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1 /*
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2 * This program is free software; you can redistribute it and/or modify
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3 * it under the terms of the GNU General Public License as published by
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4 * the Free Software Foundation; either version 3 of the License, or
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5 * (at your option) any later version.
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6 *
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7 * Written (W) 2010-2011 Jonas Behr, Regina Bohnert, Gunnar Raetsch
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8 * Copyright (C) 2010-2011 Max Planck Society
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9 */
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10
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11
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12 #include <stdio.h>
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13 #include <string.h>
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14 #include <signal.h>
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15 #include <mex.h>
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16 #include <algorithm>
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17 #include <vector>
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18 using std::vector;
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19 #include "get_reads_direct.h"
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20 #include "mex_input.h"
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21 #include "read.h"
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22
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23 #define MAXLINE 10000
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24
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25 /*
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26 * input:
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27 * 1 bam file
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28 * 2 chromosome
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29 * 3 region start (1-based index)
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30 * 4 region end (1-based index)
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31 * 5 strand (either '+' or '-' or '0')
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32 * [6] collapse flag: if true the reads are collapsed to a coverage track
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33 * [7] subsample percentage: percentage of reads to be subsampled (in per mill)
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34 * [8] intron length filter
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35 * [9] exon length filter
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36 * [10] mismatch filter
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37 * [11] bool: use mapped reads for coverage
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38 * [12] bool: use spliced reads for coverage
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39 * [13] return maxminlen
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40 * [14] return pair coverage
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41 *
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42 * output:
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43 * 1 coverage
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44 * [2] intron cell array
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45 * [3] pair coverage
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46 * [4] pair list
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47 *
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48 * example call:
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49 * [cov introns] = get_reads('polyA_left_I+_el15_mm1_spliced.bam', 'I', 10000, 12000, '-', 1, 30);
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50 */
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51 void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[]) {
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52
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53 if (nrhs<5 || nrhs>14 || (nlhs<1 || nlhs>4)) {
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54 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]);\n");
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55 return;
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56 }
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57
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58 /* obligatory arguments
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59 * **********************/
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60 char *fname = get_string(prhs[0]);
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61 //fprintf(stdout, "arg1: %s\n", fname);
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62 char *chr = get_string(prhs[1]);
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63 //fprintf(stdout, "arg2: %s\n", chr);
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64 int from_pos = get_int(prhs[2]);
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65 //fprintf(stdout, "arg3: %d\n", from_pos);
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66 int to_pos = get_int(prhs[3]);
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67 //fprintf(stdout, "arg4: %d\n", to_pos);
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68 char *strand = get_string(prhs[4]);
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69 //fprintf(stdout, "arg5: %s\n", strand);
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70
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71 if (from_pos>to_pos)
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72 mexErrMsgTxt("Start (arg 3) must be <= end (arg 4)\n");
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73
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74 if (strand[0]!='+' && strand[0]!='-' && strand[0]!='0')
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75 mexErrMsgTxt("Unknown strand (arg 5): either + or - or 0");
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76
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77 /* optional arguments
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78 * ******************/
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79 int collapse = 0;
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80 if (nrhs>=6)
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81 collapse = get_int(prhs[5]);
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82
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83 int subsample = 1000;
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84 if (nrhs>=7)
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85 subsample = get_int(prhs[6]);
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86
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87 int intron_len_filter = 1e9;
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88 if (nrhs>=8)
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89 intron_len_filter = get_int(prhs[7]);
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90
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91 int exon_len_filter = -1;
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92 if (nrhs>=9)
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93 exon_len_filter = get_int(prhs[8]);
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94
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95 int filter_mismatch = 1e9;
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96 if (nrhs>=10)
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97 filter_mismatch = get_int(prhs[9]);
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98
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99 int mapped = 1;
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100 if (nrhs>=11)
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101 mapped = get_int(prhs[10]);
