From 3815a67618f211643fc8fdec15d1e86975adec1e Mon Sep 17 00:00:00 2001 From: zzh Date: Tue, 30 Dec 2025 01:21:13 +0800 Subject: [PATCH] =?UTF-8?q?=E4=BF=AE=E6=94=B9=E5=A4=9A=E7=BB=B4=E6=95=B0?= =?UTF-8?q?=E7=BB=84=E5=AE=9E=E7=8E=B0=E6=96=B9=E5=BC=8F=EF=BC=8C=E6=9B=B4?= =?UTF-8?q?=E6=9C=89=E5=88=A9=E4=BA=8E=E8=BF=9E=E7=BB=AD=E8=AE=BF=E5=AD=98?= =?UTF-8?q?=EF=BC=8C=E4=BF=AE=E6=94=B9reclatable=E7=9A=84=E7=B4=A2?= =?UTF-8?q?=E5=BC=95=E6=AC=A1=E5=BA=8F?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- src/bqsr/bqsr_entry.cpp | 4 +- src/bqsr/covariate.cpp | 24 +++--- src/bqsr/covariate.h | 88 ++++++++++++++-------- src/bqsr/nested_array.h | 157 +++++++++++++++++----------------------- src/bqsr/recal_datum.h | 4 +- src/bqsr/recal_tables.h | 8 +- src/bqsr/recal_utils.h | 67 ++++++----------- 7 files changed, 164 insertions(+), 188 deletions(-) diff --git a/src/bqsr/bqsr_entry.cpp b/src/bqsr/bqsr_entry.cpp index f0ce7f8..c478953 100644 --- a/src/bqsr/bqsr_entry.cpp +++ b/src/bqsr/bqsr_entry.cpp @@ -85,9 +85,7 @@ void collapseQualityScoreTableToReadGroupTable(Array2D &byReadGroupT // 遍历quality table _Foreach3DK(byQualTable, qualDatum, { if (qualDatum.numObservations > 0) { - int rgKey = k1; - int eventIndex = k3; - byReadGroupTable[rgKey][eventIndex].combine(qualDatum); + byReadGroupTable(k1, k2).combine(qualDatum); } }); } diff --git a/src/bqsr/covariate.cpp b/src/bqsr/covariate.cpp index ecd31cf..0f02b62 100644 --- a/src/bqsr/covariate.cpp +++ b/src/bqsr/covariate.cpp @@ -25,7 +25,7 @@ int CycleCovariate::MAXIMUM_CYCLE_VALUE; // 对一条read计算协变量（该协变量被上一个read用过） void CovariateUtils::ComputeCovariates(SamData& sd, sam_hdr_t* header, PerReadCovariateMatrix& values, bool recordIndelValues) { - // ReadGroupCovariate::RecordValues(sd, header, values, recordIndelValues); + ReadGroupCovariate::RecordValues(sd, header, values, recordIndelValues); BaseQualityCovariate::RecordValues(sd, header, values, recordIndelValues); ContextCovariate::RecordValues(sd, header, values, recordIndelValues); CycleCovariate::RecordValues(sd, header, values, recordIndelValues); @@ -43,7 +43,7 @@ void ReadGroupCovariate::RecordValues(SamData& sd, sam_hdr_t* header, PerReadCov key = RgToId[rgVal]; } for (int i = 0; i < sd.read_len; ++i) { - CovariateUtils::SetCovariate(key, key, key, i, ReadGroupCovariate::index, values); + CovariateUtils::SetReadGroup(key, key, key, i, values); } } @@ -51,11 +51,11 @@ void ReadGroupCovariate::RecordValues(SamData& sd, sam_hdr_t* header, PerReadCov void BaseQualityCovariate::RecordValues(SamData& sd, 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) \ - do { \ - for (int i = 0; i < sd.read_len; ++i) { \ - CovariateUtils::SetCovariate(quals[i], (ins), (del), i, BaseQualityCovariate::index, values); \ - } \ +#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 INDEL_QUAL = 45; @@ -261,7 +261,7 @@ void ContextCovariate::RecordValues(SamData& sd, sam_hdr_t* header, PerReadCovar // don't bother zeroing out if we are going to overwrite the whole array for (int i = 0; i < originalReadLength; i++) { // this base has been clipped off, so zero out the covariate values here - CovariateUtils::SetCovariate(0, 0, 0, i, ContextCovariate::index, values); + CovariateUtils::SetContext(0, 0, 0, i, values); } } @@ -273,12 +273,12 @@ void ContextCovariate::RecordValues(SamData& sd, sam_hdr_t* header, PerReadCovar for (int i = 0; i < readLengthAfterClipping; i++) { const int readOffset = GetStrandedOffset(negativeStrand, i, readLengthAfterClipping); const int indelKey = indelKeys[i]; - CovariateUtils::SetCovariate(nBasePairContextAtEachCycle[i], indelKey, indelKey, readOffset, ContextCovariate::index, values); + CovariateUtils::SetContext(nBasePairContextAtEachCycle[i], indelKey, indelKey, readOffset, values); } } else { for (int i = 0; i < readLengthAfterClipping; i++) { const int readOffset = GetStrandedOffset(negativeStrand, i, readLengthAfterClipping); - CovariateUtils::SetCovariate(nBasePairContextAtEachCycle[i], 0, 0, readOffset, ContextCovariate::index, values); + CovariateUtils::SetContext(nBasePairContextAtEachCycle[i], 0, 0, readOffset, values); } } } @@ -330,12 +330,12 @@ void CycleCovariate::RecordValues(SamData& sd, sam_hdr_t* header, PerReadCovaria for (int i = 0; i < readLength; i++) { const int substitutionKey = CycleKey(sd, i, false, MAXIMUM_CYCLE_VALUE); const int indelKey = CycleKey(sd, i, true, MAXIMUM_CYCLE_VALUE); - CovariateUtils::SetCovariate(substitutionKey, indelKey, indelKey, i, CycleCovariate::index, values); + CovariateUtils::SetCycle(substitutionKey, indelKey, indelKey, i, values); } } else { for (int i = 0; i < readLength; i++) { const int substitutionKey = CycleKey(sd, i, false, MAXIMUM_CYCLE_VALUE); - CovariateUtils::SetCovariate(substitutionKey, 0, 0, i, CycleCovariate::index, values); + CovariateUtils::SetCycle(substitutionKey, 0, 0, i, values); } } } \ No newline at end of file diff --git a/src/bqsr/covariate.h b/src/bqsr/covariate.h index 2f813c8..408436a 100644 --- a/src/bqsr/covariate.h +++ b/src/bqsr/covariate.h @@ -25,12 +25,27 @@ using std::map; using std::string; using std::vector; +// 协变量的值, 4个协变量 +struct CovariateValues { + int readGroup = 0; + int baseQuality = 0; + int context = -1; + int cycle = -1; + void clear() { + readGroup = 0; + baseQuality = 0; + context = -1; + cycle = -1; + } +}; + /** * This is where we store the per-read covariates, also indexed by (event type) and (read position). * Thus the array has shape { event type } x { read position (aka cycle) } x { covariate }. * For instance, { covariate } is by default 4-dimensional (read group, base quality, context, cycle). */ -typedef vector>> PerReadCovariateMatrix; +// 三维数组，第一维是event type，第二维是read position，第三维是协变量数组(结构体)(base quality, context, cycle) +typedef vector> PerReadCovariateMatrix; // 变异类型（snp, insert, deletion） struct EventTypeValue { @@ -48,33 +63,6 @@ struct EventType { static vector EVENTS; }; -// 协变量相关的工具类 -struct CovariateUtils { - static constexpr int MAX_READ_LENGTH = 300; // 最大read长度 - static constexpr int NUM_COVARIATES = 4; - - // 初始化PerReadCovariateMatrix - static void InitPerReadCovMat(PerReadCovariateMatrix& matrix) { - matrix.resize(EventType::EVENT_SIZE); - for (int event_type = 0; event_type < EventType::EVENT_SIZE; ++event_type) { - matrix[event_type].resize(MAX_READ_LENGTH); - for (int pos = 0; pos < MAX_READ_LENGTH; ++pos) { - matrix[event_type][pos].resize(NUM_COVARIATES, 0); - } - } - } - - // 设置协变量 - static void SetCovariate(int mismatch, int insertion, int deletion, int readOffset, int covIndex, PerReadCovariateMatrix& matrix) { - matrix[EventType::BASE_SUBSTITUTION.index][readOffset][covIndex] = mismatch; - matrix[EventType::BASE_INSERTION.index][readOffset][covIndex] = insertion; - matrix[EventType::BASE_DELETION.index][readOffset][covIndex] = deletion; - } - - // 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); -}; - // Read group协变量 struct ReadGroupCovariate { static constexpr int index = 0; // 在协变量数组中的索引位置 @@ -270,8 +258,44 @@ struct CycleCovariate { static void RecordValues(SamData& ad, sam_hdr_t* header, PerReadCovariateMatrix& values, bool recordIndelValues); }; -// 好像不需要 -struct StandardCovariateList { - ReadGroupCovariate readGroupCovariate; - BaseQualityCovariate qualityScoreCovariate; +// 协变量相关的工具类 +struct CovariateUtils { + static constexpr int MAX_READ_LENGTH = 300; // 最大read长度 + static constexpr int NUM_COVARIATES = 4; + + // 初始化PerReadCovariateMatrix + static void InitPerReadCovMat(PerReadCovariateMatrix& matrix) { + matrix.resize(EventType::EVENT_SIZE); + for (int event_type = 0; event_type < EventType::EVENT_SIZE; ++event_type) { + matrix[event_type].resize(MAX_READ_LENGTH); + } + } + + // 设置协变量 + static inline void SetReadGroup(int mismatch, int insertion, int deletion, int readOffset, PerReadCovariateMatrix& matrix) { + matrix[EventType::BASE_SUBSTITUTION.index][readOffset].readGroup = mismatch; + matrix[EventType::BASE_INSERTION.index][readOffset].readGroup = insertion; + matrix[EventType::BASE_DELETION.index][readOffset].readGroup = deletion; + } + + static inline void SetBaseQual(int mismatch, int insertion, int deletion, int readOffset, PerReadCovariateMatrix& matrix) { + matrix[EventType::BASE_SUBSTITUTION.index][readOffset].baseQuality = mismatch; + matrix[EventType::BASE_INSERTION.index][readOffset].baseQuality = insertion; + matrix[EventType::BASE_DELETION.index][readOffset].baseQuality = deletion; + } + + static inline void SetContext(int mismatch, int insertion, int deletion, int readOffset, PerReadCovariateMatrix& matrix) { + matrix[EventType::BASE_SUBSTITUTION.index][readOffset].context = mismatch; + matrix[EventType::BASE_INSERTION.index][readOffset].context = insertion; + matrix[EventType::BASE_DELETION.index][readOffset].context = deletion; + } + + static inline void SetCycle(int mismatch, int insertion, int deletion, int readOffset, PerReadCovariateMatrix& matrix) { + matrix[EventType::BASE_SUBSTITUTION.index][readOffset].cycle = mismatch; + matrix[EventType::BASE_INSERTION.index][readOffset].cycle = insertion; + matrix[EventType::BASE_DELETION.index][readOffset].cycle = deletion; + } + + // 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); }; \ No newline at end of file diff --git a/src/bqsr/nested_array.h b/src/bqsr/nested_array.h