Added BEDGRAPH functionality to genomeCoverageBed. From Gordon Assaf, CSHL.

src/genomeCoverageBed/genomeCoverageBed.cpp

@@ -15,15 +15,16 @@
 /*
 	Constructor
 */
-BedCoverage::BedCoverage(string &bedFile, string &genomeFile, bool &eachBase, bool &startSites, int &max) {
+BedCoverage::BedCoverage(string &bedFile, string &genomeFile, bool &eachBase, bool &startSites, bool &bedGraph, int &max) {
 
-	this->bedFile = bedFile;
+	this->bedFile    = bedFile;
 	this->genomeFile = genomeFile;
-	this->eachBase = eachBase;
+	this->eachBase   = eachBase;
 	this->startSites = startSites;
-	this->max = max;
+	this->bedGraph   = bedGraph;
+	this->max        = max;
 
-	this->bed = new BedFile(bedFile);
+	this->bed        = new BedFile(bedFile);
 }
 
 
@@ -139,14 +140,14 @@ void BedCoverage::CoverageBeds(istream &bedInput) {
 	// process the results of the last chromosome.
 	ReportChromCoverage(chromCov, chromSizes[currChrom], currChrom, chromDepthHist);
 	
-	if (! this->eachBase) {
+	if (this->eachBase == false && this->bedGraph == false) {
 		ReportGenomeCoverage(chromSizes, chromDepthHist);
 	}
 }
 
 
 
-void BedCoverage::ReportChromCoverage(vector<DEPTH> &chromCov, int &chromSize, string &chrom, chromHistMap &chromDepthHist) {
+void BedCoverage::ReportChromCoverage(const vector<DEPTH> &chromCov, int &chromSize, string &chrom, chromHistMap &chromDepthHist) {
 	
 	if (this->eachBase) {
 		int depth = 0;  // initialize the depth
@@ -159,6 +160,9 @@ void BedCoverage::ReportChromCoverage(vector<DEPTH> &chromCov, int &chromSize, s
 			depth = depth - chromCov[pos].ends;
 		}
 	}
+	else if (this->bedGraph) {
+		ReportChromCoverageBedGraph(chromCov, chromSize, chrom);
+	}
 	else {
 		
 		int depth = 0;  // initialize the depth
@@ -232,6 +236,46 @@ void BedCoverage::ReportGenomeCoverage(map<string, int> &chromSizes, chromHistMa
 }
 
 
+void BedCoverage::ReportChromCoverageBedGraph(const vector<DEPTH> &chromCov, int &chromSize, string &chrom) {
+
+	int depth     = 0;     // initialize the depth
+	int lastStart = -1 ;
+	int lastDepth = -1 ;
+
+	for (int pos = 0; pos < chromSize; pos++) {
+		depth += chromCov[pos].starts;
+
+		if (depth == 0 && lastDepth != -1) {
+			// We've found a new block of zero coverage, so report
+			// the previous block of non-zero coverage.
+			cout << chrom << "\t" << lastStart << "\t" << pos << "\t" << lastDepth << endl;
+			lastDepth = -1;
+			lastStart = -1;
+		}
+		else if (depth > 0 && depth != lastDepth) {
+			// Coverage depth has changed, print the last interval coverage (if any)
+			if (lastDepth != -1) { 
+				cout << chrom << "\t" << lastStart << "\t" << pos << "\t" << lastDepth << endl;
+			}
+			//Set current position as the new interval start + depth
+			lastDepth = depth;
+			lastStart = pos;
+		}
+		// Default: the depth has not changed, so we will not print anything.
+		// Proceed until the depth changes.
+		
+		// Update depth
+		depth = depth - chromCov[pos].ends;
+	}
+	
+	
+	//Print information about the last position
+	if (lastDepth != -1) {
+		cout << chrom << "\t" << lastStart << "\t" << chromSize << "\t" << lastDepth << endl;
+	}
+}
+
+
 void BedCoverage::DetermineBedInput() {
 	if (bed->bedFile != "stdin") {   // process a file
 		ifstream beds(bed->bedFile.c_str(), ios::in);

src/genomeCoverageBed/genomeCoverageBed.h

@@ -34,14 +34,18 @@ class BedCoverage {
 public:
 
 	// constructor 
-	BedCoverage(string &, string &, bool &, bool &, int &);
+	BedCoverage(string &bedFile, string &genomeFile, bool &eachBase, bool &startSites, bool &bedGraph, int &max);
 
