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

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author aaronquinlan
date Thu, 03 Nov 2011 10:25:04 -0400
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1 /*****************************************************************************
2 complementBed.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 Licenced under the GNU General Public License 2.0 license.
11 ******************************************************************************/
12 #include "lineFileUtilities.h"
13 #include "complementBed.h"
14
15 BedComplement::BedComplement(string &bedFile, string &genomeFile) {
16
17 _bedFile = bedFile;
18 _genomeFile = genomeFile;
19
20 _bed = new BedFile(bedFile);
21 _genome = new GenomeFile(genomeFile);
22
23 }
24
25
26 BedComplement::~BedComplement(void) {
27 }
28
29
30 //
31 // Merge overlapping BED entries into a single entry
32 //
33 void BedComplement::ComplementBed() {
34
35 // load the "B" bed file into a map so
36 // that we can easily compare "A" to it for overlaps
37 _bed->loadBedFileIntoMapNoBin();
38
39 // get a list of the chroms in the user's genome
40 vector<string> chromList = _genome->getChromList();
41
42 // process each chrom in the genome
43 for (size_t c = 0; c < chromList.size(); ++c) {
44 string currChrom = chromList[c];
45
46 // create a "bit vector" for the chrom
47 CHRPOS currChromSize = _genome->getChromSize(currChrom);
48 vector<bool> chromMasks(currChromSize, 0);
49
50 // mask the chrom for every feature in the BED file
51 bedVector::const_iterator bItr = _bed->bedMapNoBin[currChrom].begin();
52 bedVector::const_iterator bEnd = _bed->bedMapNoBin[currChrom].end();
53 for (; bItr != bEnd; ++bItr) {
54 if (bItr->end > currChromSize) {
55 cout << "Warninge: end of BED entry exceeds chromosome length. Please correct." << endl;
56 _bed->reportBedNewLine(*bItr);
57 exit(1);
58 }
59
60 // mask all of the positions spanned by this BED entry.
61 for (CHRPOS b = bItr->start; b < bItr->end; b++)
62 chromMasks[b] = 1;
63 }
64
65 // report the unmasked, that is, complemented parts of the chrom
66 CHRPOS i = 0;
67 CHRPOS start;
68 while (i < chromMasks.size()) {
69 if (chromMasks[i] == 0) {
70 start = i;
71 while ((chromMasks[i] == 0) && (i < chromMasks.size()))
72 i++;
73
74 if (start > 0)
75 cout << currChrom << "\t" << start << "\t" << i << endl;
76 else
77 cout << currChrom << "\t" << 0 << "\t" << i << endl;
78 }
79 i++;
80 }
81 }
82 }
83