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102
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103 int spliced = 1;
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104 if (nrhs>=12)
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105 spliced = get_int(prhs[11]);
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106
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107 int maxminlen = 0;
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108 if (nrhs>=13)
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109 maxminlen = get_int(prhs[12]);
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110
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111 int pair_cov = 0;
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112 if (nrhs>=14)
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113 pair_cov = get_int(prhs[13]);
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114
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115 /* call function to get reads
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116 * **************************/
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117 char region[MAXLINE];
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118 sprintf(region, "%s:%i-%i", chr, from_pos, to_pos);
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119
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120 vector<CRead*> all_reads;
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121
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122 get_reads_from_bam(fname, region, &all_reads, strand[0], subsample);
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123
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124 /* filter reads
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125 * **************/
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126 int left = 0;
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127 int right = 0;
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128
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129 vector<CRead*> reads;
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130 for (int i=0; i<all_reads.size(); i++) {
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131 if (all_reads[i]->left)
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132 left++;
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133 if (all_reads[i]->right)
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134 right++;
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135 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)
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136 reads.push_back(all_reads[i]);
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137 }
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138
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139
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140 /* prepare output
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141 * **************/
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142 int num_rows = reads.size();
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143 int num_pos = to_pos-from_pos+1;
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144
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145 if (pair_cov==1 && nlhs>=3) {
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146 // sort reads by read_id
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147 printf("\n\nleft:%i right:%i \n\n", left, right);
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148 sort(reads.begin(), reads.end(), CRead::compare_by_read_id);
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149 }
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150
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151 // read coverages collapsed
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152 if (collapse) {
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153 plhs[0] = mxCreateNumericMatrix(1, num_pos, mxUINT32_CLASS, mxREAL);
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154 uint32_t *mask_ret = (uint32_t*) mxGetData(plhs[0]);
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155 if (num_pos>0 && mask_ret==NULL)
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156 mexErrMsgTxt("Error allocating memory\n");
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157 if (mapped && spliced) {
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158 for (int i=0; i<reads.size(); i++) {
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159 reads[i]->get_coverage(from_pos, to_pos, mask_ret);
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160 }
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161 } else {
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162 for (int i=0; i<reads.size(); i++) {
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163 ssize_t num_exons = reads[i]->block_starts.size();
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164 if ((num_exons==1 && mapped) || (num_exons>1 && spliced))
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165 reads[i]->get_coverage(from_pos, to_pos, mask_ret);
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166 }
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167 }
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168 }
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169 // reads not collapsed
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170 else {
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171 uint32_t nzmax = 0; // maximal number of nonzero elements
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172 int len = to_pos-from_pos+1;
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173 for (uint i=0; i<reads.size(); i++) {
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174 for (uint n = 0; n < reads[i]->block_starts.size(); n++) {
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175 uint32_t from, to;
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176 if (reads[i]->block_starts[n]+reads[i]->start_pos-from_pos >= 0)
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177 from = reads[i]->block_starts[n]+reads[i]->start_pos-from_pos;
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178 else
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179 from = 0;
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180 if (reads[i]->block_starts[n]+reads[i]->start_pos-from_pos+reads[i]->block_lengths[n] >= 0)
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181 to = reads[i]->block_starts[n]+reads[i]->start_pos-from_pos+reads[i]->block_lengths[n];
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182 else
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183 to = 0;
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184 for (int bp=from; bp<to&bp<len; bp++) {
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185 nzmax++;
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186 }
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187 }
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188 }
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189 // 1st row: row indices
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190 // 2nd row: column indices
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191 plhs[0] = mxCreateDoubleMatrix(2, nzmax, mxREAL);
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192 double *mask_ret = (double*) mxGetData(plhs[0]);
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193 if (nzmax>0 && mask_ret==NULL)
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194 mexErrMsgTxt("Error allocating memory\n");
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195 uint32_t mask_ret_c = 0; // counter
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196 for (uint i=0; i<reads.size(); i++) {
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197 reads[i]->get_reads_sparse(from_pos, to_pos, mask_ret, mask_ret_c, i);
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198 }
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199 if (mask_ret_c!=2*nzmax)
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200 mexErrMsgTxt("Error filling index arrays for sparse matrix\n");
