||||||
|
# Started on: December 16, 2024 at 02:43:41 AM CST
|
||||||
|
|
||||||
|
## METRICS
|
||||||
|
LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED SECONDARY_OR_SUPPLEMENTARY_RDS UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE
|
||||||
|
normal 108919 66154888 117508 161395 67414 15058359 876584 0.227945 127582703
|
||||||
|
|
||||||
|
## HISTOGRAM Double
|
||||||
|
BIN CoverageMult
|
||||||
|
1 1.010249
|
||||||
|
2 1.611750
|
||||||
|
3 1.969882
|
||||||
|
4 2.183113
|
||||||
|
5 2.310070
|
||||||
|
6 2.385660
|
||||||
|
7 2.430666
|
||||||
|
8 2.457463
|
||||||
|
9 2.473417
|
||||||
|
10 2.482917
|
||||||
|
11 2.488573
|
||||||
|
12 2.491940
|
||||||
|
13 2.493945
|
||||||
|
14 2.495139
|
||||||
|
15 2.495850
|
||||||
|
16 2.496273
|
||||||
|
17 2.496525
|
||||||
|
18 2.496675
|
||||||
|
19 2.496764
|
||||||
|
20 2.496817
|
||||||
|
21 2.496849
|
||||||
|
22 2.496868
|
||||||
|
23 2.496879
|
||||||
|
24 2.496886
|
||||||
|
25 2.496890
|
||||||
|
26 2.496892
|
||||||
|
27 2.496894
|
||||||
|
28 2.496894
|
||||||
|
29 2.496895
|
||||||
|
30 2.496895
|
||||||
|
31 2.496895
|
||||||
|
32 2.496896
|
||||||
|
33 2.496896
|
||||||
|
34 2.496896
|
||||||
|
35 2.496896
|
||||||
|
36 2.496896
|
||||||
|
37 2.496896
|
||||||
|
38 2.496896
|
||||||
|
39 2.496896
|
||||||
|
40 2.496896
|
||||||
|
41 2.496896
|
||||||
|
42 2.496896
|
||||||
|
43 2.496896
|
||||||
|
44 2.496896
|
||||||
|
45 2.496896
|
||||||
|
46 2.496896
|
||||||
|
47 2.496896
|
||||||
|
48 2.496896
|
||||||
|
49 2.496896
|
||||||
|
50 2.496896
|
||||||
|
51 2.496896
|
||||||
|
52 2.496896
|
||||||
|
53 2.496896
|
||||||
|
54 2.496896
|
||||||
|
55 2.496896
|
||||||
|
56 2.496896
|
||||||
|
57 2.496896
|
||||||
|
58 2.496896
|
||||||
|
59 2.496896
|
||||||
|
60 2.496896
|
||||||
|
61 2.496896
|
||||||
|
62 2.496896
|
||||||
|
63 2.496896
|
||||||
|
64 2.496896
|
||||||
|
65 2.496896
|
||||||
|
66 2.496896
|
||||||
|
67 2.496896
|
||||||
|
68 2.496896
|
||||||
|
69 2.496896
|
||||||
|
70 2.496896
|
||||||
|
71 2.496896
|
||||||
|
72 2.496896
|
||||||
|
73 2.496896
|
||||||
|
74 2.496896
|
||||||
|
75 2.496896
|
||||||
|
76 2.496896
|
||||||
|
77 2.496896
|
||||||
|
78 2.496896
|
||||||
|
79 2.496896
|
||||||
|
80 2.496896
|
||||||
|
81 2.496896
|
||||||
|
82 2.496896
|
||||||
|
83 2.496896
|
||||||
|
84 2.496896
|
||||||
|
85 2.496896
|
||||||
|
86 2.496896
|
||||||
|
87 2.496896
|
||||||
|
88 2.496896
|
||||||
|
89 2.496896
|
||||||
|
90 2.496896
|
||||||
|
91 2.496896
|
||||||
|
92 2.496896
|
||||||
|
93 2.496896
|
||||||
|
94 2.496896
|
||||||
|
95 2.496896
|
||||||
|
96 2.496896
|
||||||
|
97 2.496896
|
||||||
|
98 2.496896
|
||||||
|
99 2.496896
|
||||||
|
100 2.496896
|
||||||
19
src/main.cpp
19
src/main.cpp
|
|
@ -1,6 +1,7 @@
|
||||||
#include <spdlog/cfg/env.h>
|
#include <spdlog/cfg/env.h>
|
||||||
#include <spdlog/sinks/stdout_color_sinks.h>
|
#include <spdlog/sinks/stdout_color_sinks.h>
|
||||||
#include <spdlog/spdlog.h>
|
#include <spdlog/spdlog.h>
|
||||||
|
#include <time.h>
|
||||||
|
|
||||||
#include <argparse/argparse.hpp>
|
#include <argparse/argparse.hpp>
|
||||||
#include <iostream>
|
#include <iostream>
|
||||||
|
|
@ -8,9 +9,9 @@
|
||||||
#include <set>
|
#include <set>
|
||||||
#include <string>
|
#include <string>
|
||||||
|
|
||||||
|
#include "fastdup_version.h"
|
||||||
#include "markdup/md_args.h"
|
#include "markdup/md_args.h"
|
||||||
#include "util/profiling.h"
|
#include "util/profiling.h"
|
||||||
#include "fastdup_version.h"
|
|
||||||
|
|
||||||
namespace nsgv {
|
namespace nsgv {
|
||||||
extern MarkDupsArg gMdArg;
|
extern MarkDupsArg gMdArg;
|
||||||
|
|
@ -18,6 +19,16 @@ extern MarkDupsArg gMdArg;
|
||||||
|
|
||||||
int MarkDuplicates();
|
int MarkDuplicates();
|
||||||
|
|
||||||
|
string get_current_time_str() {
|
||||||
|
time_t time_val;
|
||||||
|
struct tm *at;
|
||||||
|
char now[80];
|
||||||
|
time(&time_val);
|
||||||
|
at = localtime(&time_val);
|
||||||
|
strftime(now, 79, "%B %d, %Y at %I:%M:%S %p %Z", at);
|
||||||
|
return string(now);
|
||||||
|
}
|
||||||
|
|
||||||
int main(int argc, char *argv[]) {
|
