/*
     Description: 解析knownsites vcf文件的类

     Copyright : All right reserved by ICT

     Author : Zhang Zhonghai
     Date : 2025/12/24
*/
#pragma once

#include <htslib/sam.h>

#include <deque>
#include <fstream>
#include <string>

#include "interval.h"
#include "linear_index.h"

using std::deque;
using std::ifstream;
using std::string;

// 需要支持vcf idx，tbi，csi三种索引方式
// vcf和idx是一对
// vcf.gz和tbi或csi是一对

// 解析knownSites
struct VCFParser {
    deque<Interval> knownSites;  // 已知的变异位点
    char* buf = nullptr;         // // 数据buffer
    uint32_t bufLen = 4 * 1024;  // 数据buffer长度
    LinearIndex index;           // vcf文件索引
    ifstream inStm;              // vcf文件流

    VCFParser() { Init(); }
    VCFParser(const string& vcfFileName) { Init(vcfFileName); }
    VCFParser(const string& vcfFileName, sam_hdr_t* samHeader) { Init(vcfFileName, samHeader); }

    void Init() { buf = (char*)malloc(bufLen); }
    void Init(const string& vcfFileName) {
        Init();
        inStm.open(vcfFileName, ifstream::in);
        string idxFileName = vcfFileName + ".idx";
        if (!index.ReadIndex(idxFileName))
            error("[%s] fail to load the %s index file\n", __func__, idxFileName.c_str());
    }
    void Init(const string& vcfFileName, sam_hdr_t* samHeader) {
        index.SetHeader(samHeader);
        Init(vcfFileName);
    }
};