diff --git a/src/intersectBed/intersectBed.cpp b/src/intersectBed/intersectBed.cpp
index c6b7dafe218d6d40766727cc610f7ce937683c10..87f470d747052bc87e873f43f83cbaff575fd2da 100755
--- a/src/intersectBed/intersectBed.cpp
+++ b/src/intersectBed/intersectBed.cpp
@@ -18,12 +18,14 @@
Constructor
*/
BedIntersect::BedIntersect(string &bedAFile, string &bedBFile, bool &anyHit,
-bool &writeB, float &overlapFraction, bool &noHit, bool &writeCount) {
+ bool &writeA, bool &writeB, float &overlapFraction,
+ bool &noHit, bool &writeCount) {
this->bedAFile = bedAFile;
this->bedBFile = bedBFile;
this->anyHit = anyHit;
this->noHit = noHit;
+ this->writeA = writeA;
this->writeB = writeB;
this->writeCount = writeCount;
this->overlapFraction = overlapFraction;
@@ -152,22 +154,37 @@ void BedIntersect::IntersectBed() {
if (bedA->parseBedLine(a, bedFields, lineNum)) {
vector<BED> hits;
+
bedB->binKeeperFind(bedB->bedMap[a.chrom], a.start, a.end, hits);
int numOverlaps = 0;
for (vector<BED>::iterator h = hits.begin(); h != hits.end(); ++h) {
+
int s = max(a.start, h->start);
int e = min(a.end, h->end);
+
if (s < e) {
+ // is there enough overlap (default ~ 1bp)
if ( ((float)(e-s) / (float)(a.end - a.start)) > this->overlapFraction ) {
numOverlaps++;
if (!anyHit && !noHit && !writeCount) {
if (!writeB) {
- reportAIntersect(a,s,e); cout << endl;
+ if (writeA) {
+ reportA(a); cout << endl;
+ }
+ else {
+ reportAIntersect(a,s,e); cout << endl;
+ }
}
else {
- reportAIntersect(a,s,e); cout << "\t";
- reportB(*h); cout << endl;
+ if (writeA) {
+ reportA(a); cout << "\t";
+ reportB(*h); cout << endl;
+ }
+ else {
+ reportAIntersect(a,s,e); cout << "\t";
+ reportB(*h); cout << endl;
+ }
}
}
}
@@ -198,39 +215,53 @@ void BedIntersect::IntersectBed() {
if (bedA->parseBedLine(a, bedFields, lineNum)) {
vector<BED> hits;
+
bedB->binKeeperFind(bedB->bedMap[a.chrom], a.start, a.end, hits);
int numOverlaps = 0;
for (vector<BED>::iterator h = hits.begin(); h != hits.end(); ++h) {
-
+
int s = max(a.start, h->start);
int e = min(a.end, h->end);
+
if (s < e) {
+ // is there enough overlap (default ~ 1bp)
if ( ((float)(e-s) / (float)(a.end - a.start)) > this->overlapFraction ) {
numOverlaps++;
if (!anyHit && !noHit && !writeCount) {
if (!writeB) {
- reportAIntersect(a,s,e); cout << endl;
+ if (writeA) {
+ reportA(a); cout << endl;
+ }
+ else {
+ reportAIntersect(a,s,e); cout << endl;
+ }
}
else {
- reportAIntersect(a,s,e); cout << "\t";
- reportB(*h); cout << endl;
+ if (writeA) {
+ reportA(a); cout << "\t";
+ reportB(*h); cout << endl;
+ }
+ else {
+ reportAIntersect(a,s,e); cout << "\t";
+ reportB(*h); cout << endl;
+ }
}
}
- }
- }
- if (anyHit && (numOverlaps >= 1)) {
- reportA(a); cout << endl;
- }
- else if (writeCount) {
- reportA(a); cout << "\t" << numOverlaps << endl;
- }
- else if (noHit && (numOverlaps == 0)) {
- reportA(a); cout << endl;
+ }
}
}
+ if (anyHit && (numOverlaps >= 1)) {
+ reportA(a); cout << endl;
+ }
+ else if (writeCount) {
+ reportA(a); cout << "\t" << numOverlaps << endl;
+ }
+ else if (noHit && (numOverlaps == 0)) {
+ reportA(a); cout << endl;
+ }
}
- }
+ }
}
}
// END Intersect BED3
diff --git a/src/intersectBed/intersectBed.h b/src/intersectBed/intersectBed.h
index 376634abfb90d56f804c66b40d4060137d1cc20f..5aaf600c389382eb1f6fcb6c82078a99c3d6d1c0 100755
--- a/src/intersectBed/intersectBed.h
+++ b/src/intersectBed/intersectBed.h
@@ -25,7 +25,7 @@ class BedIntersect {
public:
// constructor
- BedIntersect(string &, string &, bool &, bool &, float &, bool &, bool &);
+ BedIntersect(string &, string &, bool &, bool &, bool &, float &, bool &, bool &);
// destructor
~BedIntersect(void);
@@ -44,6 +44,7 @@ private:
string bedBFile;
string notInBFile;
bool anyHit;
+ bool writeA;
bool writeB;
bool writeCount;
float overlapFraction;
diff --git a/src/intersectBed/intersectMain.cpp b/src/intersectBed/intersectMain.cpp
