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#pragma once
#include "stdafx.h"
#include "FileOutputBuffer.h"
#include "AlignmentsQ.h"
#include "ShortReadUtil.h"
#include "ColorSpaceRead.h" // TODO: Move that so Mapping Result is undependent to that
// class conatins the result of a mapping
const int READ_BUFFER_SIZE = MAX_READ_LENGTH * 2 + 1;
const int SCORES_BUFFER_SIZE = MAX_READ_LENGTH * 10 + 1;
class CMappingResult
{
public:
CMappingResult(void);
CMappingResult(CAlignmentsQ& que, unsigned int uiReadLength);
~CMappingResult(void);
unsigned int uiReadLength;
char QNAME[FILENAME_MAX];
char RNAME[FILENAME_MAX];
char caRef[READ_BUFFER_SIZE];
char caRead[READ_BUFFER_SIZE];
char rawScores[READ_BUFFER_SIZE]; // for calculate
char QScores[SCORES_BUFFER_SIZE]; // for print
unsigned int uiGlobalMappedPos, uiRefId, uiPOS;
unsigned int uiDiff;
int mismatchScore; //Sum of quality score of mismatches bases, if quality score are available.
char strand;
unsigned int MultipleMappedNo;
char SNPtype; // If not SOLiD read, print a space. If SOLiD read, the SNP type indicated by N, C, V, T
// Attribute only for SAM
inline void getReverseReadandQual(void);
inline void setSingleEndSamFields(void);
inline void setSingleEndSamFlags(void);
inline void setPairedEndSamFields(void);
inline void setPairedEndSamFlags(bool firstRead, char mateStrand);
// For SAM format, which prints read in ref direction
char revComRead[READ_BUFFER_SIZE];
char revQScores[SCORES_BUFFER_SIZE];
int FLAG;
int MAPQ;
int ISIZE;
unsigned int uiMPOS;
char CIGAR[FILENAME_MAX];
char MRNM[FILENAME_MAX];
char TAG[FILENAME_MAX];
bool isColorRead;
private:
inline void initialization(void);
};
inline void CMappingResult::getReverseReadandQual(void)
{
// if (strand == '-')
{
strcpy(revComRead, caRead);
strcpy(revQScores, QScores);
reverseComplementKmer(revComRead);
reverseKmer(revQScores);
}
}
inline void CMappingResult::setSingleEndSamFlags(void)
{
this->FLAG = 0;
if (this->strand == '-') {
this->FLAG += 0x10;
}
}
inline void CMappingResult::setPairedEndSamFields(void)
{
// Assume flag, uiMPOS, and ISIZE are set outside
this->MAPQ = 255;
this->MRNM[0] = '=';
this->MRNM[1] = '\0';
sprintf(this->CIGAR, "%uM", this->uiReadLength);
if (this->TAG[0] != '\0' && this->TAG[0] != 'N') {
sprintf(this->TAG, "NM:i:%d\t%s", this->uiDiff, string(this->TAG).c_str());
} else {
sprintf(this->TAG, "NM:i:%d", this->uiDiff);
}
}
inline void CMappingResult::setSingleEndSamFields(void)
{
this->setSingleEndSamFlags(); // Single strang + -, 64, 80
this->MAPQ = 255;
this->MRNM[0] = '*';
this->MRNM[1] = '\0';
this->uiMPOS = 0;
this->ISIZE = 0;
sprintf(this->CIGAR, "%uM", this->uiReadLength);
sprintf(this->TAG, "NM:i:%d", this->uiDiff);
}
inline int setFlag(int flags, int digit, bool value)
{
int flag = (0x01 << digit);
if (value) {
return( flags | flag);
} else {
return( flags & (~flag));
}
}
inline string getSamRG(const char* readsName, bool bSOLiD)
{
char RG[MAX_LINE];
const char* platform = bSOLiD ? "SOLiD" : "Illumina";
sprintf(RG, "@RG\tID:%s\tSM:%s\tPU:%s ", readsName, readsName, platform);
return(string(RG));
}
