diff --git a/src/shuffleBed/shuffleBed.cpp b/src/shuffleBed/shuffleBed.cpp
index d0a39a3cf3fa4ad2dc58de0b4dcaf07479db1a06..9e36bebb22d2fb54a2d1f75ad5e9071bcd2c77fb 100644
--- a/src/shuffleBed/shuffleBed.cpp
+++ b/src/shuffleBed/shuffleBed.cpp
@@ -18,7 +18,8 @@ BedShuffle::BedShuffle(string &bedFile, string &genomeFile,
bool haveSeed, bool haveExclude,
bool haveInclude, bool sameChrom,
float overlapFraction, int seed,
- bool chooseChrom, bool isBedpe, size_t maxTries) {
+ bool chooseChrom, bool isBedpe, size_t maxTries,
+ bool noOverlapping) {
_bedFile = bedFile;
_genomeFile = genomeFile;
@@ -32,7 +33,7 @@ BedShuffle::BedShuffle(string &bedFile, string &genomeFile,
_chooseChrom = chooseChrom;
_isBedpe = isBedpe;
_maxTries = maxTries;
-
+ _noOverlapping = noOverlapping;
// use the supplied seed for the random
// number generation if given. else,
@@ -61,6 +62,12 @@ BedShuffle::BedShuffle(string &bedFile, string &genomeFile,
_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);
@@ -99,6 +106,9 @@ void BedShuffle::Shuffle() {
while (_bed->GetNextBed(bedEntry)) {
if (_bed->_status == BED_VALID) {
ChooseLocus(bedEntry);
+ if(_noOverlapping){
+ _exclude->addBEDIntoMap(bedEntry);
+ }
_bed->reportBedNewLine(bedEntry);
}
}
@@ -150,7 +160,7 @@ void BedShuffle::ShuffleWithExclusions() {
_overlapFraction, false);
tries++;
} while ((haveOverlap == true) && (tries <= _maxTries));
-
+
if (tries > _maxTries) {
cerr << "Error, line " << _bed->_lineNum
@@ -159,6 +169,10 @@ void BedShuffle::ShuffleWithExclusions() {
<< "excluded regions. Ignoring entry and moving on."
<< endl; }
else {
+ if(_noOverlapping){
+ // future entries cannot overlap this one
+ _exclude->addBEDIntoMap(bedEntry);
+ }
_bed->reportBedNewLine(bedEntry);
}
}
@@ -237,8 +251,15 @@ void BedShuffle::ShuffleWithInclusions() {
tries++;
} while ((bedEntry.end > chromSize)
&& (tries <= _maxTries));
-
- _bed->reportBedNewLine(bedEntry);
+ 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();
@@ -280,6 +301,9 @@ void BedShuffle::ShuffleWithInclusionsAndExclusions() {
<< endl; }
else {
_bed->reportBedNewLine(bedEntry);
+ if (_noOverlapping){
+ _exclude->addBEDIntoMap(bedEntry);
+ }
}
}
}
diff --git a/src/shuffleBed/shuffleBed.h b/src/shuffleBed/shuffleBed.h
index 61dc625a90fb6a53743e9ce0909a8a1a74796c6b..2623c174106ab75e2355947069659a0856a40b2c 100644
--- a/src/shuffleBed/shuffleBed.h
+++ b/src/shuffleBed/shuffleBed.h
@@ -39,7 +39,7 @@ public:
bool haveInclude, bool sameChrom,
float overlapFraction, int seed,
bool chooseChrom, bool isBedpe,
- size_t _maxTries);
+ size_t _maxTries, bool noOverlapping);
// destructor
~BedShuffle(void);
@@ -59,6 +59,7 @@ private:
bool _chooseChrom;
bool _isBedpe;
size_t _maxTries;
+ bool _noOverlapping;
// The BED file from which to compute coverage.
