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1 /* written by Jonas Behr, Regina Bohnert and Gunnar Raetsch, FML Tuebingen, Germany, 2010 */
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2
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3 #include <stdio.h>
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4 #include <string.h>
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5 #include <signal.h>
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6 #include <mex.h>
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7 #include <algorithm>
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8 #include <vector>
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9 using std::vector;
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10 #include "get_reads_direct.h"
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11 #include "mex_input.h"
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12 #include "read.h"
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13
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14 #define MAXLINE 10000
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15
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16 /*
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17 * input:
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18 * 1 bam file
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19 * 2 chromosome
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20 * 3 region start (1-based index)
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21 * 4 region end (1-based index)
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22 * 5 strand (either '+' or '-' or '0')
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23 * [6] collapse flag: if true the reads are collapsed to a coverage track
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24 * [7] subsample percentage: percentage of reads to be subsampled (in per mill)
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25 * [8] intron length filter
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26 * [9] exon length filter
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27 * [10] mismatch filter
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28 * [11] bool: use mapped reads for coverage
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29 * [12] bool: use spliced reads for coverage
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30 * [13] return maxminlen
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31 * [14] return pair coverage and pair index list
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32 * [15] only_clipped
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33 * [15] switch of pair filter
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34 *
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35 * output:
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36 * 1 coverage
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37 * [2] intron cell array
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38 * [3] pair coverage
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39 * [4] pair list
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40 *
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41 * example call:
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42 * [cov introns] = get_reads('polyA_left_I+_el15_mm1_spliced.bam', 'I', 10000, 12000, '-', 1, 30);
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43 */
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44 void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[]) {
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45
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46 if (nrhs<5 || nrhs>16 || (nlhs<1 || nlhs>4)) {
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47 fprintf(stderr, "usage: [x [introns] [pair]] = get_reads(fname, chr, start, end, strand, [collapse], [subsample], [max intron length], [min exonlength], [max mismatches], [mapped], [spliced], [maxminlen], [pair], [only clipped], [all pairs]);\n");
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48 return;
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49 }
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50
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51 /* obligatory arguments
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52 * **********************/
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53 char *fname = get_string(prhs[0]);
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54 //fprintf(stdout, "arg1: %s\n", fname);
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55 char *chr = get_string(prhs[1]);
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56 //fprintf(stdout, "arg2: %s\n", chr);
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57 int from_pos = get_int(prhs[2]);
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58 //fprintf(stdout, "arg3: %d\n", from_pos);
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59 int to_pos = get_int(prhs[3]);
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60 //fprintf(stdout, "arg4: %d\n", to_pos);
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61 char *strand = get_string(prhs[4]);
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62 //fprintf(stdout, "arg5: %s\n", strand);
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63
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64 if (from_pos>to_pos)
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65 mexErrMsgTxt("Start (arg 3) must be <= end (arg 4)\n");
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66
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67 if (strand[0]!='+' && strand[0]!='-' && strand[0]!='0')
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68 mexErrMsgTxt("Unknown strand (arg 5): either + or - or 0");
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69
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70 /* optional arguments
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71 * ******************/
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72 int collapse = 0;
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73 if (nrhs>=6)
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74 collapse = get_int(prhs[5]);
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75
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76 int subsample = 1000;
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77 if (nrhs>=7)
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78 subsample = get_int(prhs[6]);
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79
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80 int intron_len_filter = 1e9;
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81 if (nrhs>=8)
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82 intron_len_filter = get_int(prhs[7]);
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83
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84 int exon_len_filter = -1;
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85 if (nrhs>=9)
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86 exon_len_filter = get_int(prhs[8]);
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87
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88 int filter_mismatch = 1e9;
