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annotate snp_caller/src/SnipDriver.h @ 0:0fd352f62446 draft default tip

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planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
author chrisd
date Sun, 21 Feb 2016 06:05:24 -0500
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0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
chrisd
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1 #ifndef SNIP_DRIVER_H
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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2 #define SNIP_DRIVER_H
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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4 #include "Alignment.h"
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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5 #include "FastaRecord.h"
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6 #include "args.h"
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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8 #include <iostream>
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9 #include <string>
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10 #include <fstream>
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11 #include <algorithm>
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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12 #include <set>
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14 typedef decltype(nullptr) nullptr_t;
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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15 typedef std::vector<std::pair<int,char>> cigar_str;
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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17 std::set<std::string> read_pair_snips;
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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19 struct CompareSnips {
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20 bool operator()(const std::string &first, const std::string &second) {
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21 return first.length() < second.length();
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22 }
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23 };
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26 Alignment *get_mate_pair(std::vector<Alignment> &alignments, const std::string &qname, const int pnext) {
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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27 for(auto &alignment : alignments) {
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28 bool mate_pair = alignment.second_in_pair();
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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29 std::string mate_qname = alignment.qname();
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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30 int mate_pos = alignment.pos();
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32 if( (mate_pair == 1) && (mate_qname == qname) && (mate_pos == pnext)) {
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33 return &alignment;
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34 }
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35 }
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36 return nullptr;
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37 }
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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39 void parse_cigar(FastaRecord &record, Alignment &alignment) {
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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40 cigar_str cigar = alignment.get_cigar();
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42 int occurrence;
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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43 char operation;
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45 int gene_pos = alignment.pos()-1;
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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46 int read_pos = 0;
0fd352f62446 planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty
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48 char base_in_ref, base_in_read;
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50 std::string read = alignment.seq();
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51 std::string qname = alignment.qname();
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53 std::string gene = record.gene();
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54 std::string gene_id = record.gene_id();
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56 std::string snip_pattern;
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58 for(int i = 0; i < cigar.size(); i++) {
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59 occurrence = cigar[i].first;
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60 operation = cigar[i].second;
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62 if(operation == 'M' || operation == '=') {
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63 for(int k = 0; k < occurrence; k++) {
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64 if(gene_pos >= gene.length() || read_pos >= read.length()) {
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65 break;
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66 }
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67
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68 base_in_ref = gene[gene_pos];
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69 base_in_read = read[read_pos];
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71 if(base_in_ref != base_in_read) {
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72 snip_pattern = std::to_string(gene_pos) +
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73 std::string(1,base_in_ref) + "->" +
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74 std::string(1, base_in_read) + ":";
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75 read_pair_snips.insert(snip_pattern);
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76 }
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77
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78 ++gene_pos;
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79 ++read_pos;
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80 }
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81 }
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82 else if(operation == 'I') {
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83 read_pos += occurrence;
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84 gene_pos += occurrence;
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85 }
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86 else if(operation == 'S') {
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87 read_pos += occurrence;
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88 }
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89 else if(operation == 'N') {
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90 gene_pos += occurrence;
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91 }
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92 else if(operation == 'P') {
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93 read_pos += occurrence;
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94 gene_pos += occurrence;
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95 }
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96 else if(operation == 'D') {
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97 gene_pos += occurrence;
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98 }
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99 else if(operation == 'X') {
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100 read_pos += occurrence;
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101 gene_pos += occurrence;
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102 }
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103 else {
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104 std::cout << "Operation " << operation << " not handled." << std::endl;
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105 }
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106 }
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107 }
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108
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109 std::string convert_snips_to_pattern(const std::set<std::string> &read_pair_snips) {
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110 std::vector<std::string> snips;
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111 snips.assign(read_pair_snips.begin(), read_pair_snips.end());
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112
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113 CompareSnips comp;
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114 sort(snips.begin(), snips.end(), comp);
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115
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116 std::string pattern;
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117 for(const auto &snp : snips) {
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118 pattern+=snp;
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119 }
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120 return pattern;
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121 }
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122
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123 bool find_se_snips(std::vector<FastaRecord> &records,
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124 Alignment &read_pair) {
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125
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126 int fasta_record_idx = FastaRecord::find_gene(records, read_pair.rname());
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127 if(fasta_record_idx == records.size()) {
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128 return false;
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129 }
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130
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131 parse_cigar(records[fasta_record_idx], read_pair);
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132 std::string snp = convert_snips_to_pattern(read_pair_snips);
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133
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134 if(!snp.empty()) {
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135 records[fasta_record_idx].snip_database[snp]++;
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136 }
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137
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138 read_pair_snips.clear();
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139
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140 return true;
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141 }
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142
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143 bool find_pe_snips(std::vector<FastaRecord> &records,
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144 std::vector<Alignment> &alignments,
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145 Alignment &read_pair) {
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146
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147 if(read_pair.first_in_pair()) {
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148 std::string qname = read_pair.qname();
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149 int mate_start_pos = read_pair.pnext();
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150
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151 Alignment *mate_pair = get_mate_pair(alignments, qname, mate_start_pos);
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152 if(mate_pair == nullptr) {
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153 return false;
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154 }
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155 if(mate_pair->rname () != read_pair.rname()) {
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156 if(mate_pair->alternate_hits.size() == 0) {
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157 return false;
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158 }
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159
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160 bool found_alt_hit = false;
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161 for(const auto &alternative: mate_pair->alternate_hits) {
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162 if(alternative.rname == read_pair.rname()) {
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163 found_alt_hit = true;
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164 mate_pair->set_rname(alternative.rname);
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165 mate_pair->set_cigar(alternative.cigar);
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166 mate_pair->set_pos(alternative.pos);
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167 break;
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168 }
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169 }
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170 if(!found_alt_hit) {
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171 return false;
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172 }
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173 }
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174
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175
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176 int fasta_record_idx = FastaRecord::find_gene(records, read_pair.rname());
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177 if(fasta_record_idx == records.size()) {
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178 return false;
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179 }
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180
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181 parse_cigar(records[fasta_record_idx], read_pair);
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182 parse_cigar(records[fasta_record_idx], *mate_pair);
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183
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184 std::string snp = convert_snips_to_pattern(read_pair_snips);
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185
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186 if(!snp.empty()) {
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187 records[fasta_record_idx].snip_database[snp]++;
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188 }
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189
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190
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191 read_pair_snips.clear();
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192 }
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193
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194 return true;
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195 }
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196
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197 void run(std::vector<FastaRecord> &records, std::vector<Alignment> &alignments, cmd_args arg) {
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198 if(arg.samse) {
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199 for(int i = 0; i < alignments.size(); i++) {
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200 find_se_snips(records, alignments[i]);
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201 }
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202 }
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203 else {
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204 for(int i = 0; i < alignments.size(); i++) {
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205 find_pe_snips(records, alignments, alignments[i]);
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206 }
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207 }
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208 }
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209
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210 void write_header(const std::string &out_fp) {
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211 std::ofstream out(out_fp.c_str());
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212 out << "Chr,Haplotype,Frequency" << '\n';
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213 }
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215 void write_snips(std::vector<FastaRecord> &records, const std::string &out_fp) {
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216 write_header(out_fp);
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217 std::ofstream out(out_fp.c_str(), std::ofstream::app);
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218 for(const auto &record : records) {
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219 for(const auto &snip : record.snip_database) {
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220 out << record.gene_id() << "," << snip.first << "," << snip.second << '\n';
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221 }
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222 }
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223 }
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225
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226 #endif // SNIP_DRIVER_H