初步并行实现，还没完全

src/bqsr/aux_arg.cpp

@@ -0,0 +1,3 @@
+#include "aux_arg.h"
+
+int64_t AuxVar::processedReads = 0;

src/bqsr/aux_arg.h

@@ -15,13 +15,21 @@
 
 #include "util/vcf_parser.h"
 #include "recal_tables.h"
+#include "covariate.h"
+#include "util/bam_wrap.h"
+#include "util/sam_data.h"
+#include "util/stable_array.h"
+#include "util/bam_buf.h"
 
 using std::vector;
 
 // 解析后的一些参数，文件，数据等
 struct AuxVar {
-    const static int REF_CONTEXT_PAD = 3;                 // 需要做一些填充
+    //const static int REF_CONTEXT_PAD = 3;                 // 需要做一些填充
-    const static int REFERENCE_HALF_WINDOW_LENGTH = 150;  // 需要额外多取出一些ref序列，防止边界效应
+    //const static int REFERENCE_HALF_WINDOW_LENGTH = 150;  // 需要额外多取出一些ref序列，防止边界效应
+
+    static constexpr int BAM_BLOCK_NUM = 1000; // 每个线程每次处理1k个bam记录
+    static int64_t processedReads;
 
     sam_hdr_t* header = nullptr;  // bam header
     faidx_t* faidx = nullptr;     // reference index
@@ -29,7 +37,16 @@ struct AuxVar {
     int ref_len = 0;              // reference sequence length
     int offset = 0;               // 在要求的ref序列两边，多余取出的碱基数量
 
+    BamArray *bamArr = nullptr;  // bam数据数组
+
     vector<VCFParser> vcfArr;  // 从vcf中获取已知位点
 
-    RecalTables recalTables; // 每个线程对应一个recal tables
+    PerReadCovariateMatrix readCovariates;  // 每个read对应的协变量矩阵
+    RecalTables recalTables;  // 每个线程对应一个recal tables
+
+    SamData sd;
+    StableArray<int> isSNP, isIns, isDel;  // 该位置是否是SNP, indel位置，0不是，1是
+    StableArray<uint8_t> baqArray;
+    StableArray<double> snpErrors, insErrors, delErrors;
+    StableArray<uint8_t> skips;  // 该位置是否是已知位点
 };

src/bqsr/bqsr_entry.cpp

@@ -13,6 +13,7 @@ Date : 2023/10/23
 #include <htslib/sam.h>
 #include <htslib/synced_bcf_reader.h>
 #include <htslib/thread_pool.h>
+#include <klib/kthread.h>
 #include <spdlog/spdlog.h>
 
 #include <iomanip>
@@ -110,14 +111,21 @@ void roundTableValues(RecalTables& rt) {
 }
 
 // 串行bqsr
-int SerialBQSR() {
+int SerialBQSR(AuxVar &aux) {
     BamBufType inBamBuf(nsgv::gBqsrArg.DUPLEX_IO);
     inBamBuf.Init(nsgv::gInBamFp, nsgv::gInBamHeader, nsgv::gBqsrArg.MAX_MEM, bqsrReadFilterOut);
     int64_t readNumSum = 0;
     int round = 0;
     PerReadCovariateMatrix readCovariates;
     CovariateUtils::InitPerReadCovMat(readCovariates);
-    RecalTables& recalTables = nsgv::gAuxVars[0].recalTables;
+    RecalTables& recalTables = aux.recalTables;
+
+    SamData& sd = aux.sd;
+    StableArray<int>&isSNP = aux.isSNP, &isIns = aux.isIns, &isDel = aux.isDel;  // 该位置是否是SNP, indel位置，0不是，1是
+    StableArray<uint8_t> &baqArray = aux.baqArray;
+    StableArray<double> &snpErrors = aux.snpErrors, &insErrors = aux.insErrors, &delErrors = aux.delErrors;
+    StableArray<uint8_t> &skips = aux.skips;  // 该位置是否是已知位点
+
     while (true) {
         ++round;
         // 一. 读取bam数据
@@ -131,12 +139,6 @@ int SerialBQSR() {
         spdlog::info("{} reads processed in {} round", readNum, round);
 