int main(int argc, char *argv[]) {
|
||||||
// init log
|
// init log
|
||||||
spdlog::set_default_logger(spdlog::stderr_color_st("fastdup"));
|
spdlog::set_default_logger(spdlog::stderr_color_st("fastdup"));
|
||||||
|
|
@ -159,6 +170,12 @@ int main(int argc, char *argv[]) {
|
||||||
|
|
||||||
// std::cout << program << std::endl;
|
// std::cout << program << std::endl;
|
||||||
|
|
||||||
|
nsgv::gMdArg.START_TIME = get_current_time_str();
|
||||||
|
nsgv::gMdArg.CLI_STR = argv[0];
|
||||||
|
for (int i = 1; i < argc; ++i) {
|
||||||
|
nsgv::gMdArg.CLI_STR += " " + std::string(argv[i]);
|
||||||
|
}
|
||||||
|
|
||||||
try {
|
try {
|
||||||
program.parse_args(argc, argv);
|
program.parse_args(argc, argv);
|
||||||
nsgv::gMdArg.INPUT_FILE = program.get("--input");
|
nsgv::gMdArg.INPUT_FILE = program.get("--input");
|
||||||
|
|
|
||||||
|
|
@ -11,6 +11,7 @@ Date : 2023/10/23
|
||||||
#include <htslib/thread_pool.h>
|
#include <htslib/thread_pool.h>
|
||||||
#include <spdlog/spdlog.h>
|
#include <spdlog/spdlog.h>
|
||||||
|
|
||||||
|
#include <iomanip>
|
||||||
#include <vector>
|
#include <vector>
|
||||||
|
|
||||||
#include "dup_metrics.h"
|
#include "dup_metrics.h"
|
||||||
|
|
@ -36,6 +37,13 @@ PipelineArg gPipe;
|
||||||
|
|
||||||
};
|
};
|
||||||
|
|
||||||
|
// 字节缓冲区
|
||||||
|
struct ByteBuf {
|
||||||
|
uint8_t *buf = nullptr;
|
||||||
|
int size = 0; // 当前使用量
|
||||||
|
int capacity = 0; // 最大容量
|
||||||
|
};
|
||||||
|
|
||||||
/*
|
/*
|
||||||
* 获取文件名后缀
|
* 获取文件名后缀
|
||||||
*/
|
*/
|
||||||
|
|
@ -89,25 +97,283 @@ int MarkDuplicates() {
|
||||||
#endif
|
#endif
|
||||||
|
|
||||||
/* 冗余检查和标记 */
|
/* 冗余检查和标记 */
|
||||||
|
PROF_START(markdup_all);
|
||||||
pipelineMarkDups();
|
pipelineMarkDups();
|
||||||
|
PROF_END(gprof[GP_markdup_all], markdup_all);
|
||||||
|
|
||||||
/* 初始化输出文件 */
|
/* 标记冗余, 将处理后的结果写入文件 */
|
||||||
char modeout[12] = "wb";
|
char modeout[12] = "wb";
|
||||||
sam_open_mode(modeout + 1, nsgv::gMdArg.OUTPUT_FILE.c_str(), NULL);
|
sam_open_mode(modeout + 1, nsgv::gMdArg.OUTPUT_FILE.c_str(), NULL);
|
||||||
nsgv::gOutBamFp = sam_open(nsgv::gMdArg.OUTPUT_FILE.c_str(), modeout);
|
nsgv::gOutBamFp = sam_open(nsgv::gMdArg.OUTPUT_FILE.c_str(), modeout);
|
||||||
|
if (!nsgv::gOutBamFp) {
|
||||||
|
spdlog::error("[{}] create output sam/bam file failed.\n", __func__);
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
nsgv::gOutBamHeader = sam_hdr_dup(nsgv::gInBamHeader);
|
nsgv::gOutBamHeader = sam_hdr_dup(nsgv::gInBamHeader);
|
||||||
// 修改输出文件的header
|
// 修改输出文件的header
|
||||||
// sam_hdr_add_line(nsgv::gOutBamHeader, "PG", "ID", nsgv::gMdArg.PROGRAM_RECORD_ID.c_str(), "VN", FASTDUP_VERSION,
|
sam_hdr_add_line(nsgv::gOutBamHeader, "PG", "ID", nsgv::gMdArg.PROGRAM_RECORD_ID.c_str(), "VN", FASTDUP_VERSION,
|
||||||
// "CL",
|
"CL", nsgv::gMdArg.CLI_STR.c_str(), NULL);
|
||||||
// (nsgv::gMdArg.PROGRAM_RECORD_ID + " " + nsgv::gMdArg.GetArgValueString() + " " +
|
|
||||||
// nsgv::gMdArg.GetArgValueString())
|
|
||||||
// .c_str(),
|
|
||||||
// NULL);
|
|
||||||
|
|
||||||
// 用同样的线程池处理输出文件
|
// 用同样的线程数量处理输出文件
|
||||||
hts_set_opt(nsgv::gOutBamFp, HTS_OPT_BLOCK_SIZE, BAM_BLOCK_SIZE);
|
hts_set_opt(nsgv::gOutBamFp, HTS_OPT_BLOCK_SIZE, BAM_BLOCK_SIZE);
|
||||||
hts_set_opt(nsgv::gOutBamFp, HTS_OPT_THREAD_POOL, &htsPoolWrite);
|
hts_set_opt(nsgv::gOutBamFp, HTS_OPT_THREAD_POOL, &htsPoolWrite);
|
||||||
|
sam_close(nsgv::gInBamFp); // 重新打开bam文件
|
||||||
|
nsgv::gInBamFp = sam_open_format(nsgv::gMdArg.INPUT_FILE.c_str(), "r", nullptr);
|
||||||
|
if (!nsgv::gInBamFp) {
|
||||||
|
spdlog::error("[{}] load sam/bam file failed.\n", __func__);
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
hts_set_opt(nsgv::gInBamFp, HTS_OPT_BLOCK_SIZE, BAM_BLOCK_SIZE);
|
||||||
|
hts_set_opt(nsgv::gInBamFp, HTS_OPT_THREAD_POOL, &htsPoolRead);
|
||||||
|
nsgv::gInBamHeader = sam_hdr_read(nsgv::gInBamFp);
|
||||||
|
if (sam_hdr_write(nsgv::gOutBamFp, nsgv::gOutBamHeader) != 0) {
|
||||||
|
spdlog::error("failed writing header to \"{}\"", nsgv::gMdArg.OUTPUT_FILE);
|
||||||
|
sam_close(nsgv::gOutBamFp);
|
||||||
|
sam_close(nsgv::gInBamFp);