inline void setSamFlags(CMappingResult &m1, CMappingResult &m2, int m1No, int m2No, bool bInRange)
{
// potential error if one of the read is not mapped however the strand flag is still set
int flag = 1 + 0x02*(1-(int)bInRange);
m1.FLAG = flag + 0x04*((int)(m1No == 0)) + 0x08*((int)(m2No == 0)) + 0x40;
m1.FLAG += (int)(m1.strand == '-') * 0x10 + (int)(m2.strand == '-') * 0x20;
m2.FLAG = flag + 0x04*((int)(m2No == 0)) + 0x08*((int)(m1No == 0)) + 0x80;
m2.FLAG += (int)(m2.strand == '-') * 0x10 + (int)(m1.strand == '-') * 0x20;
}
inline void resetStrandSamFlag(CMappingResult &m)
{
const int strandQDigit = 4;
m.FLAG = setFlag(m.FLAG, strandQDigit, m.strand == '-');
}
inline void resetStrandSamFlags(CMappingResult &m1, CMappingResult &m2)
{
const int strandQDigit = 4;
const int strandMDigit = 5;
m1.FLAG = setFlag(m1.FLAG, strandQDigit, m1.strand == '-');
m2.FLAG = setFlag(m2.FLAG, strandQDigit, m2.strand == '-');
m1.FLAG = setFlag(m1.FLAG, strandMDigit, m2.strand == '-');
m2.FLAG = setFlag(m2.FLAG, strandMDigit, m1.strand == '-');
}
inline void setSamFlags4OnlyOneEndMapped(CMappingResult &m, bool firstRead)
{
int flag = 0x01;
m.FLAG = flag + 0x08 + (int)(m.strand == '-') * 0x40;
if (firstRead) {
m.FLAG += 0x40;
} else {
m.FLAG += 0x80;
}
}
inline void printAMappingInSam(FileOutputBuffer* AlignResult, CMappingResult& m)
{
char* SEQ = (m.strand == '+') ? m.caRead : m.revComRead;
char* QUAL = (m.strand == '+') ? m.QScores : m.revQScores;
resetStrandSamFlag(m);
// fake quality score
if (QUAL[0] == '\0') {
memset(QUAL, 'I', sizeof(char) * m.uiReadLength);
}
QUAL[m.uiReadLength] = '\0';
unsigned int uiMPOS = (m.MRNM[0] == '*' ? 0 : m.uiMPOS + 1);
sprintf(AlignResult->caBufp, "%s\t%d\t%s\t%u\t%d\t%s\t%s\t%u\t%d\t%s\t%s\t%s\n",\
m.QNAME, m.FLAG, m.RNAME, m.uiPOS + 1, m.MAPQ, m.CIGAR,\
m.MRNM, uiMPOS, m.ISIZE, SEQ, QUAL, m.TAG);
AlignResult->UpdateSize();
}
// TODO the quality score is not handled
inline void printAMappingInFastq(FileOutputBuffer* AlignResult, CMappingResult& m)
{
char readInColor[FILENAME_MAX];
char colorReadQ[FILENAME_MAX];
// fake quality score
if (m.QScores[0] == '\0') {
if (m.isColorRead) {
memset(colorReadQ, '!', sizeof(char) * m.uiReadLength);
} else {
memset(m.QScores, 'I', sizeof(char) * m.uiReadLength);
}
}
// TODO: assign m.isColorRead when maaping
// TODO: if it is color read, make color read output
const char* SEQ;
const char* QUAL;
if (m.isColorRead) {
// TODO: Move that so Mapping Result is undependent to that
basesStr2ColorStr(m.caRead, readInColor);
SEQ = readInColor;
QUAL = colorReadQ;
} else {
SEQ = m.caRead;
QUAL = m.QScores;
}
m.QScores[m.uiReadLength] = '\0';
sprintf(AlignResult->caBufp, "@%s\n%s\n+\n%s\n", m.QNAME, SEQ, QUAL);
AlignResult->UpdateSize();
}
// Assume both end are mapped to a same reference
inline bool printAPairedMappingInSam\
(FileOutputBuffer* AlignResult, CMappingResult &m1, CMappingResult &m2)
{
const bool bMapped = true;
setSamFlags(m1, m2, (int)(bMapped), (int)(bMapped), bMapped);
m1.setPairedEndSamFields();
m2.setPairedEndSamFields();
m1.uiMPOS = m2.uiPOS;
m2.uiMPOS = m1.uiPOS;
strcpy(m2.QNAME, m1.QNAME); // sam format needs a same query name for a pair.