         // 二. 遍历每个bam（read）记录，进行处理
-        SamData sd;
-        StableArray<int> isSNP, isIns, isDel;  // 该位置是否是SNP, indel位置，0不是，1是
-        StableArray<uint8_t> baqArray;
-        StableArray<double> snpErrors, insErrors, delErrors;
-        StableArray<uint8_t> skips;  // 该位置是否是已知位点
-
         for (int i = 0; i < bams.size(); ++i) {
             // 1. 对每个read，需要检查cigar是否合法，即没有两个连续的相同的cigar，而且需要将首尾的deletion处理掉，目前看好像没啥影响，我们忽略这一步
             // 2. 对质量分数长度跟碱基长度不匹配的read，缺少的质量分数用默认值补齐，先忽略，后边有需要再处理
@@ -164,7 +166,7 @@ int SerialBQSR() {
             PROF_END(gprof[GP_clip_read], clip_read);
 
             // 6. 更新每个read的platform信息，好像没啥用，暂时忽略
-            const int nErrors = RecalFuncs::calculateIsSNPOrIndel(nsgv::gAuxVars[0], sd, isSNP, isIns, isDel);
+            const int nErrors = RecalFuncs::calculateIsSNPOrIndel(aux, sd, isSNP, isIns, isDel);
 
             /*fprintf(gf[0], "%d\t", sd.read_len);
             for (int ii = 0; ii < sd.read_len; ++ii) fprintf(gf[0], "%d ", isSNP[ii]);
@@ -194,7 +196,7 @@ int SerialBQSR() {
 
             // 8. 计算这条read对应的协变量
             PROF_START(covariate);
-            CovariateUtils::ComputeCovariates(sd, nsgv::gInBamHeader, readCovariates, true);
+            CovariateUtils::ComputeCovariates(sd, aux.header, readCovariates, true);
             PROF_END(gprof[GP_covariate], covariate);
 
             // fprintf(gf[3], "%ld %ld %d %ld\n", sd.rid, readCovariates.size(), sd.read_len, readCovariates[0][0].size());
@@ -220,7 +222,7 @@ int SerialBQSR() {
 
             // 9. 计算这条read需要跳过的位置
             PROF_START(read_vcf);
-            RecalFuncs::calculateKnownSites(sd, nsgv::gAuxVars[0].vcfArr, nsgv::gInBamHeader, skips);
+            RecalFuncs::calculateKnownSites(sd, aux.vcfArr, aux.header, skips);
             for (int ii = 0; ii < sd.read_len; ++ii) {
                 skips[ii] = skips[ii] || (ContextCovariate::baseIndexMap[sd.bases[ii]] == -1) ||
                             sd.base_quals[ii] < nsgv::gBqsrArg.PRESERVE_QSCORES_LESS_THAN;
@@ -264,6 +266,109 @@ int SerialBQSR() {
     return 0;
 }
 