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
// 输出index文件
|
||||||
|
string indexFn = nsgv::gMdArg.OUTPUT_FILE + ".bai"; // min_shift = 0 是bai格式
|
||||||
|
if ("sam" == getFileExtension(nsgv::gMdArg.OUTPUT_FILE) || !nsgv::gMdArg.CREATE_INDEX) {
|
||||||
|
indexFn = "";
|
||||||
|
}
|
||||||
|
if (!indexFn.empty()) {
|
||||||
|
int index_min_shift = 0;
|
||||||
|
if (nsgv::gMdArg.INDEX_FORMAT == nsmd::IndexFormat::CSI) {
|
||||||
|
indexFn = nsgv::gMdArg.OUTPUT_FILE + ".csi";
|
||||||
|
index_min_shift = 14;
|
||||||
|
}
|
||||||
|
if (sam_idx_init(nsgv::gOutBamFp, nsgv::gOutBamHeader, 0 /*csi 14*/, indexFn.c_str()) < 0) {
|
||||||
|
spdlog::error("failed to open index \"{}\" for writing", indexFn);
|
||||||
|
sam_close(nsgv::gOutBamFp);
|
||||||
|
sam_close(nsgv::gInBamFp);
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
// 读取输入文件，标记冗余并输出
|
||||||
|
BamBufType inBuf(nsgv::gMdArg.DUPLEX_IO);
|
||||||
|
inBuf.Init(nsgv::gInBamFp, nsgv::gInBamHeader, nsgv::gMdArg.MAX_MEM);
|
||||||
|
|
||||||
|
DupIdxQueue<DupInfo> dupIdxQue, repIdxQue;
|
||||||
|
DupIdxQueue<int64_t> opticalIdxQue;
|
||||||
|
dupIdxQue.Init(&nsgv::gPipe.intersectData.dupIdxArr);
|
||||||
|
repIdxQue.Init(&nsgv::gPipe.intersectData.repIdxArr);
|
||||||
|
opticalIdxQue.Init(&nsgv::gPipe.intersectData.opticalDupIdxArr);
|
||||||
|
spdlog::info("{} duplicate reads found", dupIdxQue.Size());
|
||||||
|
|
||||||
|
uint64_t bamIdx = 0;
|
||||||
|
DupInfo dupIdx = dupIdxQue.Pop();
|
||||||
|
DupInfo repIdx = repIdxQue.Pop();
|
||||||
|
uint64_t opticalIdx = opticalIdxQue.Pop();
|
||||||
|
|
||||||
|
ByteBuf bytes;
|
||||||
|
bam1_t *bp = bam_init1();
|
||||||
|
bool isDup = false;
|
||||||
|
bool isOpticalDup = false;
|
||||||
|
bool isInDuplicateSet = false;
|
||||||
|
uint32_t representativeReadIndexInFile = 0;
|
||||||
|
uint32_t duplicateSetSize = 0;
|
||||||
|
|
||||||
|
int64_t realDupSize = 0;
|
||||||
|
|
||||||
|
// exit(0);
|
||||||
|
PROF_START(write);
|
||||||
|
while (inBuf.ReadStat() >= 0) {
|
||||||
|
PROF_START(final_read);
|
||||||
|
size_t readNum = inBuf.ReadBam();
|
||||||
|
PROF_END(gprof[GP_final_read], final_read);
|
||||||
|
PROF_PRINT_START(read_write);
|
||||||
|
for (size_t i = 0; i < readNum; ++i) {
|
||||||
|
BamWrap *bw = inBuf[i];
|
||||||
|
if (bam_copy1(bp, bw->b) == nullptr) {
|
||||||
|
spdlog::error("Can not copy sam record!");
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
bw->b = bp;
|
||||||
|
isDup = false;
|
||||||
|
isOpticalDup = false;
|
||||||
|
isInDuplicateSet = false;
|
||||||
|
|
||||||
|
// 删除原来的duplicate tag
|
||||||
|
if (nsgv::gMdArg.CLEAR_DT) {
|
||||||
|
uint8_t *oldTagVal = bam_aux_get(bw->b, nsgv::gMdArg.DUPLICATE_TYPE_TAG.c_str());
|
||||||
|
if (oldTagVal != NULL) bam_aux_del(bw->b, oldTagVal);
|
||||||
|
}
|
||||||
|
|
||||||
|
// 统计信息
|
||||||
|
if (bw->GetReadUnmappedFlag()) {
|
||||||
|
++nsgv::gMetrics.UNMAPPED_READS;
|
||||||
|
} else if (bw->IsSecondaryOrSupplementary()) {
|
||||||
|
++nsgv::gMetrics.SECONDARY_OR_SUPPLEMENTARY_RDS;
|
||||||
|
} else if (!bw->GetReadPairedFlag() || bw->GetMateUnmappedFlag()) {
|
||||||
|
++nsgv::gMetrics.UNPAIRED_READS_EXAMINED;
|
||||||
|
} else {
|
||||||
|
++nsgv::gMetrics.READ_PAIRS_EXAMINED; // will need to be divided by 2 at the end
|
||||||
|
}
|
||||||
|
|
||||||
|
/* 判断是否冗余 */
|
||||||
|
if (bamIdx == dupIdx) {
|
||||||
|
++realDupSize; // for test
|
||||||
|
isDup = true;
|
||||||
|
if (nsgv::gMdArg.TAG_DUPLICATE_SET_MEMBERS && dupIdx.dupSet != 0) {
|
||||||
|
isInDuplicateSet = true;
|
||||||
|
representativeReadIndexInFile = dupIdx.repIdx;
|
||||||
|
duplicateSetSize = dupIdx.dupSet;
|
||||||
|
}
|
||||||
|
|
||||||
|
// 为了防止小内存运行的时候，有重复的dupidx，这时候dup的repIdx和dupSetSize可能会有不同
|
||||||
|
while ((dupIdx = dupIdxQue.Pop()) == bamIdx);
|
||||||
|
if (opticalIdx == bamIdx)
|
||||||
|
isOpticalDup = true;
|
||||||
|
else if (opticalIdx < bamIdx) {
|
||||||
|
while ((opticalIdx = opticalIdxQue.Pop()) < bamIdx);
|
||||||
|
if (opticalIdx == bamIdx)
|
||||||
|
isOpticalDup = true;
|
||||||
|
}
|
||||||
|
|
||||||
|
// 添加冗余标识
|
||||||
|
bw->SetDuplicateReadFlag(true);
