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1 #include "ncListCreator.hpp"
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2
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3 NCListCreator::NCListCreator(string inputFileName): inputFileName(inputFileName) {}
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4
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5 string NCListCreator::getFileName(string chromosome) {
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6 return inputFileName.substr(0, inputFileName.find_last_of('.')) + "_" + chromosome + ".bed";
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7 }
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8
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9 void NCListCreator::splitFile () {
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10 Chromosomes chromosomes;
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11 GenomicInterval interval;
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12 map <string, ofstream> splittedFiles;
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13 map <string, ofstream>::iterator it;
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14 ifstream file;
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15 string line, fileName;
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16 string chromosome;
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17 file.open(inputFileName.c_str());
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18 if (file.is_open()) {
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19 while (file.good()) {
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20 getline(file, line);
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21 if (line.size() > 0) {
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22 interval.parseFromLine(line);
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23 chromosomes.insert(interval.chromosome);
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24 fileName = getFileName(interval.chromosome);
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25 it = splittedFiles.find(interval.chromosome);
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26 if (it == splittedFiles.end()) {
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27 ofstream outputFile;
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28 outputFile.open(fileName.c_str(), ios::out | ios::binary);
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29 interval.writeBinary(outputFile);
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30 splittedFiles[chromosome] = outputFile;
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31 }
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32 else {
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33 it->second << line << "\n";
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34 }
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35 }
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36 }
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37 file.close();
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38 for (it = splittedFiles.begin(); it != splittedFiles.end(); it++) {
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39 it->second.close();
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40 }
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41 }
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42 else {
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43 cout << "Unable to open file" << inputFileName;
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44 }
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45 }
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46
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47 void NCListCreator::run() {
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48 for (Chromosomes::iterator it = chromosomes.begin(); splittedFiles != chromosomes.end(); splittedFiles++) {
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49 buildLists(*it);
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50 }
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51 }
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52
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53 void NCListCreator::buildLists(string chromosome) {
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54 createTables(chromosome);
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55 labelLists();
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56 computeSubStart();
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57 computeAbsPosition();
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58 cleanFiles();
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59 transfer(chromosome);
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60 }
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61
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62 void NCListCreator::createTables(string chromosome) {
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63 initLists(chromosome);
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64 h = new Table(H_CELL_SIZE, nbLists);
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65 t = new Table(T_CELL_SIZE, nbLines);
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66 l = new Table(L_CELL_SIZE, nbLines);
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67 fillTables(chromosome);
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68 }
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69
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70 void NCListCreator::initLists (string chromosome) {
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71 nbLists = 0;
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72 nbLines = 0;
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73 ifstream file;
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74 file.open(getFileName(chromosome).c_str(), ios::in | ios::binary);
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75 Interval currentInterval, previousInterval;
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76 if (file.is_open()) {
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77 while (file.good()) {
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78 if (currentInterval.parseBinary(file)) {
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79 nbLines++;
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80 if (previousInterval.include(currentInterval)) {
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81 nbLists++;
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82 }
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83 }
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84 previousInterval = currentInterval;
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85 }
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86 }
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87 file.close();
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88 }
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89
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90 void NCListCreator::fillTables (string chromosome) {
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91 ifstream file;
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92 file.open(getFileName(chromosome).c_str(), ios::in | ios::binary);
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93 Interval currentInterval, previousInterval;
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94 unsigned int i = 0;
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95 if (file.is_open()) {
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96 while (file.good()) {
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97 if (currentInterval.parseBinary(file)) {
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98 t->write(currentInterval.start, i, 0);
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99 t->writeHere(currentInterval.end);
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100 t->writeHere(-1);
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101 t->writeHere(-1);
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102 }
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103 i++;
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104 }
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105 file.close();
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106 }
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107 t->write(SENTINEL, LIST, -1);
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108 l->write(SENTINEL, LIST, 0);
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109 t->write(SENTINEL, NEW, -1);
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110 }
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111
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112 void NCListCreator::labelLists () {
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113 unsigned int nextL = 0, thisL, length;
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114 unsigned int p;
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115 Interval current, parent;
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116 for (unsigned int i = 0; i < nbLines; i++) {
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117 p = i - 1;
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118 t->moveTo(p, 0);
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119 parent.readBinary(t->file);
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120 t->moveTo(i, 0);
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121 current.readBinary(t->file);
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122 while ((p != SENTINEL) && (! parent.include(current))) {
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123 p = t->read(p, PARENT);
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124 t->moveTo(p, 0);
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125 parent.readBinary(t->file);
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126 }
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127 thisL = t->read(p, LIST);
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128 if (thisL == SENTINEL) {
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129 thisL = nextL;
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130 nextL++;
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131 length = 0;
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132 t->write(p, LIST, thisL);
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133 }
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134 else {
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135 length = h->read(thisL, LENGTH);
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136 }
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137 t->write(i, PARENT, p);
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138 h->write(thisL, LENGTH, length+1);
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139 }
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140 }
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141
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142 void NCListCreator::computeSubStart () {
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143 unsigned int total = 0;
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144 for (unsigned int i = 0; i < nbLists; i++) {
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145 h->write(i, START, total);
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146 total += h->read(i, LENGTH);
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147 h->write(i, LENGTH, 0);
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148 }
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149 }
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150
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151 void NCListCreator::computeAbsPosition () {
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152 Value s, e, pt, hp, pl, nb, lp;
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153 for (unsigned int i = 0; i < nbLines; i++) {
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154 s = t->read(i, START);
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155 e = t->read(i, END);
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156 pt = t->read(i, PARENT);
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157 hp = t->read(pt, LIST);
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158 pl = t->read(pt, NEW);
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159 nb = h->read(hp, LENGTH);
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160 lp = h->read(hp, START) + nb;
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161 t->write(i, NEW, lp);
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162 l->write(lp, START, s);
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163 l->write(lp, END, e);
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164 l->write(lp, LIST, SENTINEL);
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165 l->write(lp, PARENT, pl);
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166 h->write(lp, LENGTH, nb+1);
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167 if (nb == 0) {
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168 l->write(pl, LIST, hp);
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169 }
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170 }
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171 }
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172
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173 void NCListCreator::cleanFiles () {
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174 t->destroy();
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175 }
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176
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177 void NCListCreator::transfer (string chromosome) {
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178 ncLists[chromosome] = NCList(h, l);
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179 }
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