457 lines
13 KiB
C++
457 lines
13 KiB
C++
/*
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Description: 读入sam/bam时，开辟一个大的buf，存放这些数据
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Copyright : All right reserved by ICT
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Author : Zhang Zhonghai
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Date : 2019/11/27
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*/
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#ifndef BAM_WRAP_H_
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#define BAM_WRAP_H_
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#include <map>
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#include <string>
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#include <vector>
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#include <sstream>
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#include <limits.h>
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#include <math.h>
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#include <htslib/sam.h>
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using namespace std;
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/*
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这里的成员函数命名有点混乱，特此说明，小写加下划线的函数命名，无论是静态函数，还是普通成员函数，更侧重说明
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这是类似bam的一个属性，而大写加驼峰命名的函数，更侧重说明这是通过计算得出的。
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*/
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/*
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* sam read的封装
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*/
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struct BamWrap
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{
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// 将contig左移后加上pos作为全局位置
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const static int MAX_CONTIG_LEN_SHIFT = 30;
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const static int READ_MAX_LENGTH = 200;
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const static int READ_MAX_DEPTH = 1000; // 这只是用来初始化空间用的，深度大于这个值也没关系
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// 成员变量尽量少，减少占用内存空间
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bam1_t *b;
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int64_t end_pos_; // bam的全局结束位置, 闭区间
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// 全局开始位置
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inline int64_t start_pos()
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{
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return bam_global_pos(b);
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}
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// 全局结束位置
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inline int64_t end_pos()
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{
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return end_pos_;
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}
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// 和reference对应的序列长度
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inline int16_t read_len()
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{
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return (end_pos_ - start_pos() + 1);
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}
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// 在contig内的开始位置
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inline int32_t contig_pos()
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{
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return b->core.pos;
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}
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// 在contig内部的结束位置
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inline int32_t contig_end_pos()
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{
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return bam_pos(end_pos_);
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}
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// 序列的长度（AGTC字母个数）
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inline int16_t seq_len()
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{
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return b->core.l_qseq;
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}
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// 算上开头的softclip
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inline int32_t softclip_start()
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{
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const uint32_t *cigar = bam_get_cigar(b);
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const bam1_core_t &bc = b->core;
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const char c = bam_cigar_opchr(cigar[0]);
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const int len = bam_cigar_oplen(cigar[0]);
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if (c == 'S')
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return bc.pos - len;
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return bc.pos;
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}
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// 算上结尾的softclip
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inline int32_t softclip_end()
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{
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const uint32_t *cigar = bam_get_cigar(b);
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const bam1_core_t &bc = b->core;
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const char c = bam_cigar_opchr(cigar[bc.n_cigar - 1]);
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const int len = bam_cigar_oplen(cigar[bc.n_cigar - 1]);
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if (c == 'S')
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return bam_pos(end_pos_) + len;
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return bam_pos(end_pos_);
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}
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// 算上结尾的softclip
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inline int32_t right_softclip_len()
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{
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const uint32_t *cigar = bam_get_cigar(b);
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const bam1_core_t &bc = b->core;
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const char c = bam_cigar_opchr(cigar[bc.n_cigar - 1]);
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const int len = bam_cigar_oplen(cigar[bc.n_cigar - 1]);
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if (c == 'S')
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return len;
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return 0;
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}
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// 获取序列
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inline std::string sequence()
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{
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ostringstream oss;
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char *seq = (char *)bam_get_seq(b);
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const bam1_core_t &bc = b->core;
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const char base_to_char[16] = {'N', 'A', 'C', 'N', 'G', 'N', 'N', 'N', 'T', 'N', 'N', 'N', 'N', 'N', 'N', 'N'};
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for (int i = 0; i < bc.l_qseq; ++i)
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{
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char base = base_to_char[bam_seqi(seq, i)];
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oss << base;
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}
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return std::move(oss.str());
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}
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// 获取名字
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inline const char *query_name()
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{
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return bam_get_qname(b);
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}
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// 获取cigar 字符串
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inline string cigar_str()
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{
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ostringstream oss;
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const uint32_t *cigar = bam_get_cigar(b);
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const bam1_core_t &bc = b->core;
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for (int i = 0; i < bc.n_cigar; ++i)
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{
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const char c = bam_cigar_opchr(cigar[i]);
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const int len = bam_cigar_oplen(cigar[i]);
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oss << len << c;
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}
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return std::move(oss.str());
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}
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// 占用的内存大小
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inline int16_t length()
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{
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return sizeof(*this) +
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sizeof(bam1_t) +
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b->l_data;
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}
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// 获取cigar中insert的总长度
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inline int32_t insert_cigar_len()
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{
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const uint32_t *cigar = bam_get_cigar(b);
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const bam1_core_t &bc = b->core;
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int ret = 0;
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for (int i = 0; i < bc.n_cigar; ++i)
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{
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const char c = bam_cigar_opchr(cigar[i]);
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const int len = bam_cigar_oplen(cigar[i]);
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if (c == 'I')
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ret += len;
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}
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return ret;
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}
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// 获取cigar中delete的总长度
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inline int32_t del_cigar_len()
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{
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const uint32_t *cigar = bam_get_cigar(b);
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const bam1_core_t &bc = b->core;
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int ret = 0;
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for (int i = 0; i < bc.n_cigar; ++i)
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{