|
||||||
|
|
||||||
|
uint8_t *oldTagVal = bam_aux_get(bw->b, nsgv::gMdArg.DUPLICATE_TYPE_TAG.c_str());
|
||||||
|
if (oldTagVal != NULL) bam_aux_del(bw->b, oldTagVal);
|
||||||
|
|
||||||
|
if (isOpticalDup)
|
||||||
|
bam_aux_append(bw->b, nsgv::gMdArg.DUPLICATE_TYPE_TAG.c_str(), 'Z',
|
||||||
|
nsgv::gMdArg.DUPLICATE_TYPE_SEQUENCING.size() + 1,
|
||||||
|
(const uint8_t *)nsgv::gMdArg.DUPLICATE_TYPE_SEQUENCING.c_str());
|
||||||
|
else
|
||||||
|
bam_aux_append(bw->b, nsgv::gMdArg.DUPLICATE_TYPE_TAG.c_str(), 'Z',
|
||||||
|
nsgv::gMdArg.DUPLICATE_TYPE_LIBRARY.size() + 1,
|
||||||
|
(const uint8_t *)nsgv::gMdArg.DUPLICATE_TYPE_LIBRARY.c_str());
|
||||||
|
|
||||||
|
// 计算统计信息
|
||||||
|
if (!bw->IsSecondaryOrSupplementary() && !bw->GetReadUnmappedFlag()) {
|
||||||
|
// Update the duplication metrics
|
||||||
|
if (!bw->GetReadPairedFlag() || bw->GetMateUnmappedFlag()) {
|
||||||
|
++nsgv::gMetrics.UNPAIRED_READ_DUPLICATES;
|
||||||
|
} else {
|
||||||
|
++nsgv::gMetrics.READ_PAIR_DUPLICATES; // will need to be divided by 2 at the end
|
||||||
|
}
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
bw->SetDuplicateReadFlag(false);
|
||||||
|
}
|
||||||
|
if (nsgv::gMdArg.TAG_DUPLICATE_SET_MEMBERS && bamIdx == repIdx) { // repressent
|
||||||
|
isInDuplicateSet = true;
|
||||||
|
representativeReadIndexInFile = repIdx.repIdx;
|
||||||
|
duplicateSetSize = repIdx.dupSet;
|
||||||
|
while (repIdx == bamIdx || repIdx.dupSet == 0) {
|
||||||
|
if (repIdxQue.Size() > 0)
|
||||||
|
repIdx = repIdxQue.Pop();
|
||||||
|
else {
|
||||||
|
repIdx = -1;
|
||||||
|
break;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if (nsgv::gMdArg.TAG_DUPLICATE_SET_MEMBERS && isInDuplicateSet) {
|
||||||
|
if (!bw->IsSecondaryOrSupplementary() && !bw->GetReadUnmappedFlag()) {
|
||||||
|
// cerr << bamIdx << " " << representativeReadIndexInFile << " " << duplicateSetSize << endl;
|
||||||
|
uint8_t *oldTagVal = bam_aux_get(bw->b, nsgv::gMdArg.DUPLICATE_SET_INDEX_TAG.c_str());
|
||||||
|
if (oldTagVal != NULL)
|
||||||
|
bam_aux_del(bw->b, oldTagVal);
|
||||||
|
bam_aux_append(bw->b, nsgv::gMdArg.DUPLICATE_SET_INDEX_TAG.c_str(), 'i',
|
||||||
|
sizeof(representativeReadIndexInFile), (uint8_t *)&representativeReadIndexInFile);
|
||||||
|
oldTagVal = bam_aux_get(bw->b, nsgv::gMdArg.DUPLICATE_SET_SIZE_TAG.c_str());
|
||||||
|
if (oldTagVal != NULL)
|
||||||
|
bam_aux_del(bw->b, oldTagVal);
|
||||||
|
bam_aux_append(bw->b, nsgv::gMdArg.DUPLICATE_SET_SIZE_TAG.c_str(), 'i', sizeof(duplicateSetSize),
|
||||||
|
(const uint8_t *)&duplicateSetSize);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
// 每个read都要写到output，只是添加标识，或者删掉这些冗余record
|
||||||
|
++bamIdx;
|
||||||
|
if (isDup && nsgv::gMdArg.REMOVE_DUPLICATES) {
|
||||||
|
continue;
|
||||||
|
}
|
||||||
|
if (isOpticalDup && nsgv::gMdArg.REMOVE_SEQUENCING_DUPLICATES) {
|
||||||
|
continue;
|
||||||
|
}
|
||||||
|
if (!nsgv::gMdArg.PROGRAM_RECORD_ID.empty() && nsgv::gMdArg.ADD_PG_TAG_TO_READS) {
|
||||||
|
uint8_t *oldTagVal = bam_aux_get(bw->b, "PG");
|
||||||
|
if (oldTagVal != NULL)
|
||||||
|
bam_aux_del(bw->b, oldTagVal);
|
||||||
|
bam_aux_append(bw->b, "PG", 'Z', nsgv::gMdArg.PROGRAM_RECORD_ID.size() + 1,
|
||||||
|
(const uint8_t *)nsgv::gMdArg.PROGRAM_RECORD_ID.c_str());
|
||||||
|
}
|
||||||
|
#if 0
|
||||||
|
if (sam_write1(nsgv::gOutBamFp, nsgv::gOutBamHeader, bw->b) < 0) {
|
||||||
|
spdlog::error("failed writing sam record to \"{}\"", nsgv::gMdArg.OUTPUT_FILE.c_str());
|
||||||
|
sam_close(nsgv::gOutBamFp);
|
||||||
|
sam_close(nsgv::gInBamFp);
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
#endif
|
||||||
|
}
|
||||||
|
inBuf.ClearAll();
|
||||||
|
PROF_PRINT_END(read_write);
|
||||||
|
spdlog::info("write {} reads to output", readNum);
|
||||||
|
}
|
||||||
|
bam_destroy1(bp);
|
||||||
|
|
||||||
|
// 计算统计信息
|
||||||
|
nsgv::gMetrics.READ_PAIRS_EXAMINED /= 2;
|
||||||
|
nsgv::gMetrics.READ_PAIR_DUPLICATES /= 2;
|
||||||
|
for (auto &arr : nsgv::gPipe.intersectData.opticalDupIdxArr)
|
||||||
|
nsgv::gMetrics.READ_PAIR_OPTICAL_DUPLICATES += arr.size();
|
||||||
|
