对5.1G的数据，串行结果正确了，并行结果还没测试
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@ -189,22 +189,24 @@ int SerialBQSR(AuxVar &aux) {
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sd.applyTransformations();
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PROF_END(gprof[GP_clip_read], clip_read);
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const char* qname = bam_get_qname(sd.bw->b);
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//const char* qname = bam_get_qname(sd.bw->b);
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// fprintf(gf[4], "%ld %d %d %d\n", sd.rid, sd.read_len, 1 + BamWrap::bam_pos(sd.start_pos), 1 + BamWrap::bam_pos(sd.end_pos));
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// fprintf(gf[4], "%s %d %d %d %d\n", qname, sd.bw->b->core.flag, sd.read_len, 1 + BamWrap::bam_pos(sd.start_pos), 1 + BamWrap::bam_pos(sd.end_pos));
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//fprintf(gf[4], "%s %d %d %d %d\n", qname, sd.bw->b->core.flag, sd.read_len, 1 + BamWrap::bam_pos(sd.start_pos), 1 + BamWrap::bam_pos(sd.end_pos));
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// 6. 更新每个read的platform信息，好像没啥用，暂时忽略
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// 这里计算snp和indel有点问题，snp和del结果不对，白天调试一下
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const int nErrors = RecalFuncs::calculateIsSNPOrIndel(aux, sd, isSNP, isIns, isDel);
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// fprintf(gf[0], "%d\t", sd.read_len);
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// for (int ii = 0; ii < sd.read_len; ++ii) fprintf(gf[0], "%d ", isSNP[ii]);
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// fprintf(gf[0], "\n");
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// fprintf(gf[1], "%d\t", sd.read_len);
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// for (int ii = 0; ii < sd.read_len; ++ii) fprintf(gf[1], "%d ", isIns[ii]);
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// fprintf(gf[1], "\n");
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// fprintf(gf[2], "%d\t", sd.read_len);
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// for (int ii = 0; ii < sd.read_len; ++ii) fprintf(gf[2], "%d ", isDel[ii]);
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// fprintf(gf[2], "\n");
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// fprintf(gf[4], "%s %d %ld ", bam_get_qname(sd.bw->b), sd.bw->b->core.flag, sd.rid);
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// for (int ii = 0; ii < sd.read_len; ++ii) fprintf(gf[4], "%d ", skips[ii] ? 1 : 0);
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// fprintf(gf[4], "\n");
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// fprintf(gf[0], "%s %d %ld ", bam_get_qname(sd.bw->b), sd.bw->b->core.flag, sd.rid);
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// for (int ii = 0; ii < sd.read_len; ++ii) fprintf(gf[0], "%d ", isSNP[ii]); fprintf(gf[0], "\n");
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// fprintf(gf[1], "%s %d %ld ", bam_get_qname(sd.bw->b), sd.bw->b->core.flag, sd.rid);
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// for (int ii = 0; ii < sd.read_len; ++ii) fprintf(gf[1], "%d ", isIns[ii]); fprintf(gf[1], "\n");
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// fprintf(gf[2], "%s %d %ld ", bam_get_qname(sd.bw->b), sd.bw->b->core.flag, sd.rid);
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// for (int ii = 0; ii < sd.read_len; ++ii) fprintf(gf[2], "%d ", isDel[ii]); fprintf(gf[2], "\n");
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// 7. 计算baqArray
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// BAQ = base alignment quality
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@ -257,9 +259,9 @@ int SerialBQSR(AuxVar &aux) {
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//spdlog::info("{}", ss.str());
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PROF_GP_END(read_vcf);
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// fprintf(gf[4], "%s %d %ld ", bam_get_qname(sd.bw->b), sd.bw->b->core.flag, sd.rid);
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// for (int ii = 0; ii < sd.read_len; ++ii) fprintf(gf[4], "%d ", skips[ii] ? 1 : 0);
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// fprintf(gf[4], "\n");
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// fprintf(gf[3], "%s %d %ld ", bam_get_qname(sd.bw->b), sd.bw->b->core.flag, sd.rid);
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// for (int ii = 0; ii < sd.read_len; ++ii) fprintf(gf[3], "%d ", skips[ii] ? 1 : 0);
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// fprintf(gf[3], "\n");
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// fprintf(gf[0], "%ld %d\t", sd.rid, sd.read_len);
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// for (int ii = 0; ii < sd.read_len; ++ii) fprintf(gf[0], "%d ", skips[ii] ? 1 : 0);
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@ -290,7 +292,7 @@ int SerialBQSR(AuxVar &aux) {
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collapseQualityScoreTableToReadGroupTable(recalTables.readGroupTable, recalTables.qualityScoreTable);
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roundTableValues(recalTables);
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#if 1
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#if 0
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printRecalTables(recalTables);
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#endif
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@ -304,8 +306,8 @@ int SerialBQSR(AuxVar &aux) {
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}
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// 多线程处理bam数据, tmd是乱序的？
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// static void thread_worker(void* data, long idx, int tid, int steal) {
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static void thread_worker(void* data, long idx, int tid) {
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static void thread_worker(void* data, long idx, int tid, int steal) {
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// static void thread_worker(void* data, long idx, int tid) {
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AuxVar& aux = (*(vector<AuxVar>*)data)[tid];
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auto& readCovariates = aux.readCovariates;
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RecalTables& recalTables = aux.recalTables;
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@ -315,7 +317,7 @@ static void thread_worker(void* data, long idx, int tid) {
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StableArray<double>&snpErrors = aux.snpErrors, &insErrors = aux.insErrors, &delErrors = aux.delErrors;
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StableArray<uint8_t>& skips = aux.skips; // 该位置是否是已知位点
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auto &bams = *aux.bamArr;
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// if (steal) for (auto& vcf : aux.vcfArr) vcf.knownSites.clear();
