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/**********************************************************************
* Skewer - a fast and accurate adapter trimming tool
* using the bit-masked k-difference matching algorithm
* Copyright (c) 2013-2016 by Hongshan Jiang
* hongshan.jiang@gmail.com
*
* If you use this program, please cite the paper:
* Jiang, H., Lei, R., Ding, S.W. and Zhu, S. (2014) Skewer: a fast and
* accurate adapter trimmer for next-generation sequencing paired-end reads.
* BMC Bioinformatics, 15, 182.
* http://www.biomedcentral.com/1471-2105/15/182
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
#ifndef _MATRIX_H
#define _MATRIX_H
#include <stdlib.h>
#include <deque>
#include <vector>
#include <set>
#include <string>
#include "common.h"
using namespace std;
typedef struct{
double score;
int nIndel;
INDEX idx;
}ELEMENT;
class ElementComparator
{
public:
bool operator()(const ELEMENT &elem1, const ELEMENT &elem2){
return elem1.idx.pos < elem2.idx.pos;
}
};
typedef set<ELEMENT, ElementComparator> ELEMENT_SET;
class cElementSet : public ELEMENT_SET
{
public:
bool insert(const ELEMENT& val);
};
typedef enum{
CD_NONE = 0,
CD_A = 1, // Adenosine
CD_C = 2, // Cytidine
CD_G = 3, // Guanosine
CD_T = 4, // Thymidine (or Uridine)
CD_R = 5, // puRine, A or G
CD_Y = 6, // pYrimidine, T or C
CD_S = 7, // Strong, G or C
CD_W = 8, // Weak, A or T
CD_K = 9, // Keto, G or T
CD_M = 10, // aMino, A or C
CD_B = 11, // not A
CD_D = 12, // not C
CD_H = 13, // not G
CD_V = 14, // not T
CD_N = 15, // any base
CD_CNT = CD_N+1,
CD_BASIC_CNT = 5
}CODE;
class cAdapter
{
char sequence[MAX_ADAPTER_LEN+1]; // for debug only
char barcode[MAX_ADAPTER_LEN+1];
char primer[MAX_ADAPTER_LEN+1];
bool masked[MAX_ADAPTER_LEN+1];
inline void UPDATE_COLUMN(deque<ELEMENT> & queue, uint64 &d0bits, uint64 &lbits, uint64 &unbits, uint64 &dnbits, double &penal, double &dMaxPenalty, int &iMaxIndel);
public:
size_t len;
TRIM_MODE trimMode;
bool bBestAlign;
uint64 matchBits[CD_CNT];
public:
cAdapter();
~cAdapter();
void Init(char * seq, size_t sLen, TRIM_MODE trimMode);
void Init2(char * seq, size_t sLen);
bool align(char * read, size_t rLen, uchar * qual, size_t qLen, cElementSet &result, int bc, bool bBestAlign=true);
public:
void initBarcode(int iCut);
char * getBarcode() { return barcode; }
char * getPrimer() { return primer; }
bool * getMasked() { return masked; }
};
///////////////////////////////////////
class cMatrix
{
friend class cAdapter;
static bool bShareAdapter;
static double dEpsilon, dEpsilonIndel;
static double dPenaltyPerErr;
static double dDelta, dMu;
static double penalty[256];
static bool bSensitive;
public:
static vector<bool *> fw_masked;
static vector<bool *> rv_masked;
static vector<string> fw_barcodes;
static vector<string> rv_barcodes;
static vector<string> fw_primers;
static vector<string> rv_primers;
static vector<int> rowBc;
static vector<int> colBc;
public:
static deque<cAdapter> firstAdapters;
static deque<cAdapter> secondAdapters;
static deque<cAdapter> junctionAdapters;
static vector<int> junctionLengths;
static vector< vector<int> > indices;
static int iIdxCnt;
static int iMinOverlap;
public:
cMatrix();
~cMatrix();
private:
static bool CalcRevCompScore(char * seq, char * seq2, int len, uchar * qual, uchar * qual2, size_t qLen, double &score);
static string GetRevComp(char * seq, int len);
public:
static void InitParameters(enum TRIM_MODE trimMode, double dEpsilon, double dEpsilonIndel, int baseQual, bool bShareAdapter);
static void AddAdapter(deque<cAdapter> & adapters, char * vector, size_t len, TRIM_MODE trimMode);
static void CalculateJunctionLengths();
static void CalculateIndices(vector< vector<bool> > &bMatrix, int nRow, int nCol);
static void InitBarcodes(deque<cAdapter> & fw_primers, int iCutF, deque<cAdapter> & rv_primers, int iCutR);
static bool isBlurry(char * seq, size_t len);
static bool checkQualities(uchar * quals, size_t len, int minQual);
static int trimByQuality(uchar * quals, size_t len, int minQual);
static INDEX findAdapter(char * read, size_t rLen, uchar * qual, size_t qLen);
static INDEX findAdapter2(char * read, size_t rLen, uchar * qual, size_t qLen);
static INDEX findJuncAdapter(char * read, size_t rLen, uchar * qual, size_t qLen);
static bool findAdapterWithPE(char * read, char * read2, size_t rLen, size_t rLen2, uchar * qual, uchar * qual2, size_t qLen, size_t qLen2, INDEX &index, INDEX & index2);
static int findAdaptersBidirectionally(char * read, size_t rLen, uchar * qual, size_t qLen,
char * read2, size_t rLen2, uchar * qual2, size_t qLen2, INDEX &index, INDEX &index2);
static int findAdaptersInARead(char * read, size_t rLen, uchar * qual, size_t qLen, INDEX &index);
static bool PrepareBarcode(char * barcodeSeq, int bcIdx, char * seq, int len, char * seq2, int len2, char * barcodeQual, char * qual, char * qual2);
static bool PrepareBarcode(char * barcodeSeq, int bcIdx, char * seq, int len, char * seq2, int len2);
static INDEX mergePE(char * read, char * read2, size_t rLen, uchar * qual, uchar * qual2, size_t qLen, size_t startPos, size_t jLen);
static bool combinePairSeqs(char * read, char * read2, int len, int len2, uchar * qual, uchar * qual2, int qLen, int qLen2);
};
#endif // _MATRIX_H
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