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comparison BEDTools-Version-2.14.3/src/slopBed/slopBed.cpp @ 0:dfcd8b6c1bda

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author aaronquinlan
date Thu, 03 Nov 2011 10:25:04 -0400
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1 /*****************************************************************************
2 slopBed.cpp
3
4 (c) 2009 - Aaron Quinlan
5 Hall Laboratory
6 Department of Biochemistry and Molecular Genetics
7 University of Virginia
8 aaronquinlan@gmail.com
9
10 Licensed under the GNU General Public License 2.0 license.
11 ******************************************************************************/
12 #include "lineFileUtilities.h"
13 #include "slopBed.h"
14
15
16 BedSlop::BedSlop(string &bedFile, string &genomeFile, bool forceStrand, float leftSlop, float rightSlop, bool fractional) {
17
18 _bedFile = bedFile;
19 _genomeFile = genomeFile;
20 _forceStrand = forceStrand;
21 _leftSlop = leftSlop;
22 _rightSlop = rightSlop;
23 _fractional = fractional;
24
25 _bed = new BedFile(bedFile);
26 _genome = new GenomeFile(genomeFile);
27
28 // get going, slop it up.
29 SlopBed();
30 }
31
32
33 BedSlop::~BedSlop(void) {
34
35 }
36
37
38 void BedSlop::SlopBed() {
39
40 int lineNum = 0;
41 BED bedEntry, nullBed; // used to store the current BED line from the BED file.
42 BedLineStatus bedStatus;
43
44 _bed->Open();
45 bedStatus = _bed->GetNextBed(bedEntry, lineNum);
46 while (bedStatus != BED_INVALID) {
47 if (bedStatus == BED_VALID) {
48 if (_fractional == false) {
49 AddSlop(bedEntry, (int) _leftSlop, (int) _rightSlop);
50 }
51 else {
52 int leftSlop = (int) (_leftSlop * bedEntry.size());
53 int rightSlop = (int) (_rightSlop * bedEntry.size());
54 AddSlop(bedEntry, leftSlop, rightSlop);
55 }
56 _bed->reportBedNewLine(bedEntry);
57 bedEntry = nullBed;
58 }
59 bedStatus = _bed->GetNextBed(bedEntry, lineNum);
60 }
61 _bed->Close();
62 }
63
64
65 void BedSlop::AddSlop(BED &bed, int leftSlop, int rightSlop) {
66
67 // special handling if the BED entry is on the negative
68 // strand and the user cares about strandedness.
69 CHRPOS chromSize = _genome->getChromSize(bed.chrom);
70
71 if ( (_forceStrand) && (bed.strand == "-") ) {
72 // inspect the start
73 if ( (static_cast<int>(bed.start) - rightSlop) > 0 ) bed.start -= rightSlop;
74 else bed.start = 0;
75
76 // inspect the start
77 if ( (static_cast<int>(bed.end) + leftSlop) <= static_cast<int>(chromSize)) bed.end += leftSlop;
78 else bed.end = chromSize;
79 }
80 else {
81 // inspect the start
82 if ( (static_cast<int>(bed.start) - leftSlop) > 0) bed.start -= leftSlop;
83 else bed.start = 0;
84
85 // inspect the end
86 if ( (static_cast<int>(bed.end) + rightSlop) <= static_cast<int>(chromSize)) bed.end += rightSlop;
87 else bed.end = chromSize;
88 }
89 }
90
91