nsgv::gMetrics.READ_PAIR_OPTICAL_DUPLICATES = nsgv::gMetrics.READ_PAIR_OPTICAL_DUPLICATES / 2;
|
||||||
|
nsgv::gMetrics.ESTIMATED_LIBRARY_SIZE =
|
||||||
|
estimateLibrarySize(nsgv::gMetrics.READ_PAIRS_EXAMINED - nsgv::gMetrics.READ_PAIR_OPTICAL_DUPLICATES,
|
||||||
|
nsgv::gMetrics.READ_PAIRS_EXAMINED - nsgv::gMetrics.READ_PAIR_DUPLICATES);
|
||||||
|
if (nsgv::gMetrics.UNPAIRED_READS_EXAMINED + nsgv::gMetrics.READ_PAIRS_EXAMINED != 0) {
|
||||||
|
nsgv::gMetrics.PERCENT_DUPLICATION =
|
||||||
|
(nsgv::gMetrics.UNPAIRED_READ_DUPLICATES + nsgv::gMetrics.READ_PAIR_DUPLICATES * 2) /
|
||||||
|
(double)(nsgv::gMetrics.UNPAIRED_READS_EXAMINED + nsgv::gMetrics.READ_PAIRS_EXAMINED * 2);
|
||||||
|
} else {
|
||||||
|
nsgv::gMetrics.PERCENT_DUPLICATION = 0;
|
||||||
|
}
|
||||||
|
calculateRoiHistogram(nsgv::gMetrics);
|
||||||
|
|
||||||
|
// 将统计信息写到文件里
|
||||||
|
if (!nsgv::gMdArg.METRICS_FILE.empty()) {
|
||||||
|
ofstream ofsM(nsgv::gMdArg.METRICS_FILE);
|
||||||
|
ofsM << "## StringHeader" << endl;
|
||||||
|
ofsM << "# " << nsgv::gMdArg.CLI_STR << endl;
|
||||||
|
ofsM << "## StringHeader" << endl;
|
||||||
|
ofsM << "# Started on: " << nsgv::gMdArg.START_TIME << endl << endl;
|
||||||
|
ofsM << "## METRICS"
|
||||||
|
<< endl;
|
||||||
|
ofsM << "LIBRARY\tUNPAIRED_READS_EXAMINED\tREAD_PAIRS_EXAMINED\tSECONDARY_OR_SUPPLEMENTARY_RDS\tUNMAPPED_"
|
||||||
|
"READS\tUNPAIRED_READ_DUPLICATES\tREAD_PAIR_DUPLICATES\tREAD_PAIR_OPTICAL_DUPLICATES\tPERCENT_"
|
||||||
|
"DUPLICATION\tESTIMATED_LIBRARY_SIZE"
|
||||||
|
<< endl;
|
||||||
|
ofsM << nsgv::gMetrics.LIBRARY << "\t" << nsgv::gMetrics.UNPAIRED_READS_EXAMINED << "\t" << nsgv::gMetrics.READ_PAIRS_EXAMINED
|
||||||
|
<< "\t" << nsgv::gMetrics.SECONDARY_OR_SUPPLEMENTARY_RDS << "\t" << nsgv::gMetrics.UNMAPPED_READS << "\t"
|
||||||
|
<< nsgv::gMetrics.UNPAIRED_READ_DUPLICATES << "\t" << nsgv::gMetrics.READ_PAIR_DUPLICATES << "\t"
|
||||||
|
<< nsgv::gMetrics.READ_PAIR_OPTICAL_DUPLICATES << "\t" << nsgv::gMetrics.PERCENT_DUPLICATION << "\t"
|
||||||
|
<< nsgv::gMetrics.ESTIMATED_LIBRARY_SIZE << endl
|
||||||
|
<< endl;
|
||||||
|
ofsM << "## HISTOGRAM\tDouble" << endl;
|
||||||
|
ofsM << "BIN CoverageMult" << endl;
|
||||||
|
for (int i = 1; i <= 100; ++i) {
|
||||||
|
ofsM << i << "\t" << std::fixed << std::setprecision(6) << nsgv::gMetrics.CoverageMult[i] << endl;
|
||||||
|
}
|
||||||
|
ofsM.close();
|
||||||
|
}
|
||||||
|
PROF_END(gprof[GP_write], write);
|
||||||
|
|
||||||
|
if (!indexFn.empty() && sam_idx_save(nsgv::gOutBamFp) < 0) {
|
||||||
|
spdlog::error("writing index failed");
|
||||||
|
sam_close(nsgv::gOutBamFp);
|
||||||
|
sam_close(nsgv::gInBamFp);
|
||||||
|
return -1;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* 关闭文件，收尾清理 */
|
||||||
|
sam_close(nsgv::gOutBamFp);
|
||||||
|
sam_close(nsgv::gInBamFp);
|
||||||
|
|
||||||
return 0;
|
return 0;
|
||||||
}
|
}
|
||||||
|
|
@ -256,14 +256,9 @@ struct MarkDupsArg {
|
||||||
/* Add PG tag to each read in a SAM or BAM (PGTagArgumentCollection)*/
|
/* Add PG tag to each read in a SAM or BAM (PGTagArgumentCollection)*/
|
||||||
bool ADD_PG_TAG_TO_READS = true;
|
bool ADD_PG_TAG_TO_READS = true;
|
||||||
|
|
||||||
// 解析参数
|
// 命令行字符串
|
||||||
void ParseArgument(int argc, char **argv);
|
string CLI_STR;
|
||||||
|
|
||||||
void PrintArgValue();
|
|
||||||
string GetArgValueString();
|
|
||||||
|
|
||||||
static void PrintHelp();
|
|
||||||
|
|
||||||
static void PrintVersion();
|
|
||||||
|
|
||||||
|
// 开始运行时间
|
||||||
|
string START_TIME;
|
||||||
};
|
};
|
||||||
|
|
@ -2,6 +2,7 @@
|
||||||
|
|
||||||
#include <klib/kthread.h>
|
#include <klib/kthread.h>
|
||||||
#include <pthread.h>
|
#include <pthread.h>
|
||||||
|
#include <spdlog/spdlog.h>
|
||||||
|
|
||||||
#include <algorithm>
|
#include <algorithm>
|
||||||
#include <iostream>
|
#include <iostream>
|
||||||
|
|
@ -16,7 +17,6 @@
|
||||||
#include "util/profiling.h"
|
#include "util/profiling.h"
|
||||||
#include "util/yarn.h"
|
#include "util/yarn.h"
|
||||||
|
|
||||||
using std::cout;
|
|
||||||
using std::vector;
|
using std::vector;
|
||||||
|
|
||||||
namespace nsgv {
|
namespace nsgv {
|
