串行版本还差最后一步，将信息合并到数据汇总表中
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@ -6,7 +6,7 @@ vector<double> BAQ::qual2prob(256); // 质量分数转化概率
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vector<vector<vector<double>>> BAQ::EPSILONS(256, vector<vector<double>>(256, vector<double>(SAM_MAX_PHRED_SCORE + 1))); // [ref][read][qual]
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// 计算baq数组，返回成功与否
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bool BAQ::calcBAQFromHMM(BamWrap* bw, ReadAdditionData& ad, string ref, int refOffset, vector<int>& baqArray) {
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bool BAQ::calcBAQFromHMM(BamWrap* bw, SamData& ad, string ref, int refOffset, vector<int>& baqArray) {
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// 检测ref是否覆盖了read
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if (ref.size() < refOffset + ad.read_len) {
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spdlog::error("BAQ calculation error: reference sequence length {} is less than required length {} (refOffset {} + read_len {})",
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@ -84,5 +84,5 @@ struct BAQ {
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double calcEpsilon(uint8_t ref, uint8_t read, uint8_t qualB) { return EPSILONS[ref][read][qualB]; }
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// 计算baq数组，返回成功与否
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bool calcBAQFromHMM(BamWrap* bw, ReadAdditionData& ad, string ref, int refOffset, vector<int>& baqArray);
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bool calcBAQFromHMM(BamWrap* bw, SamData& ad, string ref, int refOffset, vector<int>& baqArray);
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};
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@ -36,6 +36,9 @@ Date : 2023/10/23
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using std::deque;
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#define BAM_BLOCK_SIZE 16L * 1024 * 1024
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#define MAX_SITES_INTERVAL 100000
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const uint8_t NO_BAQ_UNCERTAINTY = (uint8_t)'@';
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const char cBaseToChar[16] = {'N', 'A', 'C', 'N', 'G', 'N', 'N', 'N', 'T', 'N', 'N', 'N', 'N', 'N', 'N', 'N'};
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@ -210,7 +213,7 @@ PosAndOperator getReadIndexForReferenceCoordinate(BamWrap *bw, int alignmentStar
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}
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// 根据adapter位置，对read进行hardclip，返回左侧或右侧减掉的base数量
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void clipByReferenceCoordinates(BamWrap *bw, int refStart, int refStop, ReadAdditionData &ad) {
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void clipByReferenceCoordinates(BamWrap *bw, int refStart, int refStop, SamData &ad) {
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int start, stop;
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// Determine the read coordinate to start and stop hard clipping
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if (refStart < 0) {
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@ -235,7 +238,7 @@ void clipByReferenceCoordinates(BamWrap *bw, int refStart, int refStop, ReadAddi
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}
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// 计算切掉adapter之后，ref相对原始ref的偏移量
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void calculateRefOffset(BamWrap *bw, ReadAdditionData &ad) {
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void calculateRefOffset(BamWrap *bw, SamData &ad) {
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const uint32_t* cigar = bam_get_cigar(bw->b);
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const bam1_core_t& bc = bw->b->core;
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int i = 0;
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@ -253,16 +256,68 @@ void calculateRefOffset(BamWrap *bw, ReadAdditionData &ad) {
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}
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// 计算clip处理之后，剩余的碱基
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void calculateReadBases(BamWrap* bw, ReadAdditionData& ad) {
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void calculateReadBases(BamWrap* bw, SamData& ad) {
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ad.bases.resize(ad.read_len);
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ad.quals.resize(ad.read_len);
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uint8_t* seq = bam_get_seq(bw->b);
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uint8_t* quals = bam_get_qual(bw->b);
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for (int i = 0; i < ad.read_len; ++i) {
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ad.bases[i] = cBaseToChar[bam_seqi(seq, i + ad.left_clip)];
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ad.quals[i] = quals[i];
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}
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}
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// 计算read两端clip之后的softstart和softend
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void calculateSoftStartEnd(BamWrap* bw, SamData& ad) {
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int64_t softStart = bw->b->core.pos + ad.ref_offset;
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int64_t softEnd = softStart - 1; // 闭区间
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const uint32_t* cigar = bam_get_cigar(bw->b);
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const bam1_core_t& bc = bw->b->core;
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int cigar_start = ad.cigar_start;
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int cigar_end = ad.cigar_end;
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bool rightTail = false;
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for (int i = ad.cigar_start; i < ad.cigar_end; ++i) {