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const char c = bam_cigar_opchr(cigar[i]);
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const int len = bam_cigar_oplen(cigar[i]);
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if (c == 'D')
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ret += len;
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}
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return ret;
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}
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// 计算sam read的终点位置
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static inline int64_t BamEndPos(const bam1_t *b)
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{
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const uint32_t *cigar = bam_get_cigar(b);
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const bam1_core_t &bc = b->core;
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int start_offset = -1;
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for (int i = 0; i < bc.n_cigar; ++i)
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{
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const char c = bam_cigar_opchr(cigar[i]);
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const int len = bam_cigar_oplen(cigar[i]);
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if (c == 'D' || c == 'N' || c == 'M' || c == '=' || c == 'X')
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start_offset += len;
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}
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return (((int64_t)b->core.tid << MAX_CONTIG_LEN_SHIFT) | (int64_t)(b->core.pos + start_offset));
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};
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bool HasWellDefinedFragmentSize()
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{
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const bam1_core_t &bc = b->core;
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bool hasWellDefinedFragmentSize = true;
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if (bc.isize == 0 ||
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!(bc.flag & BAM_FPAIRED) ||
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((bc.flag & BAM_FUNMAP) || (bc.flag & BAM_FMUNMAP)) ||
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((bool)(bc.flag & BAM_FREVERSE) == (bool)(bc.flag & BAM_FMREVERSE)))
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{
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hasWellDefinedFragmentSize = false;
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}
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else if (bc.flag & BAM_FREVERSE)
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{
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hasWellDefinedFragmentSize = contig_end_pos() > bc.mpos ? true : false;
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}
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else
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{
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hasWellDefinedFragmentSize = bc.pos <= bc.mpos + bc.isize ? true : false;
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}
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return hasWellDefinedFragmentSize;
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}
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// 计算bam的adapterBoundary
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int GetAdapterBoundary()
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{
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const bam1_core_t &bc = b->core;
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int adapterBoundary;
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if (!HasWellDefinedFragmentSize())
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adapterBoundary = INT_MIN;
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else if (bc.flag & BAM_FREVERSE)
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adapterBoundary = bc.mpos - 1;
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else
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adapterBoundary = bc.pos + abs(bc.isize); // GATK4.0 和 GATK3.5不一样，3.5的这里+1
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return adapterBoundary;
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}
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// 获取开头的I的长度
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inline int GetHeadInsertLen()
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{
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int insLen = 0;
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const uint32_t *cigar = bam_get_cigar(b);
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const bam1_core_t &bc = b->core;
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for (int i = 0; i < bc.n_cigar; ++i)
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{
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const char c = bam_cigar_opchr(cigar[i]);
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const int len = bam_cigar_oplen(cigar[i]);
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if (c == 'I')
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{
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insLen = len;
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break;
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}
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else if (c != 'H' && c != 'S')
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break;
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}
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return insLen;
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}
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// 获取soft clip开始位置(能处理H和S相连的情况，有这种情况么？, 注意开头的I要当做S？)
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inline int64_t GetSoftStart()
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{
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int64_t softStart = b->core.pos;
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const uint32_t *cigar = bam_get_cigar(b);
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const bam1_core_t &bc = b->core;
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for (int i = 0; i < bc.n_cigar; ++i)
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{
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const char c = bam_cigar_opchr(cigar[i]);
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const int len = bam_cigar_oplen(cigar[i]);
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if (c == 'S' || c == 'I')
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softStart -= len;
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else if (c != 'H')
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break;
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}
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return softStart;
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}
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// 获取unclipped开始位置(包括hardclip)
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inline int64_t GetUnclippedStart()
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{
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int64_t start = b->core.pos;
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const uint32_t *cigar = bam_get_cigar(b);
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const bam1_core_t &bc = b->core;
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for (int i = 0; i < bc.n_cigar; ++i)
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{
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const char c = bam_cigar_opchr(cigar[i]);
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const int len = bam_cigar_oplen(cigar[i]);
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if (c == 'S' || c == 'H')
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start -= len;
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else
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break;
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}
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return start;
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}
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// 获取unclipped结束位置(包括hardclip)
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inline int64_t GetUnclippedEnd()
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{
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int64_t end_pos = bam_endpos(b);
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const uint32_t *cigar = bam_get_cigar(b);
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const bam1_core_t &bc = b->core;
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for (int i = bc.n_cigar; i >= 0; --i)
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{
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const char c = bam_cigar_opchr(cigar[i]);
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const int len = bam_cigar_oplen(cigar[i]);
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if (c == 'S' || c == 'H')
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end_pos += len;
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else
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break;
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}
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return end_pos;
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}
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/* 获取碱基质量分数的加和 */
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/** Calculates a score for the read which is the sum of scores over Q15. */
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inline int GetSumOfBaseQualities()
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{
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int score = 0;
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uint8_t *qual = bam_get_qual(b);
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for (int i = 0; i < b->core.l_qseq; ++i)
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{
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if (qual[i] >= 15)
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score += qual[i];
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}
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return score;
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}
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/* 与flag相关的检测 */
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/* 没有比对上 unmapped */
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inline bool GetReadUnmappedFlag()
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{
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return b->core.flag & BAM_FUNMAP;
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}
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/* Template having multiple segments in sequencing */
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inline bool GetReadPairedFlag()
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{
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return b->core.flag & BAM_FPAIRED;
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}
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/**
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* the read fails platform/vendor quality checks.