index 0e1d3a6b637d6fcf86d533831f0db14bd295459c..400dc7ee531c6846ce5c4e61f96f6e48a3372561 100755
--- a/src/intersectBed/intersectMain.cpp
+++ b/src/intersectBed/intersectMain.cpp
@@ -25,13 +25,17 @@ int main(int argc, char* argv[]) {
// input arguments
float overlapFraction = 1E-9;
+ int slop = 0;
bool haveBedA = false;
bool haveBedB = false;
bool noHit = false;
bool anyHit = false;
+ bool writeA = false;
bool writeB = false;
bool writeCount = false;
+ bool haveFraction = false;
+ bool haveSlop = false;
// check to see if we should print out some help
if(argc <= 1) showHelp = true;
@@ -53,34 +57,38 @@ int main(int argc, char* argv[]) {
int parameterLength = (int)strlen(argv[i]);
if(PARAMETER_CHECK("-a", 2, parameterLength)) {
- haveBedA = true;
- bedAFile = argv[i + 1];
+ if ((i+1) < argc) {
+ haveBedA = true;
+ bedAFile = argv[i + 1];
+ }
i++;
}
else if(PARAMETER_CHECK("-b", 2, parameterLength)) {
- haveBedB = true;
- bedBFile = argv[i + 1];
+ if ((i+1) < argc) {
+ haveBedB = true;
+ bedBFile = argv[i + 1];
+ }
i++;
}
else if(PARAMETER_CHECK("-u", 2, parameterLength)) {
anyHit = true;
- i++;
}
else if(PARAMETER_CHECK("-f", 2, parameterLength)) {
+ haveFraction = true;
overlapFraction = atof(argv[i + 1]);
i++;
}
+ else if(PARAMETER_CHECK("-wa", 3, parameterLength)) {
+ writeA = true;
+ }
else if(PARAMETER_CHECK("-wb", 3, parameterLength)) {
writeB = true;
- i++;
}
else if(PARAMETER_CHECK("-c", 2, parameterLength)) {
writeCount = true;
- i++;
}
else if (PARAMETER_CHECK("-v", 2, parameterLength)) {
noHit = true;
- i++;
}
else {
cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
@@ -103,10 +111,15 @@ int main(int argc, char* argv[]) {
cerr << endl << "*****" << endl << "*****ERROR: Request either -wb OR -c, not both." << endl << "*****" << endl;
showHelp = true;
}
+
+ if (anyHit && writeCount) {
+ cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -c, not both." << endl << "*****" << endl;
+ showHelp = true;
+ }
if (!showHelp) {
- BedIntersect *bi = new BedIntersect(bedAFile, bedBFile, anyHit, writeB, overlapFraction, noHit, writeCount);
+ BedIntersect *bi = new BedIntersect(bedAFile, bedBFile, anyHit, writeA, writeB, overlapFraction, noHit, writeCount);
bi->IntersectBed();
return 0;
}
@@ -133,9 +146,11 @@ void ShowHelp(void) {
cerr << "OPTIONS: " << endl;
cerr << "\t" << "-u\t\t\t" << "Write ORIGINAL a.bed entry ONCE if ANY overlap bed." << endl << "\t\t\t\tIn other words, ignore multiple overlaps." << endl << endl;
cerr << "\t" << "-v \t\t\t" << "Only report those entries in A that have NO OVERLAP in B." << endl << "\t\t\t\tSimilar to grep -v." << endl << endl;
+ cerr << "\t" << "-s (100000)\t\t" << "Slop added before and after each entry in A" << endl << "\t\t\t\tUseful for finding overlaps within N bases upstream and downstream." << endl << endl;
cerr << "\t" << "-f (e.g. 0.05)\t\t" << "Minimum overlap req'd as fraction of a.bed." << endl << "\t\t\t\tDefault is 1E-9 (effectively 1bp)." << endl << endl;
cerr << "\t" << "-c \t\t\t" << "For each entry in A, report the number of hits in B while restricting to -f." << endl << "\t\t\t\tReports 0 for A entries that have no overlap with B." << endl << endl;
- cerr << "\t" << "-wb \t\t\t" << "Write the entry in B for each overlap." << endl << "\t\t\t\tUseful for knowing _what_ A overlaps. Restricted by -f." << endl << endl;
+ cerr << "\t" << "-wa \t\t\t" << "Write the original entry in A for each overlap." << endl << endl;
+ cerr << "\t" << "-wb \t\t\t" << "Write the original entry in B for each overlap." << endl << "\t\t\t\tUseful for knowing _what_ A overlaps. Restricted by -f." << endl << endl;
cerr << "NOTES: " << endl;
cerr << "\t" << "-i stdin\t\t" << "Allows intersectBed to read BED from stdin. E.g.: cat a.bed | intersectBed -a stdin -b B.bed" << endl << endl;