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1 /*****************************************************************************
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2 genomeFile.cpp
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3
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4 (c) 2009 - Aaron Quinlan
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5 Hall Laboratory
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6 Department of Biochemistry and Molecular Genetics
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7 University of Virginia
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8 aaronquinlan@gmail.com
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9
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10 Licensed under the GNU General Public License 2.0 license.
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11 ******************************************************************************/
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12 #include "lineFileUtilities.h"
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13 #include "genomeFile.h"
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14
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15
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16 GenomeFile::GenomeFile(const string &genomeFile) {
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17 _genomeFile = genomeFile;
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18 loadGenomeFileIntoMap();
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19 }
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20
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21 GenomeFile::GenomeFile(const RefVector &genome) {
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22 for (size_t i = 0; i < genome.size(); ++i) {
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23 string chrom = genome[i].RefName;
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24 int length = genome[i].RefLength;
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25
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26 _chromSizes[chrom] = length;
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27 _chromList.push_back(chrom);
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28 }
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29 }
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30
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31 // Destructor
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32 GenomeFile::~GenomeFile(void) {
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33 }
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34
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35
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36 void GenomeFile::loadGenomeFileIntoMap() {
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37
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38 string genomeLine;
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39 int lineNum = 0;
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40 vector<string> genomeFields; // vector for a GENOME entry
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41
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42 // open the GENOME file for reading
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43 ifstream genome(_genomeFile.c_str(), ios::in);
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44 if ( !genome ) {
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45 cerr << "Error: The requested genome file (" << _genomeFile << ") could not be opened. Exiting!" << endl;
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46 exit (1);
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47 }
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48
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49 while (getline(genome, genomeLine)) {
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50
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51 Tokenize(genomeLine,genomeFields); // load the fields into the vector
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52 lineNum++;
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53
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54 // ignore a blank line
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55 if (genomeFields.size() > 0) {
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56 if (genomeFields[0].find("#") == string::npos) {
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57
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58 // we need at least 2 columns
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59 if (genomeFields.size() >= 2) {
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60 char *p2End;
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61 long c2;
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62 // make sure the second column is numeric.
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63 c2 = strtol(genomeFields[1].c_str(), &p2End, 10);
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64
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65 // strtol will set p2End to the start of the string if non-integral, base 10
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66 if (p2End != genomeFields[1].c_str()) {
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67 string chrom = genomeFields[0];
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68 int size = atoi(genomeFields[1].c_str());
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69 _chromSizes[chrom] = size;
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70 _chromList.push_back(chrom);
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71 }
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72 }
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73 else {
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74 cerr << "Less than the req'd two fields were encountered in the genome file (" << _genomeFile << ")";
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75 cerr << " at line " << lineNum << ". Exiting." << endl;
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76 exit (1);
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77 }
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78 }
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79 }
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80 genomeFields.clear();
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81 }
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82 }
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83
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84
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85 int GenomeFile::getChromSize(const string &chrom) {
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86 chromToSizes::const_iterator chromIt = _chromSizes.find(chrom);
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87 if (chromIt != _chromSizes.end())
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88 return _chromSizes[chrom];
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89 else
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90 return -1; // chrom not found.
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91 }
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92
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93 vector<string> GenomeFile::getChromList() {
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94 return _chromList;
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95 }
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96
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97 int GenomeFile::getNumberOfChroms() {
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98 return _chromList.size();
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99 }
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100
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101 string GenomeFile::getGenomeFileName() {
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102 return _genomeFile;
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103 }
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