||||||
|
|
@ -247,7 +247,6 @@ static void markdups(MarkDupDataArg *arg) {
|
||||||
static inline void getIntersectData(vector<ReadEnds> &leftArr, vector<ReadEnds> &rightArr, vector<ReadEnds> *dst,
|
static inline void getIntersectData(vector<ReadEnds> &leftArr, vector<ReadEnds> &rightArr, vector<ReadEnds> *dst,
|
||||||
bool isPairCmp = false) {
|
bool isPairCmp = false) {
|
||||||
if (leftArr.empty() || rightArr.empty()) {
|
if (leftArr.empty() || rightArr.empty()) {
|
||||||
// cout << "bad size: " << leftArr.size() << '\t' << rightArr.size() << endl;
|
|
||||||
return;
|
return;
|
||||||
}
|
}
|
||||||
const size_t leftEndIdx = leftArr.size() - 1;
|
const size_t leftEndIdx = leftArr.size() - 1;
|
||||||
|
|
@ -782,7 +781,7 @@ static void *pipeRead(void *data) {
|
||||||
yarn::TWIST(pipeArg.readSig, yarn::BY, 1); // 读入了一轮数据
|
yarn::TWIST(pipeArg.readSig, yarn::BY, 1); // 读入了一轮数据
|
||||||
break;
|
break;
|
||||||
}
|
}
|
||||||
cout << "read num: " << readNum << "\t" << readNumSum << '\t' << pipeArg.readOrder << endl;
|
spdlog::info("{} reads processed in {} round", readNum, pipeArg.readOrder);
|
||||||
|
|
||||||
pipeArg.readData.bams = inBamBuf.GetBamArr();
|
pipeArg.readData.bams = inBamBuf.GetBamArr();
|
||||||
|
|
||||||
|
|
@ -794,7 +793,7 @@ static void *pipeRead(void *data) {
|
||||||
pipeArg.readOrder += 1; // for next
|
pipeArg.readOrder += 1; // for next
|
||||||
yarn::TWIST(pipeArg.readSig, yarn::BY, 1); // 读入了一轮数据
|
yarn::TWIST(pipeArg.readSig, yarn::BY, 1); // 读入了一轮数据
|
||||||
}
|
}
|
||||||
cout << "total reads: " << readNumSum << endl;
|
spdlog::info("total reads processed {}", readNumSum);
|
||||||
return 0;
|
return 0;
|
||||||
}
|
}
|
||||||
static void *pipeGenRE(void *data) {
|
static void *pipeGenRE(void *data) {
|
||||||
|
|
@ -825,7 +824,6 @@ static void *pipeGenRE(void *data) {
|
||||||
break;
|
break;
|
||||||
}
|
}
|
||||||
/* 处理bam，生成readends */
|
/* 处理bam，生成readends */
|
||||||
// cout << "genRE order: " << pipeArg.genREOrder << "\t" << pipeArg.readData.bamStartIdx << endl;
|
|
||||||
PROF_START(gen);
|
PROF_START(gen);
|
||||||
doGenRE(pipeArg);
|
doGenRE(pipeArg);
|
||||||
// usleep(200000);
|
// usleep(200000);
|
||||||
|
|
@ -836,7 +834,6 @@ static void *pipeGenRE(void *data) {
|
||||||
yarn::TWIST(pipeArg.genRESig, yarn::BY, 1);
|
yarn::TWIST(pipeArg.genRESig, yarn::BY, 1);
|
||||||
yarn::TWIST(pipeArg.readSig, yarn::BY, -1); // 使用了一次读入的数据
|
yarn::TWIST(pipeArg.readSig, yarn::BY, -1); // 使用了一次读入的数据
|
||||||
}
|
}
|
||||||
cout << "pipe gen reads" << endl;
|
|
||||||
return 0;
|
return 0;
|
||||||
}
|
}
|
||||||
static void *pipeSort(void *data) {
|
static void *pipeSort(void *data) {
|
||||||
|
|
@ -867,7 +864,6 @@ static void *pipeSort(void *data) {
|
||||||
break;
|
break;
|
||||||
}
|
}
|
||||||
/* 排序 readends */
|
/* 排序 readends */
|
||||||
// cout << "sort order: " << pipeArg.sortOrder << endl;
|
|
||||||
PROF_START(sort);
|
PROF_START(sort);
|
||||||
doSort(pipeArg);
|
doSort(pipeArg);
|
||||||
PROF_END(gprof[GP_sort], sort);
|
PROF_END(gprof[GP_sort], sort);
|
||||||
|
|
@ -879,7 +875,6 @@ static void *pipeSort(void *data) {
|
||||||
pipeArg.sortOrder += 1;
|
pipeArg.sortOrder += 1;
|
||||||
yarn::TWIST(pipeArg.sortSig, yarn::BY, 1);
|
yarn::TWIST(pipeArg.sortSig, yarn::BY, 1);
|
||||||
}
|
}
|
||||||
cout << "end pipe sort" << endl;
|
|
||||||
return 0;
|
return 0;
|
||||||
}
|
}
|
||||||
static void *pipeMarkDup(void *data) {
|
static void *pipeMarkDup(void *data) {
|
||||||
|
|
@ -910,7 +905,6 @@ static void *pipeMarkDup(void *data) {
|
||||||
break;
|
break;
|
||||||
}
|
}
|
||||||
/* 冗余检测 readends */
|
/* 冗余检测 readends */
|
||||||
// cout << "markdup order: " << pipeArg.markDupOrder << endl;
|
|
||||||
PROF_START(markdup);
|
PROF_START(markdup);
|
||||||
doMarkDup(pipeArg);
|
doMarkDup(pipeArg);
|
||||||
PROF_END(gprof[GP_markdup], markdup);
|
PROF_END(gprof[GP_markdup], markdup);
|
||||||
|
|
@ -921,7 +915,6 @@ static void *pipeMarkDup(void *data) {
|
||||||
pipeArg.markDupOrder += 1;
|
pipeArg.markDupOrder += 1;
|
||||||
yarn::TWIST(pipeArg.markDupSig, yarn::BY, 1);
|
yarn::TWIST(pipeArg.markDupSig, yarn::BY, 1);
