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/*****************************************************************************
shuffleBed.cpp
(c) 2009 - Aaron Quinlan
Hall Laboratory
Department of Biochemistry and Molecular Genetics
University of Virginia
aaronquinlan@gmail.com
Licenced under the GNU General Public License 2.0 license.
******************************************************************************/
#include "lineFileUtilities.h"
#include "shuffleBed.h"
BedShuffle::BedShuffle(string &bedFile, string &genomeFile,
string &excludeFile, string &includeFile,
bool haveSeed, bool haveExclude,
bool haveInclude, bool sameChrom,
float overlapFraction, int seed,
bool chooseChrom, bool isBedpe, size_t maxTries,
bool noOverlapping, bool preventExceedingChromEnd)
{
_bedFile = bedFile;
_genomeFile = genomeFile;
_excludeFile = excludeFile;
_includeFile = includeFile;
_sameChrom = sameChrom;
_haveExclude = haveExclude;
_haveInclude = haveInclude;
_overlapFraction = overlapFraction;
_haveSeed = haveSeed;
_chooseChrom = chooseChrom;
_isBedpe = isBedpe;
_maxTries = maxTries;
_tries = 0;
_noOverlapping = noOverlapping;
_preventExceedingChromEnd = preventExceedingChromEnd;
_cumLen = 0;
// use the supplied seed for the random
// number generation if given. else,
// roll our own.
if (_haveSeed) {
_seed = seed;
srand(seed);
}
else {
// thanks to Rob Long for the tip.
_seed = (unsigned)time(0)+(unsigned)getpid();
srand(_seed);
}
if (_isBedpe == false)
_bed = new BedFile(bedFile);
else
_bedpe = new BedFilePE(bedFile);
_genome = new GenomeFile(genomeFile);
_chroms = _genome->getChromList();
_numChroms = _genome->getNumberOfChroms();
_genomeSize = _genome->getGenomeSize();
if (_haveExclude) {
_exclude = new BedFile(excludeFile);
_exclude->loadBedFileIntoMap();
}
else if (_noOverlapping) {
// create an empty map that we add to as we iterate.
_exclude = new BedFile();
// force down correct code-path.
_haveExclude = true;
}
if (_haveInclude)
{
_include = new BedFile(includeFile);
_include->loadBedFileIntoVector();
_include->assignWeightsBasedOnSize();
// for(std::vector<BED>::iterator it = _include->bedList.begin(); it != _include->bedList.end(); it++)
// {
// _cumLen += (*it).end - (*it).start;
// }
}
if (_haveExclude == true && _haveInclude == false)
ShuffleWithExclusions();
else if (_haveExclude == false && _haveInclude == true)
ShuffleWithInclusions();
else if (_haveExclude == true && _haveInclude == true)
ShuffleWithInclusionsAndExclusions();
else
Shuffle();
}
BedShuffle::~BedShuffle(void) {
}
void BedShuffle::Shuffle() {
if (_isBedpe == false) {
BED bedEntry;
_bed->Open();
while (_bed->GetNextBed(bedEntry)) {
if (_bed->_status == BED_VALID) {
ChooseLocus(bedEntry);
if(_noOverlapping){
_exclude->addBEDIntoMap(bedEntry);
}
if (_tries <= _maxTries)
{
_bed->reportBedNewLine(bedEntry);
}
}
}
_bed->Close();
}
// BEDPE input
else {
int lineNum = 0; // current input line number
BedLineStatus status;
BEDPE bedEntry, nullBedPE;
_bedpe->Open();
while ((status =
_bedpe->GetNextBedPE(bedEntry, lineNum)) != BED_INVALID)
{
if (status == BED_VALID) {
ChoosePairedLocus(bedEntry);
_bedpe->reportBedPENewLine(bedEntry);
}
bedEntry = nullBedPE;
}
_bedpe->Close();
}
}
void BedShuffle::ShuffleWithExclusions() {
if (_isBedpe == false) {
BED bedEntry;
_bed->Open();
while (_bed->GetNextBed(bedEntry)) {
if (_bed->_status == BED_VALID) {
// keep looking as long as the chosen
// locus happens to overlap with regions
// that the user wishes to exclude.
