Added bamToBed.

Makefile

@@ -19,7 +19,7 @@ export CXX ?= g++
 #include includes/$(BLD_PLATFORM).inc
 
 # define our source subdirectories
-SUBDIRS = $(SRC_DIR)/closestBed $(SRC_DIR)/complementBed $(SRC_DIR)/coverageBed $(SRC_DIR)/intersectBed $(SRC_DIR)/mergeBed $(SRC_DIR)/genomeCoverageBed $(SRC_DIR)/fastaFromBed $(SRC_DIR)/shuffleBed $(SRC_DIR)/slopBed $(SRC_DIR)/sortBed $(SRC_DIR)/windowBed $(SRC_DIR)/subtractBed $(SRC_DIR)/linksBed $(SRC_DIR)/pairToBed $(SRC_DIR)/pairToPair $(SRC_DIR)/maskFastaFromBed
+SUBDIRS = $(SRC_DIR)/closestBed $(SRC_DIR)/complementBed $(SRC_DIR)/coverageBed $(SRC_DIR)/intersectBed $(SRC_DIR)/mergeBed $(SRC_DIR)/genomeCoverageBed $(SRC_DIR)/fastaFromBed $(SRC_DIR)/shuffleBed $(SRC_DIR)/slopBed $(SRC_DIR)/sortBed $(SRC_DIR)/windowBed $(SRC_DIR)/subtractBed $(SRC_DIR)/linksBed $(SRC_DIR)/pairToBed $(SRC_DIR)/pairToPair $(SRC_DIR)/maskFastaFromBed $(SRC_DIR)/bamToBed
 
 UTIL_SUBDIRS =  $(SRC_DIR)/utils/lineFileUtilities $(SRC_DIR)/utils/bedFile $(SRC_DIR)/utils/bedFilePE $(SRC_DIR)/utils/sequenceUtilities
 

src/bamToBed/Makefile

+CXX=		g++
+CXXFLAGS=	-Wall -O3 -m64 -g
+LIBS=		-lz
+UTILITIES_DIR = ../utils/
+OBJ_DIR = ../../obj/
+BIN_DIR = ../../bin/
+
+# -------------------
+# define our includes
+# -------------------
+INCLUDES = -I$(UTILITIES_DIR)/BamTools/  -I$(UTILITIES_DIR)/version/
+
+# ----------------------------------
+# define our source and object files
+# ----------------------------------
+SOURCES= bamToBed.cpp
+OBJECTS= $(SOURCES:.cpp=.o)
+_EXT_OBJECTS=BamReader.o BGZF.o
+EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
+BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
+PROGRAM= bamToBed
+
+
+all: $(PROGRAM)
+
+.PHONY: all
+
+
+$(PROGRAM): $(BUILT_OBJECTS) $(EXT_OBJECTS)
+	@echo "  * linking $(PROGRAM)"
+	@$(CXX) $(LDFLAGS) $(CXXFLAGS) -o $(BIN_DIR)/$@ $^ $(LIBS)
+
+$(BUILT_OBJECTS): $(SOURCES)
+	@echo "  * compiling" $(*F).cpp
+	@$(CXX) -c -o $@ $(*F).cpp $(LDFLAGS) $(CXXFLAGS) $(INCLUDES)
+
+$(EXT_OBJECTS):
+
+	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/BamTools/	
+	
+clean:
+	@echo "Cleaning up."
+	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+
+.PHONY: clean