index 587e445..d965111 100644 --- a/src/bqsr/nested_array.h +++ b/src/bqsr/nested_array.h @@ -16,129 +16,102 @@ using std::vector; template struct Array2D { - vector> data; - Array2D() { } + vector data; + int d1 = 0, d2 = 0; + int s1 = 0, cap = 0; // strides for each dimension + Array2D() {} Array2D(int dim1, int dim2) { init(dim1, dim2); } - void init(int dim1, int dim2) { data.resize(dim1); for (auto& v : data) v.resize(dim2); } - inline T& get(int k1, int k2) { return data[k1][k2]; } - // 根据关键字，在对应位置插入数据 - inline void put(const T& value, int k1, int k2) { data[k1][k2] = value; } - inline vector& operator[](size_t idx) { return data[idx]; } - inline const vector& operator[](size_t idx) const { return data[idx]; } + void init(int dim1, int dim2) { d1 = dim1; d2 = dim2; s1 = dim2; cap = d1 * d2; data.resize(cap); } + inline T& operator()(int k1, int k2) { return data[k1 * s1 + k2]; } #define _Foreach2D(array, valName, codes) \ - for (auto& arr1 : array.data) { \ - for (auto& valName : arr1) { \ - codes; \ - } \ + for (auto& valName : array.data) { \ + codes; \ } + #define _Foreach2DK(array, valName, codes) \ do { \ - int k1 = 0; \ - for (auto& arr1 : array.data) { \ - int k2 = 0; \ - for (auto& valName : arr1) { \ - codes; \ - ++k2; \ - } \ - ++k1; \ + int k1 = 0, k2 = 0, kg = 0; \ + for (auto& valName : array.data) { \ + codes; \ + ++kg; \ + k1 = kg / (array.s1); \ + k2 = kg % (array.s1); \ } \ } while (0) }; +// 不能是bool template struct Array3D { - vector>> data; + vector data; + int d1 = 0, d2 = 0, d3 = 0; + int s1 = 0, s2 = 0, cap = 0; // strides for each dimension Array3D() {} Array3D(int dim1, int dim2, int dim3) { init(dim1, dim2, dim3); } void init(int dim1, int dim2, int dim3) { - data.resize(dim1); - for (auto& v : data) v.resize(dim2); - for (auto& v1 : data) - for (auto& v2 : v1) v2.resize(dim3); + d1 = dim1; d2 = dim2; d3 = dim3; + s1 = dim2 * dim3; s2 = dim3; cap = d1 * d2 * d3; + data.resize(cap); } - inline T& get(int k1, int k2, int k3) { return data[k1][k2][k3]; } - // 根据关键字，在对应位置插入数据 - inline void put(const T& value, int k1, int k2, int k3) { data[k1][k2][k3] = value; } - inline vector>& operator[](size_t idx) { return data[idx]; } -#define _Foreach3D(array, valName, codes) \ - for (auto& arr1 : array.data) { \ - for (auto& arr2 : arr1) { \ - for (auto& valName : arr2) { \ - codes; \ - } \ - } \ + inline T& operator()(int k1, int k2, int k3) { + return data[k1 * s1 + k2 * s2 + k3]; } -#define _Foreach3DK(array, valName, codes) \ - do { \ - int k1 = 0; \ - for (auto& arr1 : array.data) { \ - int k2 = 0; \ - for (auto& arr2 : arr1) { \ - int k3 = 0; \ - for (auto& valName : arr2) { \ - codes; \ - ++k3; \ - } \ - ++k2; \ - } \ - ++k1; \ - } \ +#define _Foreach3D(array, valName, codes) \ + for (auto& valName : array.data) { \ + codes; \ + } + +#define _Foreach3DK(array, valName, codes) \ + do { \ + int k1 = 0, k2 = 0, k3 = 0, kg = 0; \ + for (auto& valName : array.data) { \ + codes; \ + ++kg; \ + const int mod1 = kg % (array.s1); \ + k1 = kg / (array.s1); \ + k2 = mod1 / (array.s2); \ + k3 = mod1 % (array.s2); \ + } \ } while (0) }; template struct Array4D { - vector>>> data; + vector data; + int d1 = 0, d2 = 0, d3 = 0, d4; + int s1 = 0, s2 = 0, s3 = 0, cap = 0; // strides for each dimension Array4D() {} Array4D(int dim1, int dim2, int dim3, int dim4) { init(dim1, dim2, dim3, dim4); } void init(int dim1, int dim2, int dim3, int dim4) { - data.resize(dim1); - for (auto& v : data) v.resize(dim2); - for (auto& v1 : data) - for (auto& v2 : v1) v2.resize(dim3); - for (auto& v1 : data) - for (auto& v2 : v1) - for (auto& v3 : v2) v3.resize(dim4); + d1 = dim1; d2 = dim2; d3 = dim3; d4 = dim4; + s1 = d2 * d3 * d4; s2 = d3 * d4; s3 = d4; cap = d1 * d2 * d3 * d4; + data.resize(cap); } - inline T& get(int k1, int k2, int k3, int k4) { return data[k1][k2][k3][k4]; } - // 根据关键字，在对应位置插入数据 - inline void put(const T& value, int k1, int k2, int k3, int k4) { data[k1][k2][k3][k4] = value; } - inline vector>>& operator[](size_t idx) { return data[idx]; } -#define _Foreach4D(array, valName, codes) \ - for (auto& arr1 : array.data) { \ - for (auto& arr2 : arr1) { \ - for (auto& arr3 : arr2) { \ - for (auto& valName : arr3) { \ - codes; \ - } \ - } \ - } \ + inline T& operator()(int k1, int k2, int k3, int k4) { return data[k1 * s1 + k2 * s2 + k3 * s3 + k4]; } + +#define _Foreach4D(array, valName, codes) \ + for (auto& valName : array.data) { \ + codes; \ } -#define _Foreach4DK(array, valName, codes) \ - do { \ - int k1 = 0; \ - for (auto& arr1 : array.data) { \ - int k2 = 0; \ - for (auto& arr2 : arr1) { \ - int k3 = 0; \ - for (auto& arr3 : arr2) { \ - int k4 = 0; \ - for (auto& valName : arr3) { \ - codes; \ - ++k4; \ - } \ - ++k3; \ - } \ - ++k2; \ - } \ - ++k1; \ - } \ +#define _Foreach4DK(array, valName, codes) \ + do { \ + int k1 = 0, k2 = 0, k3 = 0, k4 = 0, kg = 0; \ + for (auto& valName : array.data) { \ + codes; \ + ++kg; \ + const int mod1 = kg % (array.s1); \ + const int mod2 = mod1 % (array.s2); \ + k1 = kg / (array.s1); \ + k2 = mod1 / (array.s2); \ + k3 = mod2 / (array.s3); \ + k4 = mod2 % (array.s3); \ + } \ } while (0) }; -// 类似一个tensor +// 类似一个tensor，性能太低，不用了 template struct NestedArray { vector data; diff --git a/src/bqsr/recal_datum.h b/src/bqsr/recal_datum.h index 976743b..c451297 100644 --- a/src/bqsr/recal_datum.h +++ b/src/bqsr/recal_datum.h @@ -97,13 +97,13 @@ struct RecalDatum { empiricalQuality = UNINITIALIZED_EMPIRICAL_QUALITY; } - void increment(const uint64_t incObservations, const double incMismatches) { + inline void increment(const uint64_t incObservations, const double incMismatches) { numObservations += incObservations; numMismatches += (incMismatches * MULTIPLIER); // the multiplier used to avoid underflow, or something like that. empiricalQuality = UNINITIALIZED_EMPIRICAL_QUALITY; } - void increment(const uint64_t incObservations, const double incMismatches, int baseQuality) { + inline void increment(const uint64_t incObservations, const double incMismatches, int baseQuality) { numObservations += incObservations; numMismatches += (incMismatches * MULTIPLIER); // the multiplier used to avoid underflow, or something like