+static void thread_worker(void* data, long idx, int tid) {
+    AuxVar& aux = ((AuxVar*)data)[tid];
+    auto& readCovariates = aux.readCovariates;
+    RecalTables& recalTables = aux.recalTables;
+    SamData& sd = aux.sd;
+    StableArray<int>&isSNP = aux.isSNP, &isIns = aux.isIns, &isDel = aux.isDel;  // 该位置是否是SNP, indel位置，0不是，1是
+    StableArray<uint8_t>& baqArray = aux.baqArray;
+    StableArray<double>&snpErrors = aux.snpErrors, &insErrors = aux.insErrors, &delErrors = aux.delErrors;
+    StableArray<uint8_t>& skips = aux.skips;  // 该位置是否是已知位点
+    auto &bams = *aux.bamArr;
+    int startIdx = idx * aux.BAM_BLOCK_NUM;
+    int stopIdx = std::min((size_t)(idx + 1) * aux.BAM_BLOCK_NUM, bams.size());
+    for (int i = startIdx; i < stopIdx; ++i) {
+        BamWrap* bw = bams[i];
+        sd.init();
+        sd.parseBasic(bw);
+        sd.rid = i + aux.processedReads;
+        if (sd.read_len <= 0) continue;
+
+        //PROF_START(clip_read);
+        ReadTransformer::hardClipAdaptorSequence(bw, sd);
+        if (sd.read_len <= 0) continue;
+        ReadTransformer::hardClipSoftClippedBases(bw, sd);
+        if (sd.read_len <= 0) continue;
+        sd.applyTransformations();
+        // PROF_END(gprof[GP_clip_read], clip_read);
+
+        const int nErrors = RecalFuncs::calculateIsSNPOrIndel(aux, sd, isSNP, isIns, isDel);
+
+        bool baqCalculated = false;
+        if (nErrors == 0 || !nsgv::gBqsrArg.enableBAQ) {
+            baqCalculated = BAQ::flatBAQArray(sd, baqArray);
+        } else {
+            // baqCalculated = calculateBAQArray(nsgv::gAuxVars[0], baq, sd, baqArray);
+        }
+        if (!baqCalculated) continue;
+
+        // PROF_START(covariate);
+        CovariateUtils::ComputeCovariates(sd, aux.header, readCovariates, true);
+        // PROF_END(gprof[GP_covariate], covariate);
+
+        // PROF_START(read_vcf);
+        RecalFuncs::calculateKnownSites(sd, aux.vcfArr, aux.header, skips);
+        for (int ii = 0; ii < sd.read_len; ++ii) {
+            skips[ii] =
+                skips[ii] || (ContextCovariate::baseIndexMap[sd.bases[ii]] == -1) || sd.base_quals[ii] < nsgv::gBqsrArg.PRESERVE_QSCORES_LESS_THAN;
+        }
+        // PROF_GP_END(read_vcf);
+
+        // PROF_START(frac_err);
+        RecalFuncs::calculateFractionalErrorArray(isSNP, baqArray, snpErrors);
+        RecalFuncs::calculateFractionalErrorArray(isIns, baqArray, insErrors);
+        RecalFuncs::calculateFractionalErrorArray(isDel, baqArray, delErrors);
+        // PROF_GP_END(frac_err);
+
+        ReadRecalInfo info(sd, readCovariates, skips, snpErrors, insErrors, delErrors);
+
+        //PROF_START(update_info);
+        RecalUtils::updateRecalTablesForRead(info, recalTables);
+        //PROF_END(gprof[GP_update_info], update_info);
+    }
+}
+
+// 并行bqsr
+int ParallelBQSR(vector<AuxVar>& auxArr) {
+    BamBufType inBamBuf(nsgv::gBqsrArg.DUPLEX_IO);
+    inBamBuf.Init(nsgv::gInBamFp, nsgv::gInBamHeader, nsgv::gBqsrArg.MAX_MEM, bqsrReadFilterOut);
+    int64_t readNumSum = 0;
+    int round = 0;
+
+    while (true) {
+        ++round;
+        // 一. 读取bam数据
+        size_t readNum = 0;
+        if (inBamBuf.ReadStat() >= 0) readNum = inBamBuf.ReadBam();
+        if (readNum < 1) { break; }
+        auto bams = inBamBuf.GetBamArr();
+        for_each(auxArr.begin(), auxArr.end(), [&](AuxVar& aux) {
+            aux.bamArr = &bams;
+        });
+        spdlog::info("{} reads processed in {} round", readNum, round);
+
+        kt_for(nsgv::gBqsrArg.NUM_THREADS, thread_worker, auxArr.data(), (readNum + AuxVar::BAM_BLOCK_NUM - 1) / AuxVar::BAM_BLOCK_NUM);
+
+        readNumSum += readNum;
+        AuxVar::processedReads += readNum;
+        inBamBuf.ClearAll();  //
+    }
+    spdlog::info("read count: {}", readNumSum);
+
+//   // 12. 创建总结数据
+//   collapseQualityScoreTableToReadGroupTable(recalTables.readGroupTable, recalTables.qualityScoreTable);
+//   roundTableValues(recalTables);
+//
+//   // 13. 量化质量分数
+//   QuantizationInfo quantInfo(recalTables, nsgv::gBqsrArg.QUANTIZING_LEVELS);
+//
+//   // 14. 输出结果
+//   RecalUtils::outputRecalibrationReport(nsgv::gBqsrArg, quantInfo, recalTables);
+//
+    return 0;
+}
+
 // 在进行数据处理之前，初始化一些全局数据
 static void globalInit() {
     open_debug_files();
@@ -277,7 +382,8 @@ static void globalInit() {
     nsgv::gInBamHeader = sam_hdr_read(nsgv::gInBamFp);  // header
 