_tries = 0;
bool haveOverlap = false;
do
{
// choose a new locus
ChooseLocus(bedEntry);
haveOverlap = _exclude->anyHits(bedEntry.chrom,
bedEntry.start,
bedEntry.end,
bedEntry.strand,
false, false,
_overlapFraction, false);
_tries++;
} while ((haveOverlap == true) && (_tries <= _maxTries));
if (_tries > _maxTries) {
cerr << "Error, line " << _bed->_lineNum
<< ": tried " << _maxTries
<< " potential loci for entry, but could not avoid "
<< "excluded regions. Ignoring entry and moving on."
<< endl; }
else {
if(_noOverlapping){
// future entries cannot overlap this one
_exclude->addBEDIntoMap(bedEntry);
}
_bed->reportBedNewLine(bedEntry);
}
}
}
_bed->Close();
}
// BEDPE input
else {
int lineNum = 0; // current input line number
BedLineStatus status;
BEDPE bedEntry;
_bedpe->Open();
while ((status =
_bedpe->GetNextBedPE(bedEntry, lineNum)) != BED_INVALID)
{
if (status == BED_VALID) {
// keep looking as long as the chosen
// locus happens to overlap with regions
// that the user wishes to exclude.
_tries = 0;
bool haveOverlap1 = false;
bool haveOverlap2 = false;
do
{
// choose a new locus
ChoosePairedLocus(bedEntry);
haveOverlap1 = _exclude->anyHits(bedEntry.chrom1,
bedEntry.start1,
bedEntry.end1,
bedEntry.strand1,
false, false,
_overlapFraction, false);
haveOverlap2 = _exclude->anyHits(bedEntry.chrom2,
bedEntry.start2,
bedEntry.end2,
bedEntry.strand2,
false, false,
_overlapFraction, false);
_tries++;
} while (((haveOverlap1 == true) || (haveOverlap2 == true))
&& (_tries <= _maxTries));
if (_tries > _maxTries) {
cerr << "Error, line " << _bed->_lineNum
<< ": tried " << _maxTries
<< " potential loci for entry, but could not avoid "
<< "excluded regions. Ignoring entry and moving on."
<< endl;
}
else {
_bedpe->reportBedPENewLine(bedEntry);
}
}
}
_bedpe->Close();
}
}
void BedShuffle::ShuffleWithInclusions() {
BED bedEntry; // used to store the current BED line from the BED file.
CHRPOS chromSize;
_bed->Open();
while (_bed->GetNextBed(bedEntry)) {
if (_bed->_status == BED_VALID) {
_tries = 0;
// choose a new locus
do {
ChooseLocusFromInclusionFile(bedEntry);
chromSize = _genome->getChromSize(bedEntry.chrom);
_tries++;
} while ((bedEntry.end > chromSize)
&& (_tries <= _maxTries));
if (_tries > _maxTries) {
cerr << "Error, line " << _bed->_lineNum
<< ": tried " << _maxTries
<< " potential loci for entry, but could not avoid "
<< "excluded regions. Ignoring entry and moving on."
<< endl; }
else {
_bed->reportBedNewLine(bedEntry);
}
}
}
_bed->Close();
}
void BedShuffle::ShuffleWithInclusionsAndExclusions() {
BED bedEntry; // used to store the current BED line from the BED file.
_bed->Open();
while (_bed->GetNextBed(bedEntry)) {
if (_bed->_status == BED_VALID) {
// keep looking as long as the chosen
// locus happens to overlap with regions
// that the user wishes to exclude.
_tries = 0;
bool haveOverlap = false;
do
{
// choose a new locus
ChooseLocusFromInclusionFile(bedEntry);
haveOverlap = _exclude->anyHits(bedEntry.chrom,
bedEntry.start,
bedEntry.end,
bedEntry.strand,
false, false,
_overlapFraction, false);
_tries++;
} while ((haveOverlap == true) && (_tries <= _maxTries));
if (_tries > _maxTries) {
cerr << "Error, line " << _bed->_lineNum
<< ": tried " << _maxTries
<< " potential loci for entry, but could not avoid "
<< "excluded regions. Ignoring entry and moving on."