|
||||||
}
|
}
|
||||||
cout << "end pipe markdup" << endl;
|
|
||||||
return 0;
|
return 0;
|
||||||
}
|
}
|
||||||
static void *pipeIntersect(void *data) {
|
static void *pipeIntersect(void *data) {
|
||||||
|
|
@ -953,7 +946,6 @@ static void *pipeIntersect(void *data) {
|
||||||
|
|
||||||
pipeArg.intersectOrder += 1;
|
pipeArg.intersectOrder += 1;
|
||||||
}
|
}
|
||||||
cout << "end pipe intersect" << endl;
|
|
||||||
return 0;
|
return 0;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
@ -1060,56 +1052,6 @@ static void parallelPipeline() {
|
||||||
PROF_START(merge_result);
|
PROF_START(merge_result);
|
||||||
mergeAllTask(pipeArg);
|
mergeAllTask(pipeArg);
|
||||||
PROF_END(gprof[GP_merge_result], merge_result);
|
PROF_END(gprof[GP_merge_result], merge_result);
|
||||||
|
|
||||||
int64_t dupNum = 0;
|
|
||||||
int64_t opticalDupNum = 0;
|
|
||||||
for (auto &arr : pipeArg.intersectData.dupIdxArr) dupNum += arr.size();
|
|
||||||
for (auto &arr : pipeArg.intersectData.opticalDupIdxArr) opticalDupNum += arr.size();
|
|
||||||
|
|
||||||
map<int64_t, int> dup;
|
|
||||||
#if 0
|
|
||||||
int taskSeq = 0;
|
|
||||||
for (auto &arr : pipeArg.intersectData.dupIdxArr) {
|
|
||||||
for (auto idx : arr) {
|
|
||||||
if (dup.find(idx.idx) != dup.end()) {
|
|
||||||
//if (taskSeq - 1 > dup[idx])
|
|
||||||
cout << "dup index: " << dup[idx] << '\t' << taskSeq << '\t' << idx << endl;
|
|
||||||
}
|
|
||||||
dup[idx.idx] = taskSeq;
|
|
||||||
}
|
|
||||||
// cout << taskSeq << "\t" << arr.size() << endl;
|
|
||||||
taskSeq++;
|
|
||||||
}
|
|
||||||
#endif
|
|
||||||
|
|
||||||
cout << "Final read order: " << pipeArg.readOrder << endl;
|
|
||||||
cout << "Final gen order: " << pipeArg.genREOrder << endl;
|
|
||||||
cout << "Final sort order: " << pipeArg.sortOrder << endl;
|
|
||||||
cout << "Final mark order: " << pipeArg.markDupOrder << endl;
|
|
||||||
cout << "Final inter order: " << pipeArg.intersectOrder << endl;
|
|
||||||
|
|
||||||
// cout << "w read time : " << tm_arr[10].acc_seconds_elapsed() << endl;
|
|
||||||
// cout << "w gen time : " << tm_arr[11].acc_seconds_elapsed() << endl;
|
|
||||||
// cout << "w sort time : " << tm_arr[12].acc_seconds_elapsed() << endl;
|
|
||||||
// cout << "w markdup time : " << tm_arr[13].acc_seconds_elapsed() << endl;
|
|
||||||
// cout << "w intersect time: " << tm_arr[14].acc_seconds_elapsed() << endl;
|
|
||||||
//
|
|
||||||
// cout << "w1 gen time : " << tm_arr[21].acc_seconds_elapsed() << endl;
|
|
||||||
// cout << "w1 sort time : " << tm_arr[22].acc_seconds_elapsed() << endl;
|
|
||||||
// cout << "w1 markdup time : " << tm_arr[23].acc_seconds_elapsed() << endl;
|
|
||||||
//
|
|
||||||
// cout << "read time : " << tm_arr[0].acc_seconds_elapsed() << endl;
|
|
||||||
// cout << "gen time : " << tm_arr[1].acc_seconds_elapsed() << endl;
|
|
||||||
// cout << "sort time : " << tm_arr[2].acc_seconds_elapsed() << endl;
|
|
||||||
// cout << "markdup time : " << tm_arr[3].acc_seconds_elapsed() << endl;
|
|
||||||
// cout << "intersect time: " << tm_arr[4].acc_seconds_elapsed() << endl;
|
|
||||||
//
|
|
||||||
// cout << "copy time: " << tm_arr[5].acc_seconds_elapsed() << endl;
|
|
||||||
// cout << "merge al6 time: " << tm_arr[6].acc_seconds_elapsed() << endl;
|
|
||||||
//
|
|
||||||
cout << "dup num : " << dupNum << "\t" << dup.size() << endl;
|
|
||||||
cout << "optical dup num : " << opticalDupNum / 2 << "\t" << opticalDupNum << endl;
|
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
/* 并行流水线方式处理数据，标记冗余 */
|
/* 并行流水线方式处理数据，标记冗余 */
|
||||||
|
|
@ -1133,7 +1075,7 @@ void pipelineMarkDups() {
|
||||||
if (readNum < 1) {
|
if (readNum < 1) {
|
||||||
break;
|
break;
|
||||||
}
|
}
|
||||||
cout << "read num: " << readNum << "\t" << readNumSum << '\t' << pipeArg.readOrder << endl;
|
spdlog::info("{} reads processed in {} round", readNum, pipeArg.readOrder);
|
||||||
|
|
||||||
pipeArg.readData.bams = inBamBuf.GetBamArr();
|
pipeArg.readData.bams = inBamBuf.GetBamArr();
|
||||||
pipeArg.readData.bamStartIdx = readNumSum;
|
pipeArg.readData.bamStartIdx = readNumSum;
|
||||||