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89 if (nrhs>=10)
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90 filter_mismatch = get_int(prhs[9]);
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91
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92 int mapped = 1;
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93 if (nrhs>=11)
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94 mapped = get_int(prhs[10]);
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95
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96 int spliced = 1;
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97 if (nrhs>=12)
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98 spliced = get_int(prhs[11]);
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99
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100 int maxminlen = 0;
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101 if (nrhs>=13)
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102 maxminlen = get_int(prhs[12]);
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103
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104 int pair_cov = 0;
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105 if (nrhs>=14)
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106 pair_cov = get_int(prhs[13]);
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107
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108 int only_clipped = 0;
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109 if (nrhs>=15)
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110 only_clipped = get_int(prhs[14]);
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111
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112 int no_pair_filter = 0;
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113 if (nrhs>=16)
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114 no_pair_filter = get_int(prhs[15]);
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115
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116
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117 /* call function to get reads
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118 * **************************/
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119 char region[MAXLINE];
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120 sprintf(region, "%s:%i-%i", chr, from_pos, to_pos);
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121
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122 vector<CRead*> all_reads;
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123
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124 get_reads_from_bam(fname, region, &all_reads, strand[0], subsample);
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125
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126 for (int i=0; i<all_reads.size(); i++) {
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127 all_reads[i]->strip_leftright_tag() ;
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128 }
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129
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130 /* filter reads
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131 * **************/
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132 int left = 0;
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133 int right = 0;
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134
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135 vector<CRead*> reads;
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136 for (int i=0; i<all_reads.size(); i++) {
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137 if (all_reads[i]->left)
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138 left++;
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139 if (all_reads[i]->right)
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140 right++;
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141 //if (all_reads[i]->max_intron_len()<intron_len_filter && all_reads[i]->min_exon_len()>exon_len_filter && all_reads[i]->get_mismatches()<=filter_mismatch && all_reads[i]->multiple_alignment_index==0)
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142 if (all_reads[i]->max_intron_len()<intron_len_filter && all_reads[i]->min_exon_len()>exon_len_filter && all_reads[i]->get_mismatches()<=filter_mismatch && (only_clipped==0 || all_reads[i]->is_clipped))
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143 reads.push_back(all_reads[i]);
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144 }
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145
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146
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147 /* prepare output
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148 * **************/
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149 int num_rows = reads.size();
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150 int num_pos = to_pos-from_pos+1;
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151
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152 if (pair_cov==1 && nlhs>=3) {
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153 // sort reads by read_id
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154 //printf("\n\nleft:%i right:%i \n\n", left, right);
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155 //printf("\nreads[0]->read_id: %s\n", reads[0]->read_id);
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156 sort(reads.begin(), reads.end(), CRead::compare_by_read_id);
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157 }
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158
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159 // read coverages collapsed
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160 if (collapse) {
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161 plhs[0] = mxCreateNumericMatrix(1, num_pos, mxUINT32_CLASS, mxREAL);
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162 uint32_t *mask_ret = (uint32_t*) mxGetData(plhs[0]);
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163 if (num_pos>0 && mask_ret==NULL)
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164 mexErrMsgTxt("Error allocating memory\n");
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165 if (mapped && spliced) {
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166 for (int i=0; i<reads.size(); i++) {
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167 reads[i]->get_coverage(from_pos, to_pos, mask_ret);
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168 }
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169 } else {
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170 for (int i=0; i<reads.size(); i++) {
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171 ssize_t num_exons = reads[i]->block_starts.size();
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172 if ((num_exons==1 && mapped) || (num_exons>1 && spliced))
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173 reads[i]->get_coverage(from_pos, to_pos, mask_ret);
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174 }
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175 }
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176 }
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177 // reads not collapsed