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const char c = bam_cigar_opchr(cigar[i]);
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int len = bam_cigar_oplen(cigar[i]);
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if (i == ad.cigar_start) len -= ad.first_cigar_clip;
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if (i == ad.cigar_end - 1) len -= ad.last_cigar_clip;
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// if (c == 'S' || c == 'I')
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if (c == 'S')
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softStart -= len;
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else if (c != 'H')
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rightTail = true;
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if (rightTail) {
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if (consumeRefBases(c) || c == 'S')
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softEnd += len;
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}
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}
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ad.softStart() = softStart;
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ad.softEnd() = softEnd;
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}
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// 计算clip之后的cigar
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void calculateCigar(BamWrap* bw, SamData& ad) {
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ad.cigars.clear();
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const uint32_t* cigar = bam_get_cigar(bw->b);
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const bam1_core_t& bc = bw->b->core;
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int cigar_start = ad.cigar_start;
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int cigar_end = ad.cigar_end;
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for (int i = ad.cigar_start; i < ad.cigar_end; ++i) {
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const char c = bam_cigar_opchr(cigar[i]);
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int len = bam_cigar_oplen(cigar[i]);
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if (i == ad.cigar_start)
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len -= ad.first_cigar_clip;
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if (i == ad.cigar_end - 1)
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len -= ad.last_cigar_clip;
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ad.cigars.push_back({c, len});
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}
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//for(auto &cigar : ad.cigars) {
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// spdlog::info("op: {}, len: {}", cigar.op, cigar.len);
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//}
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}
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// 计算read两端softclip的碱基数量，可能会修改ad里的clip值
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void calculateSoftClip(BamWrap *bw, ReadAdditionData &ad) {
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void calculateSoftClip(BamWrap *bw, SamData &ad) {
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const uint32_t* cigar = bam_get_cigar(bw->b);
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const bam1_core_t& bc = bw->b->core;
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int readIndex = ad.left_clip;
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@ -324,10 +379,12 @@ inline void updateIndel(vector<int> &isIndel, int index) {
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}
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// 计算该read的每个碱基位置是否是SNP或Indel
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int calculateIsSNPOrIndel(AuxVar& aux, BamWrap *bw, ReadAdditionData &ad, vector<int> &isSNP, vector<int> &isIns, vector<int> &isDel) {
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int calculateIsSNPOrIndel(AuxVar& aux, BamWrap *bw, SamData &ad, vector<int> &isSNP, vector<int> &isIns, vector<int> &isDel) {
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// 1. 读取参考基因组，先看看串行运行性能，稍后可以将读入ref和vcf合并起来做成一个并行流水线步骤
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Interval interval{bw->start_pos() + ad.ref_offset, bw->end_pos()}; // 闭区间
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PROF_START(ref);
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read_ref_base(aux, interval.left, interval);
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PROF_END(gprof[GP_read_ref], ref);
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string refBases(aux.ref_seq);
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// spdlog::info("ref: {}, {}, {} - {}", aux.ref_seq, aux.ref_len, bw->contig_pos(), bw->contig_end_pos());
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@ -381,13 +438,13 @@ int calculateIsSNPOrIndel(AuxVar& aux, BamWrap *bw, ReadAdditionData &ad, vector
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}
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// 简单计算baq数组，就是全部赋值为'@' (64)
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bool flatBAQArray(BamWrap* bw, ReadAdditionData& ad, vector<int>& baqArray) {
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bool flatBAQArray(BamWrap* bw, SamData& ad, vector<int>& baqArray) {
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baqArray.resize(ad.read_len, (int)'@');
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return true;
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}
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// 计算真实的baq数组，耗时更多，好像enable-baq参数默认是关闭的，那就先不实现这个了
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bool calculateBAQArray(AuxVar& aux, BAQ& baq, BamWrap* bw, ReadAdditionData& ad, vector<int>& baqArray) {
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bool calculateBAQArray(AuxVar& aux, BAQ& baq, BamWrap* bw, SamData& ad, vector<int>& baqArray) {