that. reportedQuality = baseQuality; diff --git a/src/bqsr/recal_tables.h b/src/bqsr/recal_tables.h index 7edd7fb..d342791 100644 --- a/src/bqsr/recal_tables.h +++ b/src/bqsr/recal_tables.h @@ -34,11 +34,11 @@ struct RecalTables { void init(int _numReadGroups) { numReadGroups = _numReadGroups; // 初始化readgroup和quality两个table - readGroupTable.init(numReadGroups, eventDimension); - qualityScoreTable.init(numReadGroups, qualDimension, eventDimension); + readGroupTable.init(eventDimension, numReadGroups); + qualityScoreTable.init(eventDimension, numReadGroups, qualDimension); // 初始化context和cycle两个table - contextTable.init(numReadGroups, qualDimension, ContextCovariate::MaximumKeyValue() + 1, eventDimension); - cycleTable.init(numReadGroups, qualDimension, CycleCovariate::MaximumKeyValue() + 1, eventDimension); + contextTable.init(eventDimension, numReadGroups, qualDimension, ContextCovariate::MaximumKeyValue() + 1); + cycleTable.init(eventDimension, numReadGroups, qualDimension, CycleCovariate::MaximumKeyValue() + 1); } }; \ No newline at end of file diff --git a/src/bqsr/recal_utils.h b/src/bqsr/recal_utils.h index c300985..d925388 100644 --- a/src/bqsr/recal_utils.h +++ b/src/bqsr/recal_utils.h @@ -55,44 +55,25 @@ struct RecalUtils { Array4D& cycleTable = recalTables.cycleTable; int readLength = read.read_len; - for (int offset = 0; offset < readLength; ++offset) { - // if (read.rid == 46114) { - // fprintf(gf[3], "%d %d\n", offset, info.skips[offset] ? 1 : 0); - // } - if (!info.skips[offset]) { - // if (true){ // 不跳过当前位置 - for (int idx = 0; idx < validEventTypes.size(); ++idx) { + for (int idx = 0; idx < validEventTypes.size(); ++idx) { + for (int offset = 0; offset < readLength; ++offset) { + if (!info.skips[offset]) { // 获取四个值，readgroup / qualityscore / context / cycle EventTypeValue& event = validEventTypes[idx]; - vector& covariatesAtOffset = readCovars[event.index][offset]; + CovariateValues& cv = readCovars[event.index][offset]; uint8_t qual = info.getQual(event, offset); double isError = info.getErrorFraction(event, offset); - int readGroup = covariatesAtOffset[ReadGroupCovariate::index]; - int baseQuality = covariatesAtOffset[BaseQualityCovariate::index]; - - // 处理base quality score协变量 - // RecalUtils::IncrementDatum3keys(qualityScoreTable, qual, isError, readGroup, baseQuality, event.index); - //if (read.rid == 46114) { - // fprintf(gf[3], "%d %d %f\n", offset, baseQuality, isError); - //} - qualityScoreTable[readGroup][baseQuality][event.index].increment(1, isError, baseQuality); - - auto& d = qualityScoreTable[readGroup][baseQuality][event.index]; - // spdlog::info("isError {} : {}, mis {}, obs {}", isError, info.snp_errs[offset], d.numMismatches, d.numObservations); + // 处理quality score covariate + qualityScoreTable(event.index, cv.readGroup, cv.baseQuality).increment(1, isError, cv.baseQuality); // 处理context covariate - int contextCovariate = covariatesAtOffset[ContextCovariate::index]; - if (contextCovariate >= 