 	// destructor
 	~BedCoverage(void);
 
 	void CoverageBeds(istream &bedInput);
-	void ReportChromCoverage(vector<DEPTH> &, int &, string &, chromHistMap&);
-	void ReportGenomeCoverage(map<string, int> &, chromHistMap&);
+
+	void ReportChromCoverage(const vector<DEPTH> &, int &chromSize, string &chrom, chromHistMap&);
+
+	void ReportGenomeCoverage(map<string, int> &chromSizes, chromHistMap &chromDepthHist);
+
+	void ReportChromCoverageBedGraph(const vector<DEPTH> &chromCov, int &chromSize, string &chrom);
 
 	void DetermineBedInput();
 
@@ -51,10 +55,10 @@ private:
 	string genomeFile;
 	bool eachBase;
 	bool startSites;
+	bool bedGraph;
 	int max;
 
 	// The BED file from which to compute coverage.
 	BedFile *bed;
 	chromDepthMap chromCov;
-
 };

src/genomeCoverageBed/genomeCoverageMain.cpp

@@ -34,10 +34,11 @@ int main(int argc, char* argv[]) {
 	string genomeFile;
 	int max = 999999999;
 	
-	bool haveBed = false;
+	bool haveBed    = false;
 	bool haveGenome = false;
 	bool startSites = false;
-	bool eachBase = false;
+	bool bedGraph   = false;
+	bool eachBase   = false;
 
 	// check to see if we should print out some help
 	if(argc <= 1) showHelp = true;
@@ -75,6 +76,9 @@ int main(int argc, char* argv[]) {
 		else if(PARAMETER_CHECK("-d", 2, parameterLength)) {
 			eachBase = true;
 		}
+		else if(PARAMETER_CHECK("-bg", 3, parameterLength)) {
+			bedGraph = true;
+		}		
 		else if(PARAMETER_CHECK("-max", 4, parameterLength)) {
 			if ((i+1) < argc) {
 				max = atoi(argv[i + 1]);
@@ -92,10 +96,14 @@ int main(int argc, char* argv[]) {
 	  cerr << endl << "*****" << endl << "*****ERROR: Need both a BED (-i) and a genome (-g) file. " << endl << "*****" << endl;
 	  showHelp = true;
 	}
+	if (bedGraph && eachBase) {
+	  cerr << endl << "*****" << endl << "*****ERROR: Use -d or -bedgraph, not both" << endl << "*****" << endl;
+	  showHelp = true;
+	}
 	
 	if (!showHelp) {
 		
-		BedCoverage *bc = new BedCoverage(bedFile, genomeFile, eachBase, startSites, max);
+		BedCoverage *bc = new BedCoverage(bedFile, genomeFile, eachBase, startSites, bedGraph, max);
 		bc->DetermineBedInput();
 		
 		return 0;
@@ -119,8 +127,12 @@ void ShowHelp(void) {
 	cerr << "\t-d\t"	     	<< "Report the depth at each genome position." << endl;
 	cerr 						<< "\t\tDefault behavior is to report a histogram." << endl << endl;
 
+	cerr << "\t-bg\t"			<< "Report depth in BedGraph format. For details, see:" << endl;
+	cerr 						<< "\t\tgenome.ucsc.edu/goldenPath/help/bedgraph.html" << endl << endl;
+
 	cerr << "\t-max\t"          << "Combine all positions with a depth >= max into" << endl;
-	cerr						<< "\t\ta single bin in the histogram." << endl;
+	cerr						<< "\t\ta single bin in the histogram. Irrelevant" << endl;
+	cerr						<< "\t\tfor -d and -bedGraph" << endl;
 	cerr						<< "\t\t- (INTEGER)" << endl << endl;
 
 	cerr << "Notes: " << endl;
@@ -140,7 +152,7 @@ void ShowHelp(void) {
 	cerr << "\tOne can use the UCSC Genome Browser's MySQL database to extract" << endl;
 	cerr << "\tchromosome sizes. For example, H. sapiens:" << endl << endl;
 	cerr << "\tmysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e /" << endl;
-	cerr << "\t\"select chrom, size from hg19.chromInfo\"  > hg19.genome" << endl << endl;
+	cerr << "\t\"select chrom, size from hg19.chromInfo\" | awk 'NR>1' > hg19.genome" << endl << endl;
 		
 	
 	// end the program here