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baqArray.resize(ad.read_len, 0);
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return true;
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}
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@ -404,7 +461,7 @@ static void get_line_from_buf(char* buf, int64_t total, int64_t* cur, string* li
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}
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// 计算与read有交叉的已知位点信息， 应该要判断一下，是按照read的范围去读取vcf，还是按照一个batch read的范围去读取
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void calculateKnownSites(BamWrap* bw, ReadAdditionData& ad, vector<VCFParser> &vcfs) {
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void calculateKnownSites(BamWrap* bw, SamData& ad, vector<VCFParser> &vcfs, vector<bool> knownSites) {
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int tid = bw->contig_id();
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uint64_t startPos = bw->start_pos(); // 闭区间
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uint64_t endPos = bw->end_pos(); // 闭区间
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@ -427,6 +484,8 @@ void calculateKnownSites(BamWrap* bw, ReadAdditionData& ad, vector<VCFParser> &v
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//spdlog::info("before intervals : {}", vcf.knownSites.size());
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// 读取新的interval
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int64_t fpos, flen;
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endPos = std::max(startPos + MAX_SITES_INTERVAL, endPos);
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Interval readIntv(startPos, endPos);
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vcf.index.SearchInterval(startPos, endPos, &fpos, &flen);
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//spdlog::info("file index: {}, {}", fpos, flen);
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if (flen > 0) {
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@ -448,7 +507,9 @@ void calculateKnownSites(BamWrap* bw, ReadAdditionData& ad, vector<VCFParser> &v
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string id, ref;
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ss_line >> stid >> pos >> id >> ref;
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tid = sam_hdr_name2tid(nsgv::gInBamHeader, stid.c_str());
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if (tid >= 0 && pos > 0) {
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int64_t varStart = BamWrap::bam_global_pos(tid, pos);
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Interval varIntv(varStart, varStart + ref.size() - 1);
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if (readIntv.overlaps(varIntv)) {
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vcf.knownSites.push_back(Interval(tid, pos - 1, pos - 1 + ref.size()));
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//spdlog::info("intv-1 {}, {}, {}", tid, pos, ref.size());
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}
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@ -461,6 +522,74 @@ void calculateKnownSites(BamWrap* bw, ReadAdditionData& ad, vector<VCFParser> &v
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//}
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}
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//exit(0);
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knownSites.resize(ad.read_len);
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endPos = bw->end_pos();
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for(auto &vcf : vcfs) {
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for (auto &intv : vcf.knownSites) {
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// knownSite is outside clipping window for the read, ignore
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if (intv.right < ad.softStart())
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continue;
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if (intv.left > ad.softEnd())
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break;
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// 计算对应的位点
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ReadIdxCigar rcStart = ad.getReadIndexForReferenceCoordinate(intv.left);
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int featureStartOnRead = rcStart.readIdx == SamData::READ_INDEX_NOT_FOUND ? 0 : rcStart.readIdx;
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if (rcStart.cigarOp == 'D') {
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--featureStartOnRead;
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}
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ReadIdxCigar rcEnd = ad.getReadIndexForReferenceCoordinate(intv.right);
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int featureEndOnRead = rcEnd.readIdx == SamData::READ_INDEX_NOT_FOUND ? ad.read_len : rcEnd.readIdx;
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if (featureStartOnRead > ad.read_len) {
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featureStartOnRead = featureEndOnRead = ad.read_len;
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}
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for (int i = max(0, featureStartOnRead); i < min(ad.read_len, featureEndOnRead + 1); ++i) {
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knownSites[i] = true;
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}
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}
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}
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}
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// 应该是计算一段数据的平均值
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static void calculateAndStoreErrorsInBlock(int i, int blockStartIndex, vector<int>& errorArr, vector<double>& fracErrs) {
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int totalErrors = 0;
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for (int j = max(0, blockStartIndex - 1); j <= i; j++) {