src/bamToBed/bamToBed.cpp

+/*****************************************************************************
+  bamToBed.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 "version.h"
+#include "BamReader.h"
+#include "BamWriter.h"
+#include "BamAux.h"
+using namespace BamTools;
+
+#include <vector>
+#include <iostream>
+#include <fstream>
+#include <stdlib.h>
+
+using namespace std;
+
+
+// define our program name
+#define PROGRAM_NAME "bamToBed"
+
+// define our parameter checking macro
+#define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
+
+
+// function declarations
+void ShowHelp(void);
+void PrintBed(const BamAlignment &bam, const RefVector &refs, bool useEditDistance);
+void PrintBedPE(const BamAlignment &bam,  const RefVector &refs, bool useEditDistance);
+
+
+int main(int argc, char* argv[]) {
+
+	// our configuration variables
+	bool showHelp = false;
+
+	// input files
+	string bamFile;
+
+	bool haveBam = false;
+	bool writeBedPE = false;
+	bool useEditDistance = false;
+	
+	// check to see if we should print out some help
+	if(argc <= 1) showHelp = true;
+
+	for(int i = 1; i < argc; i++) {
+		int parameterLength = (int)strlen(argv[i]);
+
+		if((PARAMETER_CHECK("-h", 2, parameterLength)) || 
+		(PARAMETER_CHECK("--help", 5, parameterLength))) {
+			showHelp = true;
+		}
+	}
+
+	if(showHelp) ShowHelp();
+
+	// do some parsing (all of these parameters require 2 strings)
+	for(int i = 1; i < argc; i++) {
+
+		int parameterLength = (int)strlen(argv[i]);
+
+		if(PARAMETER_CHECK("-i", 2, parameterLength)) {
+			if ((i+1) < argc) {
+				haveBam = true;
+				bamFile = argv[i + 1];
+			}
+			i++;
+		}
+		else if(PARAMETER_CHECK("-bedpe", 6, parameterLength)) {
+				writeBedPE = true;
+		}
+		else if(PARAMETER_CHECK("-ed", 3, parameterLength)) {
+				useEditDistance = true;
+		}		
+		else {
+			cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
+			showHelp = true;
+		}		
+	}
+
+	// make sure we have an input files
+	if (!haveBam ) {
+		cerr << endl << "*****" << endl << "*****ERROR: Need -i (BAM) file. " << endl << "*****" << endl;
+		showHelp = true;
+	}
+	// make sure we have an input files
+	if (writeBedPE && useEditDistance) {
+		cerr << endl << "*****" << endl << "*****ERROR: Cannot use edit distance with BEDPE. " << endl << "*****" << endl;
+		showHelp = true;
+	}
+	
+	if (!showHelp) {
+
+		// open the BAM file
+		BamReader reader;
+		reader.Open(bamFile);
+
+		// get header & reference information
+		string header = reader.GetHeaderText();
+		RefVector refs = reader.GetReferenceData();
+		
+		BamAlignment bam;
+		while (reader.GetNextAlignment(bam)) {
+			if (!writeBedPE) {
+				PrintBed(bam, refs, useEditDistance);
+			}
+			else {
+				PrintBedPE(bam, refs, useEditDistance);
+			}
+		}
+		reader.Close();	
+	}	
+	else {
+		ShowHelp();
+	}
+}
+
+void ShowHelp(void) {
+
+	cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
+	
+	cerr << "Author:  Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
+
+	cerr << "Summary: Converts BAM alignments to BED6 or BEDPE format." << endl << endl;
+
+	cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -i <bam> " << endl << endl;
+
+	cerr << "Options: " << endl;
+	
+	cerr << "\t-bedpe\t"	<< "Write BEDPE format." << endl << endl;
+	
+	cerr << "\t-ed\t"		<< "Use BAM edit distance (NM tag) for score." << endl;
+	cerr 					<< "\t\tDefault is to use mapping quality." << endl;
+	cerr 					<< "\t\tNot available for BEDPE format." << endl << endl;
+	
+
+	// end the program here
+	exit(1);
+
+}
+
+
+void PrintBed(const BamAlignment &bam,  const RefVector &refs, bool useEditDistance) {
+
+	string strand = "+"; 
+	if (bam.IsReverseStrand()) strand = "-";
+	
+	if (useEditDistance == false) {
+		printf("%s\t%d\t%d\t\%s\t%d\t%s\n", refs.at(bam.RefID).RefName.c_str(), bam.Position,
+									  bam.Position + bam.Length, bam.Name.c_str(),
+									  bam.MapQuality, strand.c_str());
+	}
+	else {
+		uint8_t editDistance;
+		if (bam.GetEditDistance(editDistance)) {
+			printf("%s\t%d\t%d\t\%s\t%u\t%s\n", refs.at(bam.RefID).RefName.c_str(), bam.Position,
+										  bam.Position + bam.Length, bam.Name.c_str(),
+										  editDistance, strand.c_str());
+		}
+	}
+}
+
+
+void PrintBedPE(const BamAlignment &bam,  const RefVector &refs, bool useEditDistance) {
+
+	if (bam.InsertSize > 0) {
+		string strand1 = "+"; 
+		string strand2 = "+";
+		if (bam.IsReverseStrand()) strand1 = "-"; 
+		if (bam.IsMateReverseStrand()) strand2 = "-";	
+
+		printf("%s\t%d\t%d\t\%s\t%d\t%d\t%s\t%d\t%s\t%s\n", 
+						refs.at(bam.RefID).RefName.c_str(), bam.Position, bam.Position + bam.Length, 
+						refs.at(bam.MateRefID).RefName.c_str(), bam.MatePosition, bam.MatePosition + bam.Length,
+						bam.Name.c_str(), bam.MapQuality, strand1.c_str(), strand2.c_str());
+	}
+}
\ No newline at end of file

src/bamToBed/hmec.50.txt.pairs.conc.bam

+../intersectBed/hmec.50.txt.pairs.conc.bam
\ No newline at end of file

src/complementBed/a.bed

-chr1	50	60
+chr1	100	200
+chr1	400	500
+chr1	500	800
+

src/complementBed/genome

-chr1	100
+chr1	1000

src/intersectBed/intersectBed.cpp

@@ -248,14 +248,10 @@ void BedIntersect::IntersectBam(string bamFile) {
 		if (this->bamOutput == true) {
 			overlapsFound = FindOneOrMoreOverlap(a, hits);
 			if (overlapsFound == true) {
-				if (!this->noHit) {
-					writer.SaveAlignment(bamAlignment);
-				}
+				if (!this->noHit) writer.SaveAlignment(bamAlignment)
 			}
 			else {
-				if (this->noHit) {
-					writer.SaveAlignment(bamAlignment);
-				}
+				if (this->noHit) writer.SaveAlignment(bamAlignment);	
 			}
 		}
 		else {