Added bed12ToBed6

src/bed12ToBed6/Makefile

+CXX=		g++
+CXXFLAGS=	-Wall -O2
+LIBS=		-lz
+UTILITIES_DIR = ../utils/
+OBJ_DIR = ../../obj/
+BIN_DIR = ../../bin/
+
+# -------------------
+# define our includes
+# -------------------
+INCLUDES = -I$(UTILITIES_DIR)/bedFile/ -I$(UTILITIES_DIR)/lineFileUtilities/ -I$(UTILITIES_DIR)/version/ -I$(UTILITIES_DIR)/gzstream/ 
+
+# ----------------------------------
+# define our source and object files
+# ----------------------------------
+SOURCES= bed12ToBed6.cpp
+OBJECTS= $(SOURCES:.cpp=.o)
+_EXT_OBJECTS=bedFile.o  lineFileUtilities.o gzstream.o
+EXT_OBJECTS=$(patsubst %,$(OBJ_DIR)/%,$(_EXT_OBJECTS))
+BUILT_OBJECTS= $(patsubst %,$(OBJ_DIR)/%,$(OBJECTS))
+PROGRAM= bed12ToBed6
+
+
+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 $(UTILITIES_DIR)/lineFileUtilities/
+	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/bedFile/
+	@$(MAKE) --no-print-directory -C $(UTILITIES_DIR)/gzstream/
+			
+clean:
+	@echo "Cleaning up."
+	@rm -f $(OBJ_DIR)/* $(BIN_DIR)/*
+
+.PHONY: clean

src/bed12ToBed6/bed12ToBed6.cpp

+/*****************************************************************************
+  bed12ToBed6.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 "lineFileUtilities.h"
+#include "bedFile.h"
+#include "version.h"
+
+#include <vector>
+#include <iostream>
+#include <fstream>
+#include <stdlib.h>
+
+using namespace std;
+
+
+// define our program name
+#define PROGRAM_NAME "bed12ToBed6"
+
+// 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 DetermineBedInput(BedFile *bed);
+void ProcessBed(istream &bedInput, BedFile *bed);
+
+
+
+int main(int argc, char* argv[]) {
+
+	// our configuration variables
+	bool showHelp = false;
+
+	// input files
+	string bedFile;
+	bool haveBed         = 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) {
+				haveBed = true;
+				bedFile = argv[i + 1];
+				i++;
+			}
+		}		
+		else {
+			cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
+			showHelp = true;
+		}		
+	}
+
+	// make sure we have an input files
+	if (!haveBed ) {
+		cerr << endl << "*****" << endl << "*****ERROR: Need -i (BED) file. " << endl << "*****" << endl;
+		showHelp = true;
+	}
+
+	if (!showHelp) {
+		BedFile *bed       = new BedFile(bedFile);		
+		DetermineBedInput(bed);
+	}	
+	else {
+		ShowHelp();
+	}
+}
+
+
+void ShowHelp(void) {
+
+	cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
+	
+	cerr << "Author:  Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
+
+	cerr << "Summary: Splits BED12 features into discrete BED6 features." << endl << endl;
+
+	cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -i <bed>" << endl << endl;
+
+
+	// end the program here
+	exit(1);
+}
+
+
+void DetermineBedInput(BedFile *bed) {
+	
+	// dealing with a proper file
+	if (bed->bedFile != "stdin") {   
+
+		ifstream bedStream(bed->bedFile.c_str(), ios::in);
+		if ( !bedStream ) {
+			cerr << "Error: The requested bed file (" << bed->bedFile << ") could not be opened. Exiting!" << endl;
+			exit (1);
+		}
+		ProcessBed(bedStream, bed);
+	}
+	// reading from stdin
+	else {  					
+		ProcessBed(cin, bed);
+	}
+}
+
+
+void ProcessBed(istream &bedInput, BedFile *bed) {
+
+	// process each BED entry and convert to BAM
+	BED bedEntry, nullBed;
+	int lineNum = 0;
+	BedLineStatus bedStatus;
+	// open the BED file for reading.
+	bed->Open();
+	while ((bedStatus = bed->GetNextBed(bedEntry, lineNum)) != BED_INVALID) {        
+		if (bedStatus == BED_VALID) {
+		    
+		    bedVector bedBlocks;  // vec to store the discrete BED "blocks" from a
+            splitBedIntoBlocks(bedEntry, lineNum, bedBlocks);
+            
+            vector<BED>::const_iterator bedItr  = bedBlocks.begin();
+        	vector<BED>::const_iterator bedEnd  = bedBlocks.end();
+        	for (; bedItr != bedEnd; ++bedItr) {
+                printf ("%s\t%d\t%d\t%s\t%s\t%s\n", bedItr->chrom.c_str(), bedItr->start, bedItr->end, bedItr->name.c_str(), 
+    												bedItr->score.c_str(), bedItr->strand.c_str());
+    	    }
+			bedEntry = nullBed;
+		}
+	}
+	// close up
+	bed->Close();
+}