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totalErrors += errorArr[j];
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}
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for (int j = max(0, blockStartIndex - 1); j <= i; j++) {
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fracErrs[j] = ((double)totalErrors) / ((double)(i - max(0, blockStartIndex - 1) + 1));
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}
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}
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// 应该是用来处理BAQ的，把不等于特定BAQ分数的碱基作为一段数据统一处理
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void calculateFractionalErrorArray(vector<int>& errorArr, vector<int>& baqArr, vector<double>& fracErrs) {
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fracErrs.resize(baqArr.size());
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// errorArray和baqArray必须长度相同
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const int BLOCK_START_UNSET = -1;
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bool inBlock = false;
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int blockStartIndex = BLOCK_START_UNSET;
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int i;
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for (i = 0; i < fracErrs.size(); ++i) {
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if (baqArr[i] == NO_BAQ_UNCERTAINTY) { // 不等于NO_BAQ_UNCERTAINTY的碱基当成一段数据来处理
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if (!inBlock) {
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fracErrs[i] = errorArr[i];
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} else {
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calculateAndStoreErrorsInBlock(i, blockStartIndex, errorArr, fracErrs);
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inBlock = false; // reset state variables
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blockStartIndex = BLOCK_START_UNSET; // reset state variables
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}
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} else {
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inBlock = true;
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if (blockStartIndex == BLOCK_START_UNSET) {
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blockStartIndex = i;
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}
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}
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}
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// 处理最后一个block
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if (inBlock) {
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calculateAndStoreErrorsInBlock(i - 1, blockStartIndex, errorArr, fracErrs);
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}
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}
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// 串行bqsr
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@ -513,7 +642,7 @@ int SerialBQSR() {
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// 3. 如果bam文件之前做过bqsr，tag中包含OQ（originnal quality，原始质量分数），检查用户参数里是否指定用原始质量分数进行bqsr，如果是则将质量分数替换为OQ，否则忽略OQ，先忽略
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// 4. 对read的两端进行检测，去除（hardclip）adapter
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BamWrap *bw = bams[i];
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ReadAdditionData ad;
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SamData ad;
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ad.read_len = BamWrap::BamEffectiveLength(bw->b);
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ad.cigar_end = bw->b->core.n_cigar;
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if (ad.read_len <= 0) continue;
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@ -535,6 +664,9 @@ int SerialBQSR() {
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calculateRefOffset(bw, ad); // 计算ref_offset，就是相对比对的position，要将ref右移多少
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calculateReadBases(bw, ad); // 计算clip处理之后，剩余的碱基
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// 计算clip之后，两端的softstart和softend
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calculateSoftStartEnd(bw, ad);
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calculateCigar(bw, ad);
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//spdlog::info("read-len {} - {}: clip left {}, right {}, ref offset: {}, cigar range: [{}, {}), cigar: {}", bw->b->core.l_qseq,
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// ad.read_len, ad.left_clip, ad.right_clip, ad.ref_offset, ad.cigar_start, ad.cigar_end, bw->cigar_str());
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@ -560,7 +692,9 @@ int SerialBQSR() {
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// 到这里，基本的数据都准备好了，后续就是进行bqsr的统计了
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// 8. 计算这条read对应的协变量
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PROF_START(covariate);
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CovariateUtils::ComputeCovariates(bw, ad, nsgv::gInBamHeader, readCovariates, true);
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PROF_END(gprof[GP_covariate], covariate);
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test = readCovariates[1][0][0] + readCovariates[2][1][3];
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int end_pos = bw->contig_end_pos();
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//spdlog::info("adapter: {}, read: {}, {}, strand: {}", adapter_boundary, bw->contig_pos(), end_pos,
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@ -568,7 +702,23 @@ int SerialBQSR() {
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// 9. 计算这条read需要跳过的位置
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vector<bool> skip(ad.read_len, 0);
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calculateKnownSites(bw, ad, nsgv::gAuxVars[0].vcfArr);
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PROF_START(known_sites);