     /* 并行读取bam数据  */
-    htsThreadPool htsPoolRead = {NULL, 0};   // ，
+    htsThreadPool htsPoolRead = {NULL, 0};   //
+    int readThreadNum = min(nsgv::gBqsrArg.NUM_THREADS, 8);
     htsPoolRead.pool = hts_tpool_init(nsgv::gBqsrArg.NUM_THREADS);
     if (!htsPoolRead.pool ) {
         spdlog::error("[{}] failed to set up thread pool", __LINE__);
@@ -313,6 +419,7 @@ static void globalInit() {
         }
         // 注意初始化顺序，这个必须在协变量初始化之后，因为需要用到MaximumKeyValue
         nsgv::gAuxVars[i].recalTables.init(nsgv::gInBamHeader->hrecs->nrg);
+        CovariateUtils::InitPerReadCovMat(nsgv::gAuxVars[i].readCovariates);
     }
 
     // 0. 初始化一些全局数据
@@ -348,7 +455,8 @@ int BaseRecalibrator() {
 
     PROF_START(whole_process);
     globalInit();
-    ret = SerialBQSR();  // 串行处理数据，生成recal table
+    // ret = SerialBQSR(nsgv::gAuxVars[0]);  // 串行处理数据，生成recal table
+    ret = ParallelBQSR(nsgv::gAuxVars);  // 串行处理数据，生成recal table
     globalDestroy();
     sam_close(nsgv::gInBamFp);
     PROF_END(gprof[GP_whole_process], whole_process);

src/bqsr/covariate.cpp

@@ -31,6 +31,85 @@ void CovariateUtils::ComputeCovariates(SamData& sd, sam_hdr_t* header, PerReadCo
     CycleCovariate::RecordValues(sd, header, values, recordIndelValues);
 }
 