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if (steal) for (auto& vcf : aux.vcfArr) vcf.knownSites.clear();
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#if 1
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int startIdx = idx * aux.BAM_BLOCK_NUM;
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int stopIdx = std::min((size_t)(idx + 1) * aux.BAM_BLOCK_NUM, bams.size());
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@ -405,7 +407,7 @@ int ParallelBQSR(vector<AuxVar>& auxArr) {
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spdlog::info("{} reads processed in {} round", readNum, round);
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#if 1
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kt_for_no_steal(auxArr.size(), thread_worker, &auxArr, (readNum + AuxVar::BAM_BLOCK_NUM - 1) / AuxVar::BAM_BLOCK_NUM);
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kt_for_steal(auxArr.size(), thread_worker, &auxArr, (readNum + AuxVar::BAM_BLOCK_NUM - 1) / AuxVar::BAM_BLOCK_NUM);
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#else
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kt_for_steal(auxArr.size(), thread_worker, &auxArr, auxArr.size());
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#endif
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@ -514,6 +516,7 @@ static void globalInit() {
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RecalDatum::StaticInit();
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QualityUtils::StaticInit();
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MathUtils::StaticInit();
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BaseUtils::StaticInit();
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// 初始化需要计算的event types
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RecalUtils::initEventTypes(nsgv::gBqsrArg.computeIndelBQSRTables);
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@ -37,7 +37,7 @@ struct RecalFuncs {
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PROF_START(read_ref);
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read_ref_base(aux, interval.left, interval);
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PROF_GP_END(read_ref);
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string refBases(aux.ref_seq);
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const char *refBases = aux.ref_seq;
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// 2. 遍历cigar，计算每个碱基是否是SNP或Indel
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PROF_START(calc_snp);
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@ -48,7 +48,7 @@ struct RecalFuncs {
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if (c == 'M' || c == '=' || c == 'X') {
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for (int j = 0; j < len; ++j) {
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// 按位置将read和ref碱基进行比较，不同则是snp，注意read起始位置要加上left_clip
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int snpInt = sd.bases[readPos] == refBases[refPos] ? 0 : 1;
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int snpInt = BaseUtils::basesAreEqual(sd.bases[readPos], refBases[refPos]) ? 0 : 1;
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isSNP[readPos] = snpInt;
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nEvents += snpInt;
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readPos++;
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@ -1,3 +1,4 @@
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#include "base_utils.h"
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const char BaseUtils::cBaseToChar[16] = {'N', 'A', 'C', 'N', 'G', 'N', 'N', 'N', 'T', 'N', 'N', 'N', 'N', 'N', 'N', 'N'};
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int BaseUtils::baseIndexMap[256];
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@ -8,7 +8,28 @@
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*/
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#pragma once
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#include <cstdint>
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struct BaseUtils {
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static void StaticInit() {
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// init baseIndexMap
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for (int i = 0; i < 256; ++i) {
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baseIndexMap[i] = -1;
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}
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baseIndexMap['A'] = 0;
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baseIndexMap['a'] = 0;
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baseIndexMap['*'] = 0;
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baseIndexMap['C'] = 1;
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baseIndexMap['c'] = 1;
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baseIndexMap['G'] = 2;
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baseIndexMap['g'] = 2;
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baseIndexMap['T'] = 3;
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baseIndexMap['t'] = 3;
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}
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static int baseIndexMap[256];
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// uint8_t转碱基字符
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static const char cBaseToChar[16];
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@ -17,4 +38,19 @@ struct BaseUtils {
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// 该操作符是否消耗参考基因组的碱基
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static bool consumeRefBases(char cigar) { return cigar == 'M' || cigar == '=' || cigar == 'X' || cigar == 'D' || cigar == 'N'; }
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/**
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* Converts a simple base to a base index
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*
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* @param base [AaCcGgTt]
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* @return 0, 1, 2, 3, or -1 if the base can't be understood
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*/
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static inline int simpleBaseToBaseIndex(const char base) {
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// we want to make sure we treat the base as an unsigned byte....so that we can access this array with it.
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return baseIndexMap[(uint8_t)base];
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}
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static bool basesAreEqual(const char base1, const char base2) {
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return simpleBaseToBaseIndex(base1) == simpleBaseToBaseIndex(base2);
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}
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};
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