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calculateKnownSites(bw, ad, nsgv::gAuxVars[0].vcfArr, skip);
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for (int ii = 0; ii < ad.read_len; ++ii) {
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skip[ii] =
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skip[ii] || (ContextCovariate::baseIndexMap[ad.bases[ii]] == -1) || ad.quals[ii] < nsgv::gBqsrArg.PRESERVE_QSCORES_LESS_THAN;
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}
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PROF_END(gprof[GP_read_vcf], known_sites);
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// 10. 根据BAQ进一步处理snp，indel，得到处理后的数据
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vector<double> snpErrors, insErrors, delErrors;
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calculateFractionalErrorArray(isSNP, baqArray, snpErrors);
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calculateFractionalErrorArray(isIns, baqArray, insErrors);
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calculateFractionalErrorArray(isDel, baqArray, delErrors);
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// aggregate all of the info into our info object, and update the data
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// 11. 合并之前计算的数据，得到info，并更新bqsr table数据
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}
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#if 0
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@ -9,7 +9,7 @@
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struct ReadData {
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vector<BamWrap *> bams; // read step output
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int64_t bamStartIdx = 0; // bam，bam
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int64_t taskSeq = 0; //
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int64_t taskSeq = 0; //
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};
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struct GenREData {
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@ -22,16 +22,16 @@ int CycleCovariate::MAXIMUM_CYCLE_VALUE;
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// for CovariateUtils
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// 对一条read计算协变量（该协变量被上一个read用过）
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void CovariateUtils::ComputeCovariates(BamWrap* bw, ReadAdditionData& ad, sam_hdr_t* header, PerReadCovariateMatrix& values,
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void CovariateUtils::ComputeCovariates(BamWrap* bw, SamData& ad, sam_hdr_t* header, PerReadCovariateMatrix& values,
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bool recordIndelValues) {
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//ReadGroupCovariate::RecordValues(bw, ad, header, values, recordIndelValues);
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//BaseQualityCovariate::RecordValues(bw, ad, header, values, recordIndelValues);
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//ContextCovariate::RecordValues(bw, ad, header, values, recordIndelValues);
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//CycleCovariate::RecordValues(bw, ad, header, values, recordIndelValues);
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ReadGroupCovariate::RecordValues(bw, ad, header, values, recordIndelValues);
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BaseQualityCovariate::RecordValues(bw, ad, header, values, recordIndelValues);
|
||||
ContextCovariate::RecordValues(bw, ad, header, values, recordIndelValues);
|
||||
CycleCovariate::RecordValues(bw, ad, header, values, recordIndelValues);
|
||||
}
|
||||
|
||||
// ReadGroupCovariate 协变量的方法
|
||||
void ReadGroupCovariate::RecordValues(BamWrap* bw, ReadAdditionData& ad, sam_hdr_t* header, PerReadCovariateMatrix& values, bool recordIndelValues) {
|
||||
void ReadGroupCovariate::RecordValues(BamWrap* bw, SamData& ad, sam_hdr_t* header, PerReadCovariateMatrix& values, bool recordIndelValues) {
|
||||
uint8_t *rgStr = bam_aux_get(bw->b, "RG");
|
||||
char* rgVal = nullptr;
|
||||
if (rgStr) rgVal = bam_aux2Z(rgStr);
|
||||
|
|
@ -47,7 +47,7 @@ void ReadGroupCovariate::RecordValues(BamWrap* bw, ReadAdditionData& ad, sam_hdr
|
|||
}
|
||||
|
||||
// BaseQualityCovariate 协变量的方法
|
||||
void BaseQualityCovariate::RecordValues(BamWrap* bw, ReadAdditionData& ad, sam_hdr_t* header, PerReadCovariateMatrix& values,
|
||||
void BaseQualityCovariate::RecordValues(BamWrap* bw, SamData& ad, sam_hdr_t* header, PerReadCovariateMatrix& values,
|
||||
bool recordIndelValues) {
|
||||
// 在前面的处理过后，quals应该和base长度一致了
|
||||
#define __bq_set_cov(ins, del) \
|
||||
|
|
@ -98,7 +98,7 @@ static char SimpleComplement(const char base) {
|
|||
}
|
||||
|
||||
// 获取去除低质量分数碱基之后的read碱基序列（将低质量分数的碱基变成N）
|
||||
void ContextCovariate::GetStrandedClippedBytes(BamWrap* bw, ReadAdditionData& ad, string& clippedBases, uint8_t lowQTail) {
|
||||
void ContextCovariate::GetStrandedClippedBytes(BamWrap* bw, SamData& ad, string& clippedBases, uint8_t lowQTail) {
|
||||
uint8_t* quals = bam_get_qual(bw->b) + ad.left_clip;
|
||||
|
||||
if (bw->GetReadNegativeStrandFlag()) { // 反向互补
|
||||
|
|
@ -218,7 +218,7 @@ void ContextCovariate::GetReadContextAtEachPosition(const string& bases, const i
|
|||
}
|
||||
}
|
||||
|
||||
void ContextCovariate::RecordValues(BamWrap* bw, ReadAdditionData& ad, sam_hdr_t* header, PerReadCovariateMatrix& values, bool recordIndelValues) {
|
||||
void ContextCovariate::RecordValues(BamWrap* bw, SamData& ad, sam_hdr_t* header, PerReadCovariateMatrix& values, bool recordIndelValues) {
|
||||
const int originalReadLength = ad.read_len;
|
||||
|
||||
// store the original bases and then write Ns over low quality ones
|
||||
|
|
@ -270,7 +270,7 @@ void ContextCovariate::RecordValues(BamWrap* bw, ReadAdditionData& ad, sam_hdr_t
|
|||
* @param maxCycle max value of the base to compute the key for
|
||||
* (this method throws UserException if the computed absolute value of the cycle number is higher than this value).