+/*
+// kernel fusion
+void CovariateUtils::ComputeCovariates(SamData& sd, sam_hdr_t* header, PerReadCovariateMatrix& values, bool recordIndelValues) {
+#define __bq_set_all_cov_indel(ins, del)                                                                                                          \
+    do {                                                                                                                                          \
+        for (int i = 0; i < sd.read_len; ++i) {                                                                                                   \
+            const int vi = negativeStrand ? sd.read_len - 1 - i : i;                                                                             \
+            const int cycleM = CycleCovariate::CycleKey(sd, i, false, CycleCovariate::MAXIMUM_CYCLE_VALUE);                                       \
+            const int cycleIndel = CycleCovariate::CycleKey(sd, i, true, CycleCovariate::MAXIMUM_CYCLE_VALUE);                                    \
+            CovariateUtils::SetAllCovs(crg, quals[i], nBasePairContextAtEachCycle[vi], cycleM, crg, (ins), indelKeys[vi], cycleIndel, crg, (del), \
+                                       indelKeys[vi], cycleIndel, i, values);                                                                     \
+        }                                                                                                                                         \
+    } while (0)
+
+#define __bq_set_all_cov(ins, del)                                                                                                             \
+    do {                                                                                                                                       \
+        for (int i = 0; i < sd.read_len; ++i) {                                                                                                \
+            const int vi = negativeStrand ? sd.read_len - 1 - i : i;                                                                           \
+            const int cycleM = CycleCovariate::CycleKey(sd, i, false, CycleCovariate::MAXIMUM_CYCLE_VALUE);                                    \
+            CovariateUtils::SetAllCovs(crg, quals[i], nBasePairContextAtEachCycle[vi], cycleM, crg, (ins), 0, 0, crg, (del), 0, 0, i, values); \
+        }                                                                                                                                      \
+    } while (0)
+
+    // 1. read group
+    uint8_t* rgStr = bam_aux_get(sd.bw->b, "RG");
+    char* rgVal = nullptr;
+    if (rgStr) rgVal = bam_aux2Z(rgStr);
+    int crg = 0;
+    if (rgVal == nullptr || ReadGroupCovariate::RgToId.find(rgVal) == ReadGroupCovariate::RgToId.end()) {
+        spdlog::error("The RG tag value for read can not be found in header!");
+    } else {
+        crg = ReadGroupCovariate::RgToId[rgVal];
+    }
+
+    // 2. base quality
+    // 在前面的处理过后，quals应该和base长度一致了
+#define __bq_set_cov(ins, del)                                              \
+    do {                                                                    \
+        for (int i = 0; i < sd.read_len; ++i) {                             \
+            CovariateUtils::SetBaseQual(quals[i], (ins), (del), i, values); \
+        }                                                                   \
+    } while (0)
+
+    const int readLength = sd.read_len;
+    const bool negativeStrand = sd.bw->GetReadNegativeStrandFlag();
+    const int INDEL_QUAL = 45;
+    auto& quals = sd.base_quals;
+    auto& strandedClippedBases = sd.strandedClippedBases;
+    strandedClippedBases.copy(sd.bases);
+    ContextCovariate::GetStrandedClippedBytes(sd, strandedClippedBases, ContextCovariate::lowQualTail);
+    auto& nBasePairContextAtEachCycle = sd.nBasePairContextAtEachCycle;
+    ContextCovariate::GetReadContextAtEachPosition(strandedClippedBases, ContextCovariate::mismatchesContextSize, ContextCovariate::mismatchesKeyMask,
+                                                   nBasePairContextAtEachCycle);
+    if (recordIndelValues) {
+        // context
+        auto& indelKeys = sd.indelKeys;
+        ContextCovariate::GetReadContextAtEachPosition(strandedClippedBases, ContextCovariate::indelsContextSize, ContextCovariate::indelsKeyMask,
+                                                       indelKeys);
+        // cycle cov is in the loop
+
+        // quality
+        uint8_t* insQualPtr = bam_aux_get(sd.bw->b, "BI");  // base qualities for insertions
+        uint8_t* delQualPtr = bam_aux_get(sd.bw->b, "BD");  // base qualities for deletions
+        if (insQualPtr == nullptr && delQualPtr == nullptr) {
+            __bq_set_all_cov_indel(INDEL_QUAL, INDEL_QUAL);
+        } else if (insQualPtr == nullptr) {
+            uint8_t* delQuals = (uint8_t*)bam_aux2Z(delQualPtr) + sd.left_clip;
+            __bq_set_all_cov_indel(INDEL_QUAL, delQuals[i]);
+        } else {
+            uint8_t* insQuals = (uint8_t*)bam_aux2Z(insQualPtr) + sd.left_clip;
+            __bq_set_all_cov_indel(insQuals[i], INDEL_QUAL);
+        }
+    } else {
+        __bq_set_all_cov(0, 0);
+    }
+
+}
+*/
+
 // ReadGroupCovariate 协变量的方法
 void ReadGroupCovariate::RecordValues(SamData& sd, sam_hdr_t* header, PerReadCovariateMatrix& values, bool recordIndelValues) {
     uint8_t *rgStr = bam_aux_get(sd.bw->b, "RG");
@@ -99,7 +178,7 @@ static char SimpleComplement(const char base) {
     }
 }
 