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201 }
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202 // introns
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203 if (maxminlen==0 && nlhs>=2) {
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204 vector<int> intron_list;
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205 for (int i=0; i<reads.size(); i++) {
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206 reads[i]->get_introns(&intron_list);
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207 }
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208
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209 plhs[1] = mxCreateNumericMatrix(2, intron_list.size()/2, mxUINT32_CLASS, mxREAL);
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210 uint32_t *p_intron_list = (uint32_t*) mxGetData(plhs[1]);
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211 for (int p = 0; p<intron_list.size(); p++) {
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212 p_intron_list[p] = intron_list[p];
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213 }
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214 intron_list.clear();
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215 } else if (nlhs>=2) {
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216 vector<uint32_t> intron_starts;
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217 vector<uint32_t> intron_ends;
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218 vector<uint32_t> block_len1;
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219 vector<uint32_t> block_len2;
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220 for (int i=0; i<reads.size(); i++) {
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221 reads[i]->get_introns(&intron_starts, &intron_ends, &block_len1, &block_len2);
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222 }
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223
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224 plhs[1] = mxCreateNumericMatrix(4, intron_starts.size(), mxINT32_CLASS, mxREAL);
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225 uint32_t *p_intron_list = (uint32_t*) mxGetData(plhs[1]);
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226 for (int p = 0; p<intron_starts.size(); p++) {
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227 p_intron_list[4*p] = intron_starts[p];
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228 p_intron_list[(4*p)+1] = intron_ends[p];
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229 p_intron_list[(4*p)+2] = block_len1[p];
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230 p_intron_list[(4*p)+3] = block_len2[p];
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231 }
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232 intron_starts.clear() ;
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233 intron_ends.clear() ;
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234 block_len1.clear() ;
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235 block_len2.clear() ;
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236 }
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237 if (pair_cov==1 && nlhs>=3) {
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238 plhs[2] = mxCreateNumericMatrix(1, num_pos, mxUINT32_CLASS, mxREAL);
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239 uint32_t *p_pair_map = (uint32_t*) mxGetData(plhs[2]);
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240 if (num_pos>0 && p_pair_map==NULL)
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241 mexErrMsgTxt("Error allocating memory\n");
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242
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243 vector<int> pair_ids;
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244
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245 int take_cnt = 0;
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246 int discard_cnt = 0;
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247 // find consecutive reads with the same id
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248 for (int i=0; i<((int) reads.size())-1; i++) {
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249 int j = i+1;
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250 while(j<reads.size() && strcmp(reads[i]->read_id, reads[j]->read_id) == 0) {
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251 if ((reads[i]->left && reads[j]->right) || (reads[j]->left && reads[i]->right) && (reads[i]->reverse != reads[j]->reverse)) {
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252 if (reads[i]->get_last_position()==-1 || reads[j]->get_last_position()==-1)
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253 break;
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254 if (reads[i]->get_last_position()<reads[j]->start_pos && reads[j]->start_pos-reads[i]->get_last_position()<60000) {
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255 int from = std::max(0, reads[i]->get_last_position()-from_pos);
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256 int to = std::min(num_pos-1, reads[j]->start_pos-from_pos);
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257 pair_ids.push_back(i);
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258 pair_ids.push_back(j);
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259 for (int k=from; k<to; k++)
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260 p_pair_map[k]++;
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261 take_cnt++;
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262 } 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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263 int from = std::max(0, reads[j]->get_last_position()-from_pos);
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264 int to = std::min(num_pos-1, reads[i]->start_pos-from_pos);
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265 pair_ids.push_back(i);
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266 pair_ids.push_back(j);
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267 for (int k=from; k<to; k++)
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268 p_pair_map[k]++;
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269 take_cnt++;
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270 } else
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271 discard_cnt++;
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272 }
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273 else
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274 discard_cnt++;
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275 j++;
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276 }
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277 }
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278 printf("take:%i, discard:%i \n", take_cnt, discard_cnt);
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279
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280 if (nlhs>=4) {
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281 plhs[3] = mxCreateNumericMatrix(2, pair_ids.size()/2, mxUINT32_CLASS, mxREAL);
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282 uint32_t *pair_ids_ret = (uint32_t*) mxGetData(plhs[3]);
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283 if (pair_ids.size()>0 && pair_ids_ret==NULL)
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284 mexErrMsgTxt("Error allocating memory\n");
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285 for (int i=0; i<pair_ids.size(); i++) {
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286 pair_ids_ret[i] = pair_ids[i];
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287 }
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288 }
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289 }
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290 for (int i=0; i<all_reads.size(); i++)
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291 delete all_reads[i];
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292 }
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293
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