|
||||
*/
|
||||
int CycleCovariate::CycleKey(BamWrap* bw, ReadAdditionData& ad, const int baseNumber, const bool indel, const int maxCycle) {
|
||||
int CycleCovariate::CycleKey(BamWrap* bw, SamData& ad, const int baseNumber, const bool indel, const int maxCycle) {
|
||||
const bool isNegStrand = bw->GetReadNegativeStrandFlag();
|
||||
const bool isSecondInPair = (bw->b->core.flag & BAM_FPAIRED) && (bw->b->core.flag & BAM_FREAD2);
|
||||
const int readLength = ad.read_len;
|
||||
|
|
@ -299,7 +299,7 @@ int CycleCovariate::CycleKey(BamWrap* bw, ReadAdditionData& ad, const int baseNu
|
|||
}
|
||||
|
||||
// Used to pick out the covariate's value from attributes of the read
|
||||
void CycleCovariate::RecordValues(BamWrap* bw, ReadAdditionData& ad, sam_hdr_t* header, PerReadCovariateMatrix& values, bool recordIndelValues) {
|
||||
void CycleCovariate::RecordValues(BamWrap* bw, SamData& ad, sam_hdr_t* header, PerReadCovariateMatrix& values, bool recordIndelValues) {
|
||||
const int readLength = ad.read_len;
|
||||
// Note: duplicate the loop to void checking recordIndelValues on every iteration
|
||||
if (recordIndelValues) {
|
||||
|
|
|
|||
|
|
@ -69,7 +69,7 @@ struct CovariateUtils {
|
|||
}
|
||||
|
||||
// 对一条read计算协变量（该协变量被上一个read用过）
|
||||
static void ComputeCovariates(BamWrap* bw, ReadAdditionData& ad, sam_hdr_t* header, PerReadCovariateMatrix& values, bool recordIndelValues);
|
||||
static void ComputeCovariates(BamWrap* bw, SamData& ad, sam_hdr_t* header, PerReadCovariateMatrix& values, bool recordIndelValues);
|
||||
};
|
||||
|
||||
// Read group协变量
|
||||
|
|
@ -78,13 +78,13 @@ struct ReadGroupCovariate {
|
|||
static map<string, int> RgToId; // read group name到id的映射
|
||||
static map<int, string> IdToRg; // id到read group name的映射
|
||||
|
||||
static void RecordValues(BamWrap* bw, ReadAdditionData& ad, sam_hdr_t* header, PerReadCovariateMatrix& values, bool recordIndelValues);
|
||||
static void RecordValues(BamWrap* bw, SamData& ad, sam_hdr_t* header, PerReadCovariateMatrix& values, bool recordIndelValues);
|
||||
};
|
||||
|
||||
// Base quality协变量
|
||||
struct BaseQualityCovariate {
|
||||
static constexpr int index = 1; // 在协变量数组中的索引位置
|
||||
static void RecordValues(BamWrap* bw, ReadAdditionData& ad, sam_hdr_t* header, PerReadCovariateMatrix& values, bool recordIndelValues);
|
||||
static void RecordValues(BamWrap* bw, SamData& ad, sam_hdr_t* header, PerReadCovariateMatrix& values, bool recordIndelValues);
|
||||
};
|
||||
|
||||
// Context协变量
|
||||
|
|
@ -162,14 +162,14 @@ struct ContextCovariate {
|
|||
}
|
||||
|
||||
// 获取去除低质量分数碱基之后的read碱基序列（将低质量分数的碱基变成N）
|
||||
static void GetStrandedClippedBytes(BamWrap* bw, ReadAdditionData& ad, string& clippedBases, uint8_t lowQTail);
|
||||
static void GetStrandedClippedBytes(BamWrap* bw, SamData& ad, string& clippedBases, uint8_t lowQTail);
|
||||
// Creates a int representation of a given dna string.
|
||||
static int KeyFromContext(const string& dna, const int start, const int end);
|
||||
// For each position of the read, calculate the n-base-pair *read* base context (as opposed to the reference context).
