Multiple changes.

	1. Added BAM support to windowBed.
	2. Forced correct BEDPE ordering for bamToBed.
	3. Added default overlapFraction = 0.0 to bedFile prototype.

src/bamToBed/bamToBed.cpp

@@ -15,6 +15,7 @@
 using namespace BamTools;
 
 #include <vector>
+#include <algorithm>	// for swap()
 #include <iostream>
 #include <fstream>
 #include <stdlib.h>
@@ -38,7 +39,7 @@ void ConvertBamToBedpe(const string &bamFile, const bool &useEditDistance);
 					
 void PrintBed(const BamAlignment &bam, const RefVector &refs, bool useEditDistance);
 void PrintBed12(const BamAlignment &bam, const RefVector &refs, bool useEditDistance, string color = "255,0,0");
-void PrintBedPE(const BamAlignment &bam1, const BamAlignment &bam1,
+void PrintBedPE(const BamAlignment &bam1, const BamAlignment &bam2,
                 const RefVector &refs, bool useEditDistance);
 
 void ParseCigarBed12(const vector<CigarOp> &cigar, vector<int> &blockStarts, 
@@ -153,7 +154,7 @@ void ShowHelp(void) {
 	cerr << "\t-ed\t"		<< "Use BAM edit distance (NM tag) for BED score." << endl;
 	cerr 					<< "\t\t- Default for BED is to use mapping quality." << endl;
 	cerr 					<< "\t\t- Default for BEDPE is to use the minimum of" << endl;
-	cerr 					<< "\t\t  of the two mapping qualities for the pair." << endl;
+	cerr 					<< "\t\t  the two mapping qualities for the pair." << endl;
 	cerr 					<< "\t\t- When -ed is used with -bedpe, the total edit" << endl;
 	cerr 					<< "\t\t  distance from the two mates is reported." << endl << endl;
 
@@ -394,7 +395,16 @@ void PrintBedPE(const BamAlignment &bam1, const BamAlignment &bam2, const RefVec
 			cerr << "The edit distance tag (NM) was not found in the BAM file.  Please disable -ed.  Exiting\n";
 			exit(1);
 		}
-	}		
+	}
+	
+	// swap the ends if necessary
+	if ( chrom1 > chrom2 || ((chrom1 == chrom2) && (start1 > start2)) ) {
+		swap(chrom1, chrom2);
+		swap(start1, start2);
+		swap(end1, end2);
+		swap(strand1, strand2);
+		if (useEditDistance == true) swap(editDistance1, editDistance2);		
+	}
 
 	// report BEDPE using min mapQuality
 	if (useEditDistance == false) {
@@ -422,6 +432,7 @@ void PrintBedPE(const BamAlignment &bam1, const BamAlignment &bam2, const RefVec
 	}
 }
 
+
 // deprecated.
 bool IsCorrectMappingForBEDPE (const BamAlignment &bam) {
 

src/intersectBed/intersectMain.cpp

@@ -232,7 +232,7 @@ void ShowHelp(void) {
 	cerr << "\t-wao\t"			<< "Write the original A and B entries plus the number of base" << endl;
 	cerr 						<< "\t\tpairs of overlap between the two features." << endl;
 	cerr						<< "\t\t- Overlapping features restricted by -f and -r." << endl;
-	cerr						<< "\t\t  However, A features w/o overlap are also reported" << endl << endl;
+	cerr						<< "\t\t  However, A features w/o overlap are also reported" << endl;
 	cerr						<< "\t\t  with a NULL B feature and overlap = 0." << endl << endl;
 					
 	cerr << "\t-u\t"      		<< "Write the original A entry _once_ if _any_ overlaps found in B." << endl;

src/utils/bedFile/bedFile.h

@@ -178,11 +178,11 @@ public:
 
 	// return true if at least one overlap was found.  otherwise, return false.
 	bool FindOneOrMoreOverlapsPerBin(string chrom, int start, int end, string strand, 
-										bool forceStrand, float overlapFraction);
+										bool forceStrand, float overlapFraction = 0.0);
 
 	// return true if at least one __reciprocal__ overlap was found.  otherwise, return false.
 	bool FindOneOrMoreReciprocalOverlapsPerBin(string chrom, int start, int end, string strand, 
-													bool forceStrand, float overlapFraction);
+													bool forceStrand, float overlapFraction = 0.0);
 	