-static void ClipLowQualEndsWithN(string& bases, const StableArray<uint8_t> &quals, uint8_t lowQTail, bool isNegativeStrand) {
+static void ClipLowQualEndsWithN(StableArray<char>& bases, const StableArray<uint8_t>& quals, uint8_t lowQTail, bool isNegativeStrand) {
     // 处理左边
     int left = 0;
     int readLen = bases.size();
@@ -118,10 +197,10 @@ static void ClipLowQualEndsWithN(string& bases, const StableArray<uint8_t> &qual
                 break;
         }
     }
-    if (left == readLen) {
+    //if (left == readLen) {
-        bases.clear();
+    //    bases.clear();
-        return;
+    //    return;
-    }
+    //}
     // 处理右边
     int right = (int)bases.size() - 1;
     if (isNegativeStrand) {
@@ -139,13 +218,12 @@ static void ClipLowQualEndsWithN(string& bases, const StableArray<uint8_t> &qual
                 break;
         }
     }
-    if (right < left)
+    // if (right < left)
-        bases.clear();
+    //     bases.clear();
-
 }
 
 // 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(SamData& sd, string& clippedBases, uint8_t lowQTail) {
+void ContextCovariate::GetStrandedClippedBytes(SamData& sd, StableArray<char>& clippedBases, uint8_t lowQTail) {
     if (sd.bw->GetReadNegativeStrandFlag()) {  // 反向互补
         for (int i = 0; i < sd.read_len; ++i) clippedBases[i] = SimpleComplement(sd.bases[sd.read_len - 1 - i]);
     }
@@ -160,7 +238,7 @@ void ContextCovariate::GetStrandedClippedBytes(SamData& sd, string& clippedBases
  * @param end    the end position in the array (exclusive)
  * @return the key representing the dna sequence
  */
-int ContextCovariate::KeyFromContext(const string& dna, const int start, const int end) {
+int ContextCovariate::KeyFromContext(const StableArray<char>& dna, const int start, const int end) {
     int key = end - start;
     int bitOffset = LENGTH_BITS;
     for (int i = start; i < end; i++) {
@@ -188,7 +266,7 @@ int ContextCovariate::KeyFromContext(const string& dna, const int start, const i
  * @return a list that has the same length as the read and contains the (preceding) n-base context at each position.
  *
  */
-void ContextCovariate::GetReadContextAtEachPosition(const string& bases, const int contextSize, const int mask, vector<int>& keys) {
+void ContextCovariate::GetReadContextAtEachPosition(const StableArray<char>& bases, const int contextSize, const int mask, StableArray<int>& keys) {
     int readLength = bases.size();
     keys.resize(readLength);
     int keyIdx = 0;
@@ -245,11 +323,13 @@ void ContextCovariate::RecordValues(SamData& sd, sam_hdr_t* header, PerReadCovar
     const int originalReadLength = sd.read_len;
 
     // store the original bases and then write Ns over low quality ones
-    string strandedClippedBases(sd.bases.arr.data(), sd.read_len);
+    // string strandedClippedBases(sd.bases.arr.data(), sd.read_len);
+    auto &strandedClippedBases = sd.strandedClippedBases;
+    strandedClippedBases.copy(sd.bases);
     // GetStrandedClippedBytes(bw, sd, strandedClippedBases, 30); // 注意这里的lowQualTail数值
     GetStrandedClippedBytes(sd, strandedClippedBases, lowQualTail);  // 命名我之前看到过这个30的？
     // spdlog::info("bases: {}", strandedClippedBases);
-    vector<int> nBasePairContextAtEachCycle;
+    auto& nBasePairContextAtEachCycle = sd.nBasePairContextAtEachCycle;
     GetReadContextAtEachPosition(strandedClippedBases, mismatchesContextSize, mismatchesKeyMask, nBasePairContextAtEachCycle);
 