|
||||
static void GetReadContextAtEachPosition(const string& bases, const int contextSize, const int mask, vector<int>& keys);
|
||||
|
||||
// 设置协变量的值
|
||||
static void RecordValues(BamWrap* bw, ReadAdditionData& ad, sam_hdr_t* header, PerReadCovariateMatrix& values, bool recordIndelValues);
|
||||
static void RecordValues(BamWrap* bw, SamData& ad, sam_hdr_t* header, PerReadCovariateMatrix& values, bool recordIndelValues);
|
||||
};
|
||||
|
||||
// Cycle协变量
|
||||
|
|
@ -203,7 +203,7 @@ struct CycleCovariate {
|
|||
}
|
||||
|
||||
// Computes the encoded value of CycleCovariate's key for the given position at the read.
|
||||
static int CycleKey(BamWrap* bw, ReadAdditionData& ad, const int baseNumber, const bool indel, const int maxCycle);
|
||||
static int CycleKey(BamWrap* bw, SamData& ad, const int baseNumber, const bool indel, const int maxCycle);
|
||||
|
||||
static void RecordValues(BamWrap* bw, ReadAdditionData& ad, sam_hdr_t* header, PerReadCovariateMatrix& values, bool recordIndelValues);
|
||||
static void RecordValues(BamWrap* bw, SamData& ad, sam_hdr_t* header, PerReadCovariateMatrix& values, bool recordIndelValues);
|
||||
};
|
||||
|
|
@ -11,16 +11,61 @@
|
|||
#include <htslib/sam.h>
|
||||
#include <limits.h>
|
||||
#include <math.h>
|
||||
#include <stdlib.h>
|
||||
|
||||
#include <map>
|
||||
#include <queue>
|
||||
#include <sstream>
|
||||
#include <string>
|
||||
#include <vector>
|
||||
|
||||
using namespace std;
|
||||
|
||||
struct Cigar {
|
||||
char op = '0';
|
||||
int len = 0;
|
||||
// 该操作符是否消耗read的碱基
|
||||
static bool ConsumeReadBases(char cigar) { return cigar == 'M' || cigar == '=' || cigar == 'X' || cigar == 'I' || cigar == 'S'; }
|
||||
// 该操作符是否消耗参考基因组的碱基
|
||||
static bool ConsumeRefBases(char cigar) { return cigar == 'M' || cigar == '=' || cigar == 'X' || cigar == 'D' || cigar == 'N'; }
|
||||
};
|
||||
|
||||
struct ReadIdxCigar {
|
||||
int readIdx = 0; // 在read序列中的位置
|
||||
char cigarOp = '0'; // 当前位置对应的cigar
|
||||
};
|
||||
|
||||
// 不用经常释放array的内存空间，减少频繁的内存开辟和释放操作
|
||||
template <class T>
|
||||
struct FastArray {
|
||||
vector<T> arr;
|
||||
size_t idx;
|
||||
void clear() { idx = 0; }
|
||||
size_t size() { return idx; }
|
||||
void push_back(const T& val) {
|
||||
if (idx < arr.size()) {
|
||||
arr[idx++] = val;
|
||||
} else {
|
||||
arr.push_back(val);
|
||||
idx++;
|
||||
}
|
||||
}
|
||||
struct iterator {
|
||||
typename std::vector<T>::iterator it;
|
||||
iterator(typename std::vector<T>::iterator _it) : it(_it) {}
|
||||
iterator& operator++() { ++it; return *this;}
|
||||
iterator& operator--() { --it; return *this;}
|
||||
T& operator*() const { return *it; }
|
||||
bool operator!=(const iterator& other) const { return it != other.it; }
|
||||
bool operator==(const iterator& other) const { return it == other.it; }
|
||||
};
|
||||
|
||||
iterator begin() { return arr.begin(); }
|
||||
iterator end() { return arr.begin() + idx; }
|
||||
};
|
||||
|
||||
// 对原始bam数据的补充，比如对两端进行hardclip等
|
||||
struct ReadAdditionData {
|
||||
struct SamData {
|
||||
int read_len = 0; // read长度，各种clip之后的长度
|
||||
int cigar_start = 0; // cigar起始位置，闭区间
|