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178 else {
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179 uint32_t nzmax = 0; // maximal number of nonzero elements
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180 int len = to_pos-from_pos+1;
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181 for (uint i=0; i<reads.size(); i++)
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182 {
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183 ssize_t num_exons = reads[i]->block_starts.size();
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184 if (!((mapped && spliced) || (num_exons==1 && mapped) || (num_exons>1 && spliced)))
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185 {
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186 continue;
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187 }
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188 for (uint n = 0; n < reads[i]->block_starts.size(); n++)
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189 {
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190 uint32_t from, to;
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191 if (reads[i]->block_starts[n]+reads[i]->start_pos-from_pos >= 0)
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192 from = reads[i]->block_starts[n]+reads[i]->start_pos-from_pos;
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193 else
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194 from = 0;
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195 if (reads[i]->block_starts[n]+reads[i]->start_pos-from_pos+reads[i]->block_lengths[n] >= 0)
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196 to = reads[i]->block_starts[n]+reads[i]->start_pos-from_pos+reads[i]->block_lengths[n];
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197 else
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198 to = 0;
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199 for (int bp=from; bp<to&bp<len; bp++)
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200 {
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201 nzmax++;
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202 }
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203 }
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204 }
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205 // 1st row: row indices
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206 // 2nd row: column indices
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207 plhs[0] = mxCreateDoubleMatrix(2, nzmax, mxREAL);
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208 double *mask_ret = (double*) mxGetData(plhs[0]);
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209 if (nzmax>0 && mask_ret==NULL)
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210 mexErrMsgTxt("Error allocating memory\n");
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211 uint32_t mask_ret_c = 0; // counter
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212 for (uint i=0; i<reads.size(); i++)
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213 {
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214 ssize_t num_exons = reads[i]->block_starts.size();
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215 if (!((mapped && spliced) || (num_exons==1 && mapped) || (num_exons>1 && spliced)))
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216 {
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217 continue;
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218 }
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219 reads[i]->get_reads_sparse(from_pos, to_pos, mask_ret, mask_ret_c, i);
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220 }
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221 if (mask_ret_c!=2*nzmax)
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222 mexErrMsgTxt("Error filling index arrays for sparse matrix\n");
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223 }
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224 // introns
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225 if (maxminlen==0 && nlhs>=2) {
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226 vector<int> intron_list;
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227 for (int i=0; i<reads.size(); i++) {
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228 reads[i]->get_introns(&intron_list);
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229 }
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230
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231 plhs[1] = mxCreateNumericMatrix(2, intron_list.size()/2, mxUINT32_CLASS, mxREAL);
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232 uint32_t *p_intron_list = (uint32_t*) mxGetData(plhs[1]);
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233 for (int p = 0; p<intron_list.size(); p++) {
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234 p_intron_list[p] = intron_list[p];
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235 }
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236 intron_list.clear();
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237 } else if (nlhs>=2) {
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238 vector<uint32_t> intron_starts;
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239 vector<uint32_t> intron_ends;
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240 vector<uint32_t> block_len1;
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241 vector<uint32_t> block_len2;
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242 for (int i=0; i<reads.size(); i++) {
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243 reads[i]->get_introns(&intron_starts, &intron_ends, &block_len1, &block_len2);
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244 }
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245
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246 plhs[1] = mxCreateNumericMatrix(4, intron_starts.size(), mxINT32_CLASS, mxREAL);
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247 uint32_t *p_intron_list = (uint32_t*) mxGetData(plhs[1]);
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248 for (int p = 0; p<intron_starts.size(); p++) {
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249 p_intron_list[4*p] = intron_starts[p];
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250 p_intron_list[(4*p)+1] = intron_ends[p];
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251 p_intron_list[(4*p)+2] = block_len1[p];
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252 p_intron_list[(4*p)+3] = block_len2[p];
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253 }
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254 intron_starts.clear() ;
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255 intron_ends.clear() ;
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256 block_len1.clear() ;
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257 block_len2.clear() ;
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258 }
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259 if (pair_cov==1 && nlhs>=3) {
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260 plhs[2] = mxCreateNumericMatrix(1, num_pos, mxUINT32_CLASS, mxREAL);
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261 uint32_t *p_pair_map = (uint32_t*) mxGetData(plhs[2]);