 
 	// Given a chrom, start, end and strand for a single feature,

src/windowBed/Makefile

@@ -9,14 +9,14 @@ BIN_DIR = ../../bin/
 # -------------------
 # define our includes
 # -------------------
-INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/
+INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/BamTools/ -I$(UTILITIES_DIR)/gzstream/
 
 # ----------------------------------
 # define our source and object files
 # ----------------------------------
 SOURCES= windowMain.cpp windowBed.cpp
 OBJECTS= $(SOURCES:.cpp=.o)
-_EXT_OBJECTS=bedFile.o lineFileUtilities.o gzstream.o
+_EXT_OBJECTS=bedFile.o lineFileUtilities.o BamReader.o BamWriter.o BGZF.o gzstream.o
 EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
 BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
 PROGRAM= windowBed
@@ -37,7 +37,8 @@ $(BUILT_OBJECTS): $(SOURCES)
 $(EXT_OBJECTS):
 	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
 	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/lineFileUtilities/
-	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream.o/
+	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/	
+	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
 		
 clean:
 	@echo "Cleaning up."

src/windowBed/windowBed.cpp

@@ -16,8 +16,8 @@
 /*
 	Constructor
 */
-BedWindow::BedWindow(string &bedAFile, string &bedBFile, int &leftSlop, int &rightSlop, bool &anyHit, bool &noHit, 
-					bool &writeCount, bool &strandWindows, bool &matchOnStrand) {
+BedWindow::BedWindow(string bedAFile, string bedBFile, int leftSlop, int rightSlop, bool anyHit, bool noHit, 
+					bool writeCount, bool strandWindows, bool matchOnStrand, bool bamInput, bool bamOutput) {
 
 	_bedAFile      = bedAFile;
 	_bedBFile      = bedBFile;
@@ -30,12 +30,26 @@ BedWindow::BedWindow(string &bedAFile, string &bedBFile, int &leftSlop, int &rig
 	_writeCount    = writeCount;
 	_strandWindows = strandWindows;	
 	_matchOnStrand = matchOnStrand;
+	_bamInput      = bamInput;
+	_bamOutput     = bamOutput;
 		
 	_bedA          = new BedFile(bedAFile);
 	_bedB          = new BedFile(bedBFile);
 	
-	// do the work
-	WindowIntersectBed();
+	// dealing with a proper file
+	if (_bedA->bedFile != "stdin") {   
+		if (_bamInput == false) 
+			WindowIntersectBed();
+		else
+			WindowIntersectBam(_bedA->bedFile);
+	}
+	// reading from stdin
+	else {  
+		if (_bamInput == false)
+			WindowIntersectBed();
+		else
+			WindowIntersectBam("stdin");			
+	}
 }
 
 
@@ -48,7 +62,7 @@ BedWindow::~BedWindow(void) {
 
 
 
-void BedWindow::FindWindowOverlaps(BED &a, vector<BED> &hits) {
+void BedWindow::FindWindowOverlaps(const BED &a, vector<BED> &hits) {
 	
 	/* 
 		Adjust the start and end of a based on the requested window
@@ -58,31 +72,8 @@ void BedWindow::FindWindowOverlaps(BED &a, vector<BED> &hits) {
 	// according to the slop requested (slop = 0 by default)
 	int aFudgeStart = 0;
 	int aFudgeEnd;
+	AddWindow(a, aFudgeStart, aFudgeEnd);
 
-	// Does the user want to treat the windows based on strand?
-	// If so, 
-	// if "+", then left is left and right is right
-	// if "-", the left is right and right is left.
-	if (_strandWindows) {
-		if (a.strand == "+") {
-			if ((a.start - _leftSlop) > 0) aFudgeStart = a.start - _leftSlop;
-			else aFudgeStart = 0;
-			aFudgeEnd = a.end + _rightSlop;
-		}
-		else {
-			if ((a.start - _rightSlop) > 0) aFudgeStart = a.start - _rightSlop;
-			else aFudgeStart = 0;
-			aFudgeEnd = a.end + _leftSlop;
-		}
-	}
-	// If not, add the windows irrespective of strand
-	else {
-		if ((a.start - _leftSlop) > 0) aFudgeStart = a.start - _leftSlop;
-		else aFudgeStart = 0;
-		aFudgeEnd = a.end + _rightSlop;
-	}
-	
-	
 	/* 
 		Now report the hits (if any) based on the window around a.
 	*/
@@ -122,6 +113,19 @@ void BedWindow::FindWindowOverlaps(BED &a, vector<BED> &hits) {
 	}
 }
 
