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1 /*****************************************************************************
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2 slopBed.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 "slopBed.h"
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14
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15
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16 BedSlop::BedSlop(string &bedFile, string &genomeFile, bool forceStrand, float leftSlop, float rightSlop, bool fractional) {
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17
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18 _bedFile = bedFile;
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19 _genomeFile = genomeFile;
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20 _forceStrand = forceStrand;
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21 _leftSlop = leftSlop;
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22 _rightSlop = rightSlop;
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23 _fractional = fractional;
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24
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25 _bed = new BedFile(bedFile);
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26 _genome = new GenomeFile(genomeFile);
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27
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28 // get going, slop it up.
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29 SlopBed();
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30 }
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31
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32
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33 BedSlop::~BedSlop(void) {
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34
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35 }
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36
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37
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38 void BedSlop::SlopBed() {
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39
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40 int lineNum = 0;
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41 BED bedEntry, nullBed; // used to store the current BED line from the BED file.
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42 BedLineStatus bedStatus;
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43
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44 _bed->Open();
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45 bedStatus = _bed->GetNextBed(bedEntry, lineNum);
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46 while (bedStatus != BED_INVALID) {
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47 if (bedStatus == BED_VALID) {
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48 if (_fractional == false) {
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49 AddSlop(bedEntry, (int) _leftSlop, (int) _rightSlop);
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50 }
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51 else {
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52 int leftSlop = (int) (_leftSlop * bedEntry.size());
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53 int rightSlop = (int) (_rightSlop * bedEntry.size());
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54 AddSlop(bedEntry, leftSlop, rightSlop);
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55 }
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56 _bed->reportBedNewLine(bedEntry);
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57 bedEntry = nullBed;
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58 }
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59 bedStatus = _bed->GetNextBed(bedEntry, lineNum);
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60 }
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61 _bed->Close();
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62 }
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63
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64
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65 void BedSlop::AddSlop(BED &bed, int leftSlop, int rightSlop) {
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66
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67 // special handling if the BED entry is on the negative
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68 // strand and the user cares about strandedness.
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69 CHRPOS chromSize = _genome->getChromSize(bed.chrom);
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70
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71 if ( (_forceStrand) && (bed.strand == "-") ) {
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72 // inspect the start
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73 if ( (static_cast<int>(bed.start) - rightSlop) > 0 ) bed.start -= rightSlop;
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74 else bed.start = 0;
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75
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76 // inspect the start
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77 if ( (static_cast<int>(bed.end) + leftSlop) <= static_cast<int>(chromSize)) bed.end += leftSlop;
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78 else bed.end = chromSize;
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79 }
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80 else {
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81 // inspect the start
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82 if ( (static_cast<int>(bed.start) - leftSlop) > 0) bed.start -= leftSlop;
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83 else bed.start = 0;
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84
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85 // inspect the end
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86 if ( (static_cast<int>(bed.end) + rightSlop) <= static_cast<int>(chromSize)) bed.end += rightSlop;
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87 else bed.end = chromSize;
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88 }
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89 }
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90
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91
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