     const int readLengthAfterClipping = strandedClippedBases.size();
@@ -268,7 +348,7 @@ void ContextCovariate::RecordValues(SamData& sd, sam_hdr_t* header, PerReadCovar
     const bool negativeStrand = sd.bw->GetReadNegativeStrandFlag();
     // Note: duplicated the loop to avoid checking recordIndelValues on each iteration
     if (recordIndelValues) {
-        vector<int> indelKeys;
+        auto& indelKeys = sd.indelKeys;
         GetReadContextAtEachPosition(strandedClippedBases, indelsContextSize, indelsKeyMask, indelKeys);
         for (int i = 0; i < readLengthAfterClipping; i++) {
             const int readOffset = GetStrandedOffset(negativeStrand, i, readLengthAfterClipping);

src/bqsr/covariate.h

@@ -199,11 +199,11 @@ 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(SamData& ad, string& clippedBases, uint8_t lowQTail);
+    static void GetStrandedClippedBytes(SamData& ad, StableArray<char>& 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);
+    static int KeyFromContext(const StableArray<char>& 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);
+    static void GetReadContextAtEachPosition(const StableArray<char>& bases, const int contextSize, const int mask, StableArray<int>& keys);
 
     // 设置协变量的值
     static void RecordValues(SamData& ad, sam_hdr_t* header, PerReadCovariateMatrix& values, bool recordIndelValues);
@@ -296,6 +296,25 @@ struct CovariateUtils {
         matrix[EventType::BASE_DELETION.index][readOffset].cycle = deletion;
     }
 
+    static inline void SetAllCovs(int m1, int i1, int d1, int m2, int i2, int d2, int m3, int i3, int d3, int m4, int i4, int d4, int readOffset,
+                                  PerReadCovariateMatrix& matrix) {
+        CovariateValues *cvp = &matrix[EventType::BASE_SUBSTITUTION.index][readOffset];
+        cvp->readGroup = m1;
+        cvp->baseQuality = m2;
+        cvp->context = m3;
+        cvp->cycle = m4;
+        cvp = &matrix[EventType::BASE_INSERTION.index][readOffset];
+        cvp->readGroup = i1;
+        cvp->baseQuality = i2;
+        cvp->context = i3;
+        cvp->cycle = i4;
+        cvp = &matrix[EventType::BASE_DELETION.index][readOffset];
+        cvp->readGroup = d1;
+        cvp->baseQuality = d2;
+        cvp->context = d3;
+        cvp->cycle = d4;
+    }
+
     // 对一条read计算协变量（该协变量被上一个read用过）
     static void ComputeCovariates(SamData& ad, sam_hdr_t* header, PerReadCovariateMatrix& values, bool recordIndelValues);
 };

src/util/sam_data.h

@@ -56,6 +56,11 @@ struct SamData {
     StableArray<uint8_t> del_quals;   // delete质量分数, BD (大部分应该都没有)
     StableArray<Cigar> cigars;
 
+    // 用作临时buffer
+    StableArray<char> strandedClippedBases; // for context covariate
+    StableArray<int> nBasePairContextAtEachCycle; // for context covariate
+    StableArray<int> indelKeys; // for context covariate
+
     int64_t& softStart() { return start_pos; }
     int64_t& softEnd() { return end_pos; }
 

src/util/stable_array.h

@@ -19,7 +19,7 @@ struct StableArray {
     vector<T> arr;
     size_t idx = 0;
     void clear() { idx = 0; }
-    size_t size() { return idx; }
+    size_t size() const { return idx; }
     bool empty() { return idx == 0; }
     void reserve(size_t _size) {
         if (arr.size() < _size)
@@ -49,6 +49,12 @@ struct StableArray {
             idx++;
         }
     }
+    void copy(const StableArray<T>& other) {
+        resize(other.size());
+        for (size_t i = 0; i < other.size(); ++i) {
+            arr[i] = other.arr[i];
+        }
+    }
     inline T& operator[](size_t pos) { return arr[pos]; }
     //inline const T& operator[](size_t pos) { return arr[pos]; }
     inline const T& operator[](size_t pos) const { return arr[pos]; }