diff --git a/src/shuffleBed/shuffleBedMain.cpp b/src/shuffleBed/shuffleBedMain.cpp
index 2a7fea25a57b6c6e1be669dcd5d652406bb95984..cea9e4d5e85cbf77f3031970a6644be292fd15dd 100644
--- a/src/shuffleBed/shuffleBedMain.cpp
+++ b/src/shuffleBed/shuffleBedMain.cpp
@@ -46,6 +46,7 @@ int shuffle_main(int argc, char* argv[]) {
bool chooseChrom = false;
bool isBedpe = false;
size_t maxTries = 1000;
+ bool noOverlapping = false;
for(int i = 1; i < argc; i++) {
@@ -121,6 +122,9 @@ int shuffle_main(int argc, char* argv[]) {
else if(PARAMETER_CHECK("-bedpe", 6, parameterLength)) {
isBedpe = true;
}
+ else if(PARAMETER_CHECK("-noOverlapping", 14, parameterLength)) {
+ noOverlapping = true;
+ }
else {
cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
showHelp = true;
@@ -139,7 +143,7 @@ int shuffle_main(int argc, char* argv[]) {
haveInclude, sameChrom,
overlapFraction, seed,
chooseChrom, isBedpe,
- maxTries);
+ maxTries, noOverlapping);
delete bc;
return 0;
}
@@ -194,6 +198,7 @@ void shuffle_help(void) {
cerr << "\t-maxTries\t" << "\n\t\tMax. number of attempts to find a home for a shuffled interval" << endl;
cerr << "\t\tin the presence of -incl or -excl." << endl;
cerr << "\t\tDefault = 1000." << endl;
+ cerr << "\t-noOverlapping\t" << "\n\t\tdont allow shuffled intervals to overlap." << endl;
cerr << "Notes: " << endl;
cerr << "\t(1) The genome file should tab delimited and structured as follows:" << endl;
diff --git a/src/utils/bedFile/bedFile.cpp b/src/utils/bedFile/bedFile.cpp
index 521f43d97ce0c937d0febdc208cbb648c7b13bb9..ea993affada562802248ebfeee62c74f431b963f 100644
--- a/src/utils/bedFile/bedFile.cpp
+++ b/src/utils/bedFile/bedFile.cpp
@@ -83,6 +83,18 @@ BedFile::BedFile(string &bedFile)
_total_length(0)
{}
+BedFile::BedFile(void)
+: _isGff(false),
+ _isVcf(false),
+ _typeIsKnown(false),
+ _merged_start(-1),
+ _merged_end(-1),
+ _merged_chrom(""),
+ _prev_start(-1),
+ _prev_chrom(""),
+ _total_length(0)
+{}
+
// Destructor
BedFile::~BedFile(void) {
}
@@ -656,6 +668,11 @@ void BedFile::loadBedFileIntoMap() {
Close();
}
+void BedFile::addBEDIntoMap(BED bedEntry) {
+ BIN bin = getBin(bedEntry.start, bedEntry.end);
+ bedMap[bedEntry.chrom][bin].push_back(bedEntry);
+}
+
void BedFile::loadBedCovFileIntoMap() {
diff --git a/src/utils/bedFile/bedFile.h b/src/utils/bedFile/bedFile.h
index 029b7e98837d3ee577b7a205e5ec3d3d0325d6f9..37d8dda799ce0e6110eda3ec04be230dda2637f0 100644
--- a/src/utils/bedFile/bedFile.h
+++ b/src/utils/bedFile/bedFile.h
@@ -380,6 +380,7 @@ public:
// Constructor
BedFile(string &);
+ BedFile(void);
// Destructor
~BedFile(void);
@@ -418,6 +419,9 @@ public:
// vector of BEDs
void loadBedFileIntoMap();
+ // load a BED entry into and existing map
+ void addBEDIntoMap(BED bedEntry);
+
// load a BED file into a map keyed by chrom, then bin. value is
// vector of BEDCOVs
void loadBedCovFileIntoMap();