||||
int cigar_end = 0; // cigar结束位置，开区间
|
||||
|
|
@ -29,7 +74,41 @@ struct ReadAdditionData {
|
|||
int left_clip = 0; // 左侧被切掉的碱基长度
|
||||
int right_clip = 0; // 右侧被切掉的碱基长度
|
||||
int ref_offset = 0; // 切除adapter和softclip之后(softclip应该不影响)，相对原始ref比对位置（contig_pos）的偏移量
|
||||
string bases; // 处理之后的read的碱基
|
||||
|
||||
// 记录一下bqsr运算过程中用到的数据，回头提前计算一下，修正现在的复杂逻辑
|
||||
static constexpr int READ_INDEX_NOT_FOUND = -1;
|
||||
string bases; // 处理之后的read的碱基
|
||||
vector<uint8_t> quals; // 对应的质量分数
|
||||
int64_t start_pos; // 因为soft clip都被切掉了，这里的softstart应该就是切掉之后的匹配位点，闭区间
|
||||
int64_t end_pos; // 同上，闭区间
|
||||
FastArray<Cigar> cigars;
|
||||
int64_t& softStart() { return start_pos; }
|
||||
int64_t& softEnd() { return end_pos; }
|
||||
|
||||
// functions
|
||||
ReadIdxCigar getReadIndexForReferenceCoordinate(int64_t refPos) {
|
||||
ReadIdxCigar rc;
|
||||
if (refPos < start_pos)
|
||||
return rc;
|
||||
int firstReadPosOfElement = 0; // inclusive
|
||||
int firstRefPosOfElement = start_pos; // inclusive
|
||||
int lastReadPosOfElement = 0; // exclusive
|
||||
int lastRefPosOfElement = start_pos; // exclusive
|
||||
// advance forward through all the cigar elements until we bracket the reference coordinate
|
||||
for (auto& cigar : cigars) {
|
||||
firstReadPosOfElement = lastReadPosOfElement;
|
||||
firstRefPosOfElement = lastRefPosOfElement;
|
||||
lastReadPosOfElement += Cigar::ConsumeReadBases(cigar.op) ? cigar.len : 0;
|
||||
lastRefPosOfElement += Cigar::ConsumeRefBases(cigar.op) || cigar.op == 'S' ? cigar.len : 0;
|
||||
if (firstRefPosOfElement <= refPos && refPos < lastRefPosOfElement) { // refCoord falls within this cigar element
|
||||
int readPosAtRefCoord = firstReadPosOfElement + (Cigar::ConsumeReadBases(cigar.op) ? (refPos - firstRefPosOfElement) : 0);
|
||||
rc.cigarOp = cigar.op;
|
||||
rc.readIdx = readPosAtRefCoord;
|
||||
return rc;
|
||||
}
|
||||
}
|
||||
return rc;
|
||||
}
|
||||
};
|
||||
|
||||
/*
|
||||
|
|
|
|||
|
|
@ -54,11 +54,11 @@ int DisplayProfiling(int nthread) {
|
|||
// 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(read_ref);
|
||||
PRINT_GP(read_vcf);
|
||||
PRINT_GP(covariate);
|
||||
//PRINT_GP(markdup);
|
||||
//PRINT_GP(intersect);
|
||||
// PRINT_GP(merge_result);
|
||||
// PRINT_GP(sort_pair);
|
||||
// PRINT_GP(sort_frag);
|
||||
|
|
@ -68,10 +68,10 @@ int DisplayProfiling(int nthread) {
|
|||
// PRINT_GP(merge_markdup);
|
||||
// PRINT_GP(merge_update);
|
||||
// PRINT_GP(merge_add);
|
||||
PRINT_GP(markdup_all);
|
||||
//PRINT_GP(markdup_all);
|
||||
// PRINT_GP(final_read);
|
||||
PRINT_GP(write);
|
||||
PRINT_GP(whole_process);
|
||||
//PRINT_GP(write);
|
||||
// PRINT_GP(whole_process);
|
||||
|
||||
// PRINT_TP(gen, nthread);
|
||||
// PRINT_TP(sort_frag, nthread);
|
||||
|
|
|
|||
|
|
@ -40,6 +40,9 @@ extern uint64_t gprof[LIM_GLOBAL_PROF_TYPE];
|
|||
enum { GP_0 = 0, GP_1, GP_2, GP_3, GP_4, GP_5, GP_6, GP_7, GP_8, GP_9, GP_10 };
|
||||
enum {
|
||||
GP_read_wait = 11,
|
||||
GP_covariate,
|
||||
GP_read_ref,
|
||||
GP_read_vcf,
|
||||
GP_gen_wait,
|
||||
GP_sort_wait,
|
||||
GP_markdup_wait,
|
||||
|
|
|
|||
Loading…
Reference in New Issue