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//
// sffread.hpp
// Mothur
//
// Created by Sarah Westcott on 6/9/20.
// Copyright © 2020 Schloss Lab. All rights reserved.
//
#ifndef sffread_hpp
#define sffread_hpp
#include "mothurout.h"
#include "endiannessmacros.h"
#include "utils.hpp"
/* This class is a representation of a sff read.
https://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=show&f=formats&m=doc&s=format#sff
readHeader:
read_header_length uint16_t
name_length uint16_t
number_of_bases uint32_t
clip_qual_left uint16_t
clip_qual_right uint16_t
clip_adapter_left uint16_t
clip_adapter_right uint16_t
name char[name_length]
eight_byte_padding uint8_t[*]
readInfo:
flowgram_values uint*_t[number_of_flows]
flow_index_per_base uint8_t[number_of_bases]
bases char[number_of_bases]
quality_scores uint8_t[number_of_bases]
eight_byte_padding uint8_t[*]
*/
class SffRead {
public:
SffRead(ifstream&, int);
SffRead(int num);
~SffRead();
bool readSff(ifstream& in);
bool isOkay() { return good; }
void printFasta(ofstream& out, bool trim);
void printQuality(ofstream& out, bool trim);
void printFlow(ofstream& out);
void printSff(ofstream& out);
void printSffTxt(ofstream& out);
//read header info
string getName() { return name; }
string getTimeStamp() { return timestamp; }
string getRegion() { return region; }
string getXY() { return xy; }
unsigned short getHeaderLength() { return headerLength; }
unsigned short getNameLength() { return nameLength; }
unsigned short getClipQualLeft() { return clipQualLeft; }
unsigned short getClipQualRight() { return clipQualRight; }
unsigned short getClipAdapterLeft() { return clipAdapterLeft; }
unsigned short getClipAdapterRight() { return clipAdapterRight; }
unsigned int getNumBases() { return numBases; }
//read info
vector<unsigned short> getFlowgrams() { return flowgram; }
vector<unsigned int> getFlowIndex() { return flowIndex; }
vector<unsigned int> getQualScores() { return qualScores; }
string getBases() { return bases; }
void setName(string n) { name = n; }
void setTimeStamp(string n) { timestamp = n; }
void setRegion(string n) { region = n; }
void setXY(string n) { xy = n; }
void setHeaderLength(unsigned short n) { headerLength = n; }
void setNameLength(unsigned short n) { nameLength = n; }
void setClipQualLeft(unsigned short n) { clipQualLeft = n; }
void setClipQualRight(unsigned short n) { clipQualRight = n; }
void setClipAdapterLeft(unsigned short n) { clipAdapterLeft = n; }
void setClipAdapterRight(unsigned short n) { clipAdapterRight = n; }
void setNumBases(unsigned int n) { numBases = n; }
//read info
void setFlowgrams(vector<unsigned short> n) { flowgram = n; }
void setFlowIndex(vector<unsigned int> n) { flowIndex = n; }
void setQualScores(vector<unsigned int> n) { qualScores = n; }
void setBases(string n) { bases = n; }
private:
MothurOut* m;
vector<char*> entireRead;
//header fields
unsigned short headerLength;
unsigned short nameLength;
unsigned int numBases;
unsigned short clipQualLeft;
unsigned short clipQualRight;
unsigned short clipAdapterLeft;
unsigned short clipAdapterRight;
string name; //length depends on nameLength
string timestamp;
string region;
string xy;
//readFields
vector<unsigned short> flowgram;
vector<unsigned int> flowIndex;
string bases;
vector<unsigned int> qualScores;
int numFlows, padSize1, padSize2;
unsigned long long size;
bool good;
void printSffTxtHeader(ofstream& out);
int decodeName(string&, string&, string&, string);
bool sanityCheck();
};
#endif /* sffread_hpp */
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