/***************************************************************************** windowMakerMain.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 "windowMaker.h" #include "version.h" using namespace std; // define our program name #define PROGRAM_NAME "bedtools makewindows" // define our parameter checking macro #define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen) // function declarations void windowmaker_help(void); int windowmaker_main(int argc, char* argv[]) { // our configuration variables bool showHelp = false; // input files string inputFile; WindowMaker::INPUT_FILE_TYPE inputFileType = WindowMaker::GENOME_FILE; WindowMaker::ID_METHOD idMethod = WindowMaker::ID_NONE; // parms uint32_t size = 0; uint32_t step = 0; uint32_t count = 0; bool haveGenome = false; bool haveBed = false; bool haveSize = false; bool haveCount = false; 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) windowmaker_help(); // 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("-g", 2, parameterLength)) { if ((i+1) < argc) { haveGenome = true; inputFile = argv[i + 1]; inputFileType = WindowMaker::GENOME_FILE; i++; } } else if(PARAMETER_CHECK("-b", 2, parameterLength)) { if ((i+1) < argc) { haveBed = true; inputFile = argv[i + 1]; inputFileType = WindowMaker::BED_FILE; i++; } } else if(PARAMETER_CHECK("-w", 2, parameterLength)) { if ((i+1) < argc) { haveSize = true; size = atoi(argv[i + 1]); step = size; i++; } } else if(PARAMETER_CHECK("-s", 2, parameterLength)) { if ((i+1) < argc) { step = atoi(argv[i + 1]); i++; } } else if(PARAMETER_CHECK("-n", 2, parameterLength)) { if ((i+1) < argc) { haveCount = true; count = atoi(argv[i + 1]); i++; } } else if(PARAMETER_CHECK("-i", 2, parameterLength)) { if ((i+1) < argc) { if (strcmp(argv[i+1],"winnum")==0) idMethod = WindowMaker::ID_WINDOW_NUMBER; else if (strcmp(argv[i+1],"srcwinnum")==0) idMethod = WindowMaker::ID_SOURCE_ID_WINDOW_NUMBER; else if (strcmp(argv[i+1],"src")==0) idMethod = WindowMaker::ID_SOURCE_ID; else { cerr << endl << "*****ERROR: Invalid ID method (" << argv[i+1] << "). Possible values are: winnum, srcwinnum" << endl << endl ; showHelp = true; } i++; } } else { cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl; showHelp = true; } } // make sure we have both input files if (!haveGenome && !haveBed) { cerr << endl << "*****" << endl << "*****ERROR: Need -g (genome file) or -b (BED file) for interval source. " << endl << "*****" << endl; showHelp = true; } if (haveGenome && haveBed) { cerr << endl << "*****" << endl << "*****ERROR: Can't combine -g (genome file) and -b (BED file). Please use one or the other." << endl << "*****" << endl; showHelp = true; } if (!haveSize && !haveCount) { cerr << endl << "*****" << endl << "*****ERROR: Need -w (window size) or -n (number of windows). " << endl << "*****" << endl; showHelp = true; } if (haveSize && haveCount) { cerr << endl << "*****" << endl << "*****ERROR: Can't combine -w (window size) and -n (number of windows). Please use one or the other. " << endl << "*****" << endl; showHelp = true; } if (!showHelp) { WindowMaