369 lines
11 KiB
C
369 lines
11 KiB
C
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/*
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Description: sam/bam，buf，
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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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#pragma once
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#include <htslib/sam.h>
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#include <limits.h>
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#include <math.h>
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#include <map>
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#include <sstream>
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#include <string>
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#include <vector>
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using namespace std;
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/*
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，，，，，
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bam，，。
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*/
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/*
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* sam read
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*/
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struct BamWrap {
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// contigpos
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const static int MAX_CONTIG_LEN_SHIFT = 40; // id，
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const static int READ_MAX_LENGTH = 200;
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const static int READ_MAX_DEPTH = 1000; // ，
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// ，
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bam1_t *b;
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int64_t end_pos_; // bam,
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//
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inline int64_t start_pos() { return bam_global_pos(b); }
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//
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inline int64_t end_pos() { return end_pos_; }
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// reference
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inline int16_t read_len() { return (end_pos_ - start_pos() + 1); }
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// contig
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inline int32_t contig_pos() { return b->core.pos; }
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// contig
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inline int32_t contig_end_pos() { return bam_pos(end_pos_); }
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// （AGTC）
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inline int16_t seq_len() { return b->core.l_qseq; }
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// softclip
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inline int32_t softclip_start() {
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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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// softclip
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inline int32_t softclip_end() {
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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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// softclip
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inline int32_t right_softclip_len() {
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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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//
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inline std::string sequence() {
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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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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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//
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inline const char *query_name() { return bam_get_qname(b); }
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// cigar
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inline string cigar_str() {
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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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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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//
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inline int16_t length() { return sizeof(*this) + sizeof(bam1_t) + b->l_data; }
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// cigarinsert
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inline int32_t insert_cigar_len() {
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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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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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// cigardelete
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inline int32_t del_cigar_len() {
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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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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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// sam read
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static inline int64_t BamEndPos(const bam1_t *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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int start_offset = -1;
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for (int i = 0; i < bc.n_cigar; ++i) {
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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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const bam1_core_t &bc = b->core;
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bool hasWellDefinedFragmentSize = true;
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if (bc.isize == 0 || !(bc.flag & BAM_FPAIRED) || ((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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hasWellDefinedFragmentSize = false;
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} else if (bc.flag & BAM_FREVERSE) {
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hasWellDefinedFragmentSize = contig_end_pos() > bc.mpos ? true : false;
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} else {
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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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// bamadapterBoundary
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int GetAdapterBoundary() {
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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 GATK3.5，3.5+1
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return adapterBoundary;
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}
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// I
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inline int GetHeadInsertLen() {
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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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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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insLen = len;
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break;
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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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// soft clip(HS，？,
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// IS？)
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inline int64_t GetSoftStart() {
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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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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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// unclipped(hardclip)
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inline int64_t GetUnclippedStart() {
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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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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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// unclipped(hardclip)
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inline int64_t GetUnclippedEnd() {
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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 - 1; i >= 0; --i) {
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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 - 1;
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}
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/* */
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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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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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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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/* flag */
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/* unmapped */
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inline bool GetReadUnmappedFlag() { return b->core.flag & BAM_FUNMAP; }
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/* Template having multiple segments in sequencing */
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inline bool GetReadPairedFlag() { return b->core.flag & BAM_FPAIRED; }
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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() { return b->core.flag & BAM_FQCFAIL; }
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/**
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* the mate is unmapped.
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*/
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bool GetMateUnmappedFlag() { return b->core.flag & BAM_FMUNMAP; }
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/**
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* @return whether the alignment is secondary (an alternative alignment of
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* the read).
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*/
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bool IsSecondaryAlignment() { return b->core.flag & BAM_FSECONDARY; }
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/**
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* @return whether the alignment is supplementary (a split alignment such as
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* a chimeric alignment).
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*/
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bool GetSupplementaryAlignmentFlag() { return b->core.flag & BAM_FSUPPLEMENTARY; }
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/*
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* Tests if this record is either a secondary and/or supplementary
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* alignment;
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*/
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bool IsSecondaryOrSupplementary() { return IsSecondaryAlignment() || GetSupplementaryAlignmentFlag(); }
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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() { return b->core.flag & BAM_FREAD1; }
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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() { return b->core.flag & BAM_FREVERSE; }
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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() { return b->core.flag & BAM_FMREVERSE; }
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/* */
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inline int GetReferenceLength() {
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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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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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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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// bam，
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static inline int64_t bam_global_pos(bam1_t *b) {
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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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return (((int64_t)tid << MAX_CONTIG_LEN_SHIFT) | (int64_t)pos);
|
|||
|
|
}
|
|||
|
|
// bam
|
|||
|
|
static inline int32_t bam_tid(int64_t global_pos) {
|
|||
|
|
const int64_t mask = ~(((int64_t)1 << MAX_CONTIG_LEN_SHIFT) - 1);
|
|||
|
|
const int64_t high_tid = global_pos & mask;
|
|||
|
|
return (int32_t)(high_tid >> MAX_CONTIG_LEN_SHIFT);
|
|||
|
|
}
|
|||
|
|
// bam()
|
|||
|
|
static inline int32_t bam_pos(int64_t global_pos) {
|
|||
|
|
const int64_t mask = ((int64_t)1 << MAX_CONTIG_LEN_SHIFT) - 1;
|
|||
|
|
return (int32_t)(global_pos & mask);
|
|||
|
|
}
|
|||
|
|
|
|||
|
|
//
|
|||
|
|
void SetDuplicateReadFlag(bool flag) { setFlag(flag, BAM_FDUP); }
|
|||
|
|
|
|||
|
|
void setFlag(bool flag, int bit) {
|
|||
|
|
if (flag)
|
|||
|
|
this->b->core.flag |= bit;
|
|||
|
|
else
|
|||
|
|
this->b->core.flag &= ~bit;
|
|||
|
|
}
|
|||
|
|
};
|
|||
|
|
|
|||
|
|
typedef std::map<const std::string, std::vector<BamWrap *>> SampleBamMap;
|