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*/
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inline bool GetReadFailsVendorQualityCheckFlag()
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{
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return b->core.flag & BAM_FQCFAIL;
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}
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/**
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* the mate is unmapped.
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*/
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bool GetMateUnmappedFlag()
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{
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return b->core.flag & BAM_FMUNMAP;
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}
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/**
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* @return whether the alignment is secondary (an alternative alignment of the read).
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*/
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bool IsSecondaryAlignment()
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{
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return b->core.flag & BAM_FSECONDARY;
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}
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/**
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* @return whether the alignment is supplementary (a split alignment such as a chimeric alignment).
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*/
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bool GetSupplementaryAlignmentFlag()
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{
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return b->core.flag & BAM_FSUPPLEMENTARY;
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}
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/*
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* Tests if this record is either a secondary and/or supplementary alignment;
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*/
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bool IsSecondaryOrSupplementary()
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{
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return IsSecondaryAlignment() || GetSupplementaryAlignmentFlag();
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}
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/**
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* the read is the first read in a pair.
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*/
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bool GetFirstOfPairFlag()
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{
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return b->core.flag & BAM_FREAD1;
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}
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/**
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* strand of the query (false for forward; true for reverse strand).
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*/
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bool GetReadNegativeStrandFlag()
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{
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return b->core.flag & BAM_FREVERSE;
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}
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/**
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* strand of the mate (false for forward; true for reverse strand).
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*/
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bool GetMateNegativeStrandFlag()
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{
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return b->core.flag & BAM_FMREVERSE;
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}
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/* 其他的一些信息 */
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inline int GetReferenceLength()
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{
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int length = 0;
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const uint32_t *cigar = bam_get_cigar(b);
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const bam1_core_t &bc = b->core;
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for (int i = 0; i < bc.n_cigar; ++i)
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{
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const char c = bam_cigar_opchr(cigar[i]);
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const int len = bam_cigar_oplen(cigar[i]);
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switch (c)
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{
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case 'M':
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case 'D':
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case 'N':
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case '=':
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case 'X':
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length += len;
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break;
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default:
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break;
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}
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}
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return length;
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}
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// 计算bam的全局位置，算上染色体序号和比对位置
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static inline int64_t bam_global_pos(bam1_t *b)
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{
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return (((int64_t)b->core.tid << MAX_CONTIG_LEN_SHIFT) | (int64_t)b->core.pos);
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}
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static inline int64_t bam_global_pos(int tid, int pos)
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{
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return (((int64_t)tid << MAX_CONTIG_LEN_SHIFT) | (int64_t)pos);
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}
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// 根据全局位置获取bam的染色体序号
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static inline int32_t bam_tid(int64_t global_pos)
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{
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const int64_t mask = ~(((int64_t)1 << MAX_CONTIG_LEN_SHIFT) - 1);
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const int64_t high_tid = global_pos & mask;
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return (int32_t)(high_tid >> MAX_CONTIG_LEN_SHIFT);
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}
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// 根据全局位置获取bam的比对位置(染色体内)
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static inline int32_t bam_pos(int64_t global_pos)
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{
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const int64_t mask = ((int64_t)1 << MAX_CONTIG_LEN_SHIFT) - 1;
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return (int32_t)(global_pos & mask);
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}
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};
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typedef std::map<const std::string, std::vector<BamWrap *>> SampleBamMap;
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#endif |