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262 if (num_pos>0 && p_pair_map==NULL)
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263 mexErrMsgTxt("Error allocating memory\n");
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264
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265 vector<int> pair_ids;
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266
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267 int take_cnt = 0;
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268 int discard_cnt = 0;
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269 int discard_strand_cnt = 0;
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270 //printf("reads.size(): %i\n", reads.size());
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271 // find consecutive reads with the same id
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272 for (int i=0; i<((int) reads.size())-1; i++)
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273 {
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274 //printf("reads[%i]->read_id: %s\n", i, reads[i]->read_id);
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275 int j = i+1;
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276 while(j<reads.size() && strcmp(reads[i]->read_id, reads[j]->read_id) == 0)
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277 {
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278 if ((reads[i]->left && reads[j]->right) || (reads[j]->left && reads[i]->right) && (reads[i]->reverse != reads[j]->reverse))
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279 {
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280 if (reads[i]->get_last_position()==-1 || reads[j]->get_last_position()==-1)
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281 break;
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282 if (false)//(reads[i]->strand[0]=='0' && reads[j]->strand[0]=='0' )
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283 {
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284 // discard pairs without strand information
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285 discard_strand_cnt++;
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286 }
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287 else if (reads[i]->get_last_position()<reads[j]->start_pos && reads[j]->start_pos-reads[i]->get_last_position()<60000)
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288 {
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289 int from = std::max(0, reads[i]->get_last_position()-from_pos);
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290 int to = std::min(num_pos-1, reads[j]->start_pos-from_pos);
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291 pair_ids.push_back(i);
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292 pair_ids.push_back(j);
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293 for (int k=from; k<to; k++)
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294 p_pair_map[k]++;
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295 take_cnt++;
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296 }
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297 else if (reads[i]->start_pos>reads[j]->get_last_position() && reads[j]->get_last_position()-reads[i]->start_pos<60000)
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298 {
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299 int from = std::max(0, reads[j]->get_last_position()-from_pos);
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300 int to = std::min(num_pos-1, reads[i]->start_pos-from_pos);
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301 pair_ids.push_back(i);
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302 pair_ids.push_back(j);
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303 for (int k=from; k<to; k++)
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304 p_pair_map[k]++;
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305 take_cnt++;
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306 }
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307 else
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308 {
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309 if (no_pair_filter>0 && reads[i]->start_pos<reads[j]->start_pos)
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310 {
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311 pair_ids.push_back(i);
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312 pair_ids.push_back(j);
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313 take_cnt++;
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314 }
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315 else if (no_pair_filter>0)
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316 {
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317 pair_ids.push_back(j);
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318 pair_ids.push_back(i);
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319 take_cnt++;
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320 }
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321 else
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322 discard_cnt++;
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323 //printf("istart:%i, ilast:%i jstart:%i, jlast: %i\n", reads[i]->start_pos, reads[i]->get_last_position(), reads[j]->start_pos, reads[j]->get_last_position());
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324 }
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325 }
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326 else
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327 discard_cnt++;
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328 j++;
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329 }
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330 }
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331 //printf("take:%i, discard:%i discard_strand_cnt:%i\n", take_cnt, discard_cnt+discard_strand_cnt, discard_strand_cnt);
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332
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333 if (nlhs>=4) {
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334 plhs[3] = mxCreateNumericMatrix(2, pair_ids.size()/2, mxUINT32_CLASS, mxREAL);
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335 uint32_t *pair_ids_ret = (uint32_t*) mxGetData(plhs[3]);
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336 if (pair_ids.size()>0 && pair_ids_ret==NULL)
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337 mexErrMsgTxt("Error allocating memory\n");
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338 for (int i=0; i<pair_ids.size(); i++) {
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339 pair_ids_ret[i] = pair_ids[i];
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340 }
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341 }
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342 }
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343 for (int i=0; i<all_reads.size(); i++)
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344 delete all_reads[i];
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345 }
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346
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