+
+bool BedWindow::FindOneOrMoreWindowOverlaps(const BED &a) {
+	
+	// update the current feature's start and end
+	// according to the slop requested (slop = 0 by default)
+	int aFudgeStart = 0;
+	int aFudgeEnd;
+	AddWindow(a, aFudgeStart, aFudgeEnd);
+	
+	bool overlapsFound = _bedB->FindOneOrMoreOverlapsPerBin(a.chrom, a.start, a.end, a.strand, _matchOnStrand);
+	return overlapsFound;
+}
+
  
 void BedWindow::WindowIntersectBed() {
 
@@ -148,3 +152,99 @@ void BedWindow::WindowIntersectBed() {
 }
 
 
+void BedWindow::WindowIntersectBam(string bamFile) {
+
+	// load the "B" bed file into a map so
+	// that we can easily compare "A" to it for overlaps
+	_bedB->loadBedFileIntoMap();
+	
+	// open the BAM file
+	BamReader reader;
+	BamWriter writer;
+	reader.Open(bamFile);
+
+	// get header & reference information
+	string header  = reader.GetHeaderText();
+	RefVector refs = reader.GetReferenceData();
+
+	// open a BAM output to stdout if we are writing BAM
+	if (_bamOutput == true) {
+		// open our BAM writer
+		writer.Open("stdout", header, refs);
+	}
+
+	vector<BED> hits;					// vector of potential hits
+	// reserve some space
+	hits.reserve(100);
+	
+	_bedA->bedType = 6;
+	BamAlignment bam;	
+	bool overlapsFound;
+	// get each set of alignments for each pair.
+	while (reader.GetNextAlignment(bam)) {
+		
+		if (bam.IsMapped()) {	
+			BED a;
+			a.chrom = refs.at(bam.RefID).RefName;
+			a.start = bam.Position;
+			a.end   = bam.GetEndPosition(false);
+
+			// build the name field from the BAM alignment.
+			a.name = bam.Name;
+			if (bam.IsFirstMate()) a.name += "/1";
+			if (bam.IsSecondMate()) a.name += "/2";
+
+			a.score  = ToString(bam.MapQuality);
+			a.strand = "+"; if (bam.IsReverseStrand()) a.strand = "-"; 
+	
+			if (_bamOutput == true) {
+				overlapsFound = FindOneOrMoreWindowOverlaps(a);
+				if (overlapsFound == true) {
+					if (_noHit == false)
+						writer.SaveAlignment(bam);
+				}
+				else {
+					if (_noHit == true) 
+						writer.SaveAlignment(bam);	
+				}
+			}
+			else {
+				FindWindowOverlaps(a, hits);
+				hits.clear();
+			}
+		}
+	}
+	
+	// close the relevant BAM files.
+	reader.Close();
+	if (_bamOutput == true) {
+		writer.Close();
+	}
+}
+
+
+void BedWindow::AddWindow(const BED &a, int &fudgeStart, int &fudgeEnd) {
+	// Does the user want to treat the windows based on strand?
+	// If so, 
+	// if "+", then left is left and right is right
+	// if "-", the left is right and right is left.
+	if (_strandWindows) {
+		if (a.strand == "+") {
+			if ((a.start - _leftSlop) > 0) fudgeStart = a.start - _leftSlop;
+			else fudgeStart = 0;
+			fudgeEnd = a.end + _rightSlop;
+		}
+		else {
+			if ((a.start - _rightSlop) > 0) fudgeStart = a.start - _rightSlop;
+			else fudgeStart = 0;
+			fudgeEnd = a.end + _leftSlop;
+		}
+	}
+	// If not, add the windows irrespective of strand
+	else {
+		if ((a.start - _leftSlop) > 0) fudgeStart = a.start - _leftSlop;
+		else fudgeStart = 0;
+		fudgeEnd = a.end + _rightSlop;
+	}
+}
+

src/windowBed/windowBed.h

@@ -12,6 +12,11 @@
 #ifndef WINDOWBED_H
 #define WINDOWBED_H
 
+#include "BamReader.h"
+#include "BamWriter.h"
+#include "BamAux.h"
+using namespace BamTools;
+
 #include "bedFile.h"
 #include <vector>
 #include <iostream>
@@ -27,8 +32,8 @@ class BedWindow {
 public:
 