printAMappingInSam(AlignResult, m1);
printAMappingInSam(AlignResult, m2);
return(true);
}
inline void printAMappingInPerM(FileOutputBuffer* AlignResult, CMappingResult& m, bool bPrintNM)
{
bool bPrintNoOfMis = (bPrintNM || m.QScores[0] == '\0');
int mis = (bPrintNoOfMis ? (int)m.uiDiff : m.mismatchScore);
if (m.QScores[0] == '\0') {
sprintf(AlignResult->caBufp, "%s\t%s\t%s\t%d\t%s\t%c\t%d\t%u\t%s\n",\
m.QNAME, m.caRead, m.RNAME, m.uiPOS, m.caRef,\
m.strand, mis, m.MultipleMappedNo,"*");
} else {
sprintf(AlignResult->caBufp, "%s\t%s\t%s\t%d\t%s\t%c\t%d\t%u\t%s\n",\
m.QNAME, m.caRead, m.RNAME, m.uiPOS, m.caRef,\
m.strand, mis, m.MultipleMappedNo, m.QScores);
}
AlignResult->UpdateSize();
}
inline string getCategory(char strand1, char strand2, int ISIZE, int disLB, int disUB)
{
char category[4];
category[3] = '\0';
category[0] = (strand1 == strand2) ? 'A' : 'B';
category[1] = (strand1 == '-') ? 'B' : 'A';
if (ISIZE > disUB) {
category[2] = 'B';
} else if (ISIZE < disLB) {
category[2] = 'C';
} else {
category[2] = 'A';
}
return(string(category));
}
inline bool hasQScores(CMappingResult &m)
{
// TODO Has a better judgement
return(m.QScores[0] != '\0');
}
//
inline bool printAPairedMappingInPerM\
(FileOutputBuffer* AlignResult, CMappingResult &m1, CMappingResult &m2, int mappedPairedNo, bool bPrintNM = false)
{
bool bPrintNoOfMis = (bPrintNM || !hasQScores(m1) || !hasQScores(m2));
int mis1 = (bPrintNoOfMis ? (int)m1.uiDiff : m1.mismatchScore);
int mis2 = (bPrintNoOfMis ? (int)m2.uiDiff : m2.mismatchScore);
int totalMis = mis1 + mis2;
if(m1.caRef[0] == '\0' || m2.caRef[0] == '\0') {
if(m1.QScores == (char *)'\0' || m2.QScores == (char *)'\0') {
sprintf(AlignResult->caBufp, "%s\t%s\t%s\t%d\t%d\t%d\t%s\t%s\t%u\t%u\t%c\t%c\t%d\n",
m1.QNAME, m1.caRead, m2.caRead, mis1, mis2,
totalMis, m1.RNAME, m2.RNAME, m1.uiPOS, m2.uiPOS, m1.strand, m2.strand, mappedPairedNo);
} else {
sprintf(AlignResult->caBufp, "%s\t%s\t%s\t%s\t%s\t%d\t%d\t%d\t%s\t%s\t%u\t%u\t%c\t%c\t%d\n",
m1.QNAME, m1.caRead, m2.caRead, m1.QScores, m2.QScores, mis1, mis2,
totalMis, m1.RNAME, m2.RNAME, m1.uiPOS, m2.uiPOS, m1.strand, m2.strand, mappedPairedNo);
}
} else {
if(m1.QScores == (char *)'\0' || m2.QScores == (char *)'\0') {
sprintf(AlignResult->caBufp, "%s\t%s\t%s\t%d\t%d\t%d\t%s\t%s\t%u\t%u\t%c\t%c\t%d\t%s\t%s\n",
m1.QNAME, m1.caRead, m2.caRead, mis1, mis2,
totalMis, m1.RNAME, m2.RNAME, m1.uiPOS, m2.uiPOS, m1.strand, m2.strand, mappedPairedNo, m1.caRef, m2.caRef);
} else {
sprintf(AlignResult->caBufp, "%s\t%s\t%s\t%s\t%s\t%d\t%d\t%d\t%s\t%s\t%u\t%u\t%c\t%c\t%d\t%s\t%s\n",
m1.QNAME, m1.caRead, m2.caRead, m1.QScores, m2.QScores, mis1, mis2,
totalMis, m1.RNAME, m2.RNAME, m1.uiPOS, m2.uiPOS, m1.strand, m2.strand, mappedPairedNo, m1.caRef, m2.caRef);
}
}
AlignResult->UpdateSize();
return(true);
}
inline void printAMappingInGff(FileOutputBuffer* AlignResult, CMappingResult& m,\
int score, string& rTag)
{
sprintf(AlignResult->caBufp, "%s\tsolid\tread\t%d\t%d\t%d\t%c\t.\tg=%s;q=%s;r=%s",
m.QNAME, m.uiPOS + 1, m.uiPOS + m.uiReadLength, score, m.strand,\
m.caRead, m.QScores, rTag.c_str());
AlignResult->UpdateSize();
}
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