|
|
@ -1158,32 +1100,4 @@ void pipelineMarkDups() {
|
||||||
pipeArg.readOrder += 1; // for next
|
pipeArg.readOrder += 1; // for next
|
||||||
}
|
}
|
||||||
mergeAllTask(pipeArg);
|
mergeAllTask(pipeArg);
|
||||||
|
|
||||||
int64_t dupNum = 0;
|
|
||||||
int64_t opticalDupNum = 0;
|
|
||||||
for (auto &arr : pipeArg.intersectData.dupIdxArr) dupNum += arr.size();
|
|
||||||
for (auto &arr : pipeArg.intersectData.opticalDupIdxArr) opticalDupNum += arr.size();
|
|
||||||
|
|
||||||
map<int64_t, int> dup;
|
|
||||||
#if 0
|
|
||||||
int taskSeq = 0;
|
|
||||||
for (auto &arr : pipeArg.intersectData.dupIdxArr) {
|
|
||||||
for (auto idx : arr) {
|
|
||||||
if (dup.find(idx.idx) != dup.end()) {
|
|
||||||
cout << "dup index: " << dup[idx] << '\t' << taskSeq << '\t' << idx << endl;
|
|
||||||
}
|
|
||||||
dup[idx.idx] = taskSeq;
|
|
||||||
}
|
|
||||||
taskSeq++;
|
|
||||||
}
|
|
||||||
#endif
|
|
||||||
|
|
||||||
cout << "total reads: " << readNumSum << endl;
|
|
||||||
cout << "Final read order: " << pipeArg.readOrder << endl;
|
|
||||||
cout << "Final gen order: " << pipeArg.genREOrder << endl;
|
|
||||||
cout << "Final sort order: " << pipeArg.sortOrder << endl;
|
|
||||||
cout << "Final mark order: " << pipeArg.markDupOrder << endl;
|
|
||||||
cout << "Final inter order: " << pipeArg.intersectOrder << endl;
|
|
||||||
cout << "dup num : " << dupNum << "\t" << dup.size() << endl;
|
|
||||||
cout << "optical dup num : " << opticalDupNum / 2 << "\t" << opticalDupNum << endl;
|
|
||||||
}
|
}
|
||||||
|
|
@ -32,6 +32,7 @@ struct PhysicalLocation {
|
||||||
int16_t tile = -1;
|
int16_t tile = -1;
|
||||||
// int32_t x = -1;
|
// int32_t x = -1;
|
||||||
// int32_t y = -1;
|
// int32_t y = -1;
|
||||||
|
// This is a bug in picard Markduplicates, because some tile coordinates exceede the range of int16_t
|
||||||
int16_t x = -1;
|
int16_t x = -1;
|
||||||
int16_t y = -1;
|
int16_t y = -1;
|
||||||
};
|
};
|
||||||
|
|
|
||||||
|
|
@ -68,6 +68,9 @@ int DisplayProfiling(int nthread) {
|
||||||
PRINT_GP(merge_markdup);
|
PRINT_GP(merge_markdup);
|
||||||
PRINT_GP(merge_update);
|
PRINT_GP(merge_update);
|
||||||
PRINT_GP(merge_add);
|
PRINT_GP(merge_add);
|
||||||
|
PRINT_GP(markdup_all);
|
||||||
|
PRINT_GP(final_read);
|
||||||
|
PRINT_GP(write);
|
||||||
|
|
||||||
PRINT_TP(gen, nthread);
|
PRINT_TP(gen, nthread);
|
||||||
PRINT_TP(sort_frag, nthread);
|
PRINT_TP(sort_frag, nthread);
|
||||||
|
|
|
||||||
|
|
@ -25,9 +25,15 @@ extern uint64_t gprof[LIM_GLOBAL_PROF_TYPE];
|
||||||
#define PROF_START(tmp_time) uint64_t prof_tmp_##tmp_time = RealtimeMsec()
|
#define PROF_START(tmp_time) uint64_t prof_tmp_##tmp_time = RealtimeMsec()
|
||||||
#define PROF_START_AGAIN(tmp_time) prof_tmp_##tmp_time = RealtimeMsec()
|
#define PROF_START_AGAIN(tmp_time) prof_tmp_##tmp_time = RealtimeMsec()
|
||||||
#define PROF_END(result, tmp_time) result += RealtimeMsec() - prof_tmp_##tmp_time
|
#define PROF_END(result, tmp_time) result += RealtimeMsec() - prof_tmp_##tmp_time
|
||||||
|
#define PROF_PRINT_START(tmp_time) uint64_t tmp_time = RealtimeMsec()
|
||||||
|
#define PROF_PRINT_END(tmp_time) \
|
||||||
|
tmp_time = RealtimeMsec() - tmp_time; \
|
||||||
|
fprintf(stderr, "time %-15s: %0.2lfs\n", #tmp_time, tmp_time * 1.0 / proc_freq)
|
||||||
#else
|
#else
|
||||||
#define PROF_START(tmp_time)
|
#define PROF_START(tmp_time)
|
||||||
#define PROF_END(result, tmp_time)
|
#define PROF_END(result, tmp_time)
|
||||||
|
#define PROF_PRINT_START(tmp_time)
|
||||||
|
#define PROF_PRINT_END(tmp_time)
|
||||||
#endif
|
#endif
|
||||||
|
|
||||||
// GLOBAL
|
// GLOBAL
|
||||||
|
|
@ -51,7 +57,10 @@ enum {
|
||||||
GP_merge_match,
|
GP_merge_match,
|
||||||
GP_merge_markdup,
|
GP_merge_markdup,
|
||||||
GP_merge_update,
|
GP_merge_update,
|
||||||
GP_merge_add
|
GP_merge_add,
|
||||||
|
GP_markdup_all,
|
||||||
|
GP_final_read,
|
||||||
|
GP_write
|
||||||
};
|
};
|
||||||
// THREAD
|
// 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 };
|
enum { TP_0 = 0, TP_1, TP_2, TP_3, TP_4, TP_5, TP_6, TP_7, TP_8, TP_9, TP_10 };
|
||||||
|
|
|
||||||
Loading…
Reference in New Issue