 	// constructor 
-	BedWindow(string &bedAFile, string &bedBFile, int &leftSlop, int &rightSlop, bool &anyHit, bool &noHit, 
-			  bool &writeCount, bool &strandWindows, bool &matchOnStrand);
+	BedWindow(string bedAFile, string bedBFile, int leftSlop, int rightSlop, bool anyHit, bool noHit, 
+			  bool writeCount, bool strandWindows, bool matchOnStrand, bool bamInput, bool bamOutput);
 
 	// destructor
 	~BedWindow(void);
@@ -44,13 +49,18 @@ private:
 	bool _noHit;
 	bool _strandWindows;
 	bool _matchOnStrand;
+	bool _bamInput;
+	bool _bamOutput;
 
 	// instance of a bed file class.
 	BedFile *_bedA, *_bedB;
 	
 	// methods
 	void WindowIntersectBed();
-	void FindWindowOverlaps(BED &a, vector<BED> &hits);
+	void WindowIntersectBam(string bamFile);	
+	void FindWindowOverlaps(const BED &a, vector<BED> &hits);
+	bool FindOneOrMoreWindowOverlaps(const BED &a);	
+	void AddWindow(const BED &a, int &fudgeStart, int &fudgeEnd);	
 
 };
 #endif /* WINDOWBED_H */

src/windowBed/windowMain.cpp

@@ -14,7 +14,6 @@
 
 using namespace std;
 
-
 // define the version
 #define PROGRAM_NAME "windowBed"
 
@@ -24,6 +23,7 @@ using namespace std;
 // function declarations
 void ShowHelp(void);
 
+
 int main(int argc, char* argv[]) {
 
 	// our configuration variables
@@ -47,6 +47,8 @@ int main(int argc, char* argv[]) {
 	bool haveRight = false;
 	bool strandWindows = false;
 	bool matchOnStrand = false;
+	bool inputIsBam         = false;
+	bool outputIsBam        = true;	
 
 	// check to see if we should print out some help
 	if(argc <= 1) showHelp = true;
@@ -74,12 +76,23 @@ int main(int argc, char* argv[]) {
 				i++;
 			}
 		}
+		else if(PARAMETER_CHECK("-abam", 5, parameterLength)) {
+			if ((i+1) < argc) {
+				haveBedA = true;
+				inputIsBam = true;
+				bedAFile = argv[i + 1];
+				i++;		
+			}	
+		}
 		else if(PARAMETER_CHECK("-b", 2, parameterLength)) {
 			if ((i+1) < argc) {
 				haveBedB = true;
 				bedBFile = argv[i + 1];
 				i++;
 			}
+		}
+		else if(PARAMETER_CHECK("-bed", 4, parameterLength)) {
+			outputIsBam = false;
 		}	
 		else if(PARAMETER_CHECK("-u", 2, parameterLength)) {
 			anyHit = true;
@@ -161,7 +174,8 @@ int main(int argc, char* argv[]) {
 	}
 	
 	if (!showHelp) {
-		BedWindow *bi = new BedWindow(bedAFile, bedBFile, leftSlop, rightSlop, anyHit, noHit, writeCount, strandWindows, matchOnStrand);
+		BedWindow *bi = new BedWindow(bedAFile, bedBFile, leftSlop, rightSlop, anyHit, 
+		                              noHit, writeCount, strandWindows, matchOnStrand, inputIsBam, outputIsBam);
 		delete bi;
 		return 0;
 	}
@@ -170,6 +184,7 @@ int main(int argc, char* argv[]) {
 	}
 }
 
+
 void ShowHelp(void) {
 
 	cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
@@ -183,6 +198,12 @@ void ShowHelp(void) {
 	cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -a <a.bed> -b <b.bed>" << endl << endl;
 
 	cerr << "Options: " << endl;
+	
+	cerr << "\t-abam\t"			<< "The A input file is in BAM format.  Output will be BAM as well." << endl << endl;
+
+	cerr << "\t-bed\t"			<< "When using BAM input (-abam), write output as BED. The default" << endl;
+	cerr 						<< "\t\tis to write output in BAM when using -abam." << endl << endl;
+	
 	cerr << "\t-w\t"			<< "Base pairs added upstream and downstream of each entry" << endl;
 	cerr						<< "\t\tin A when searching for overlaps in B." << endl;
 	cerr						<< "\t\t- Creates symterical \"windows\" around A." << endl;		
@@ -220,5 +241,4 @@ void ShowHelp(void) {
 
 	// end the program here
 	exit(1);
-
-}
+}
\ No newline at end of file