<< endl; }
else {
_bed->reportBedNewLine(bedEntry);
if (_noOverlapping){
_exclude->addBEDIntoMap(bedEntry);
}
}
}
}
_bed->Close();
}
void BedShuffle::ChooseLocus(BED &bedEntry) {
string randomChrom;
CHRPOS randomStart;
CHRPOS chromSize;
string chrom = bedEntry.chrom;
CHRPOS start = bedEntry.start;
CHRPOS end = bedEntry.end;
CHRPOS length = end - start;
// choose a position randomly among the _entire_ genome.
if (_chooseChrom == false)
{
_tries = 0;
do
{
// we need to combine two consecutive calls to rand()
// because RAND_MAX is 2^31 (2147483648), whereas
// mammalian genomes are obviously much larger.
uint32_t randStart = ((((long) rand()) << 31) | rand()) %
_genomeSize;
// use the above randomStart (e.g., for human 0..3.1billion)
// to identify the chrom and start on that chrom.
pair<string, int> location = _genome->projectOnGenome(randStart);
bedEntry.chrom = location.first;
bedEntry.start = location.second;
bedEntry.end = bedEntry.start + length;
chromSize = _genome->getChromSize(location.first);
if ((bedEntry.end > chromSize) &&
(_preventExceedingChromEnd == false))
{
bedEntry.end = chromSize;
break;
}
_tries++;
} while ((bedEntry.end > chromSize) && (_tries <= _maxTries));
// keep looking if we have exceeded the end of the chrom.
if (_tries > _maxTries) {
cerr << "Error, line " << _bed->_lineNum
<< ": tried " << _maxTries
<< " potential loci for entry, but could not avoid "
<< "excluded regions. Ignoring entry and moving on."
<< endl;
}
}
// OLD, quite arguably flawed, method.
// 1. Choose a chrom randomly (i.e., not weighted by size)
// 2. Choose a position on that chrom randomly
else
{
do
{
if (_sameChrom == false) {
randomChrom = _chroms[rand() % _numChroms];
chromSize = _genome->getChromSize(randomChrom);
randomStart = rand() % chromSize;
bedEntry.chrom = randomChrom;
bedEntry.start = randomStart;
bedEntry.end = randomStart + length;
}
else {
chromSize = _genome->getChromSize(chrom);
randomStart = rand() % chromSize;
bedEntry.start = randomStart;
bedEntry.end = randomStart + length;
}
if ((bedEntry.end > chromSize) &&
(_preventExceedingChromEnd == false))
{
bedEntry.end = chromSize;
break;
}
} while (bedEntry.end > chromSize);
}
}
void BedShuffle::ChoosePairedLocus(BEDPE &b) {
CHRPOS foot1_len = b.end1 - b.start1;
CHRPOS foot2_len = b.end2 - b.start2;
CHRPOS length = b.end2 - b.start1;
if (b.chrom1 == b.chrom2)
{
CHRPOS chromSize;
do
{
uint32_t randStart = ((((long) rand()) << 31) | rand()) %
_genomeSize;
pair<string, int> location = _genome->projectOnGenome(randStart);
b.chrom1 = location.first;
b.chrom2 = location.first;
b.start1 = location.second;
b.end1 = b.start1 + foot1_len;
b.end2 = b.start1 + length;
b.start2 = b.end2 - foot2_len;
chromSize = _genome->getChromSize(location.first);
} while ((b.end1 > chromSize) ||
(b.start2 > chromSize) ||
(b.end2 > chromSize));
// keep looking if we have exceeded the end of the chrom.
}
else
{
CHRPOS chromSize1, chromSize2;
do
{
uint32_t rand1Start = ((((long) rand()) << 31) | rand()) %
_genomeSize;
uint32_t rand2Start = ((((long) rand()) << 31) | rand()) %
_genomeSize;
pair<string, int> location1 = _genome->projectOnGenome(rand1Start);
pair<string, int> location2 = _genome->projectOnGenome(rand2Start);
b.chrom1 = location1.first;
b.chrom2 = location2.first;
b.start1 = location1.second;
b.start2 = location2.second;
b.end1 = b.start1 + foot1_len;
b.end2 = b.start2 + foot2_len;
chromSize1 = _genome->getChromSize(location1.first);
chromSize2 = _genome->getChromSize(location2.first);
} while ((b.end1 > chromSize1) ||
(b.end2 > chromSize2));
// keep looking if we have exceeded the end of the chrom.
}
}
void BedShuffle::ChooseLocusFromInclusionFile(BED &bedEntry)
{
// choose an -incl interval randomly, yet weighted by the size of the incl interval.
size_t length = (bedEntry.end - bedEntry.start);
double runif =((double)rand()/(double)RAND_MAX);
BED *includeInterval = _include->sizeWeightedSearch(runif);
// choose a random start within the -incl interval and reconstruct shuffled record
CHRPOS randomStart = includeInterval->start + (rand() % (includeInterval->size()));
bedEntry.chrom = includeInterval->chrom;
bedEntry.start = randomStart;
bedEntry.end = randomStart + length;
}
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