0) - contextTable[readGroup][baseQuality][contextCovariate][event.index].increment(1, isError, baseQuality); - // RecalUtils::IncrementDatum4keys(nsgv::gRecalTables.contextTable, qual, isError, readGroup, baseQuality, contextCovariate, - // event.index); + if (cv.context >= 0) + contextTable(event.index, cv.readGroup, cv.baseQuality, cv.context).increment(1, isError, cv.baseQuality); + // 处理cycle covariate - int cycleCovariate = covariatesAtOffset[CycleCovariate::index]; - if (cycleCovariate >= 0) - cycleTable[readGroup][baseQuality][cycleCovariate][event.index].increment(1, isError, baseQuality); - // RecalUtils::IncrementDatum4keys(nsgv::gRecalTables.cycleTable, qual, isError, readGroup, baseQuality, cycleCovariate, - // event.index); + if (cv.cycle >= 0) + cycleTable(event.index, cv.readGroup, cv.baseQuality, cv.cycle).increment(1, isError, cv.baseQuality); } } } @@ -207,8 +188,8 @@ struct RecalUtils { RecalDatum &dat = const_cast(datum); if (dat.getNumObservations() > 0) { table.addRowData({ - ReadGroupCovariate::IdToRg[k1], - ReportUtil::ToString(EventType::EVENTS[k2].representation), + ReadGroupCovariate::IdToRg[k2], + ReportUtil::ToString(EventType::EVENTS[k1].representation), ReportUtil::ToString(dat.getEmpiricalQuality(), 4), ReportUtil::ToString(dat.getReportedQuality(), 4), ReportUtil::ToString(dat.getNumObservations()), @@ -233,9 +214,9 @@ struct RecalUtils { RecalDatum &dat = const_cast(datum); if (dat.getNumObservations() > 0) { table.addRowData({ - ReadGroupCovariate::IdToRg[k1], - ReportUtil::ToString(k2), - ReportUtil::ToString(EventType::EVENTS[k3].representation), + ReadGroupCovariate::IdToRg[k2], + ReportUtil::ToString(k3), + ReportUtil::ToString(EventType::EVENTS[k1].representation), ReportUtil::ToString(dat.getEmpiricalQuality(), 4), ReportUtil::ToString(dat.getNumObservations()), ReportUtil::ToString(dat.getNumMismatches(), 2) @@ -260,11 +241,11 @@ struct RecalUtils { RecalDatum &dat = const_cast(datum); if (dat.getNumObservations() > 0) { table.addRowData({ - ReadGroupCovariate::IdToRg[k1], - ReportUtil::ToString(k2), - ReportUtil::ToString(ContextCovariate::ContextFromKey(k3)), + ReadGroupCovariate::IdToRg[k2], + ReportUtil::ToString(k3), + ReportUtil::ToString(ContextCovariate::ContextFromKey(k4)), "Context", - ReportUtil::ToString(EventType::EVENTS[k4].representation), + ReportUtil::ToString(EventType::EVENTS[k1].representation), ReportUtil::ToString(dat.getEmpiricalQuality(), 4), ReportUtil::ToString(dat.getNumObservations()), ReportUtil::ToString(dat.getNumMismatches(), 2) @@ -276,11 +257,11 @@ struct RecalUtils { RecalDatum &dat = const_cast(datum); if (dat.getNumObservations() > 0) { table.addRowData({ - ReadGroupCovariate::IdToRg[k1], - ReportUtil::ToString(k2), - ReportUtil::ToString(CycleCovariate::CycleFromKey(k3)), + ReadGroupCovariate::IdToRg[k2], + ReportUtil::ToString(k3), + ReportUtil::ToString(CycleCovariate::CycleFromKey(k4)), "Cycle", - ReportUtil::ToString(EventType::EVENTS[k4].representation), + ReportUtil::ToString(EventType::EVENTS[k1].representation), ReportUtil::ToString(dat.getEmpiricalQuality(), 4), ReportUtil::ToString(dat.getNumObservations()), ReportUtil::ToString(dat.getNumMismatches(), 2)