44 lines
1.3 KiB
C
44 lines
1.3 KiB
C
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/*
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Description: 保存bqsr计算的各种数据，根据这些数据生成bqsr table
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Copyright : All right reserved by ICT
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Author : Zhang Zhonghai
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Date : 2025/12/24
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*/
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#pragma once
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#include "covariate.h"
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#include "nested_array.h"
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#include "recal_datum.h"
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struct RecalTables {
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int qualDimension = 94; // MAX_SAM_QUAL_SCORE(93) + 1
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int eventDimension = EventType::EVENT_SIZE;
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int numReadGroups;
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// These two tables are special
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Array2D<RecalDatum> readGroupTable;
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Array3D<RecalDatum> qualityScoreTable;
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// additional tables
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Array4D<RecalDatum> contextTable;
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Array4D<RecalDatum> cycleTable;
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// NestedArray<int> testArr;
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RecalTables() {}
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RecalTables(int _numReadGroups) { init(_numReadGroups); }
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void init(int _numReadGroups) {
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numReadGroups = _numReadGroups;
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// 初始化readgroup和quality两个table
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readGroupTable.init(numReadGroups, eventDimension);
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qualityScoreTable.init(numReadGroups, qualDimension, eventDimension);
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// 初始化context和cycle两个table
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contextTable.init(numReadGroups, qualDimension, ContextCovariate::MaximumKeyValue() + 1, eventDimension);
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cycleTable.init(numReadGroups, qualDimension, CycleCovariate::MaximumKeyValue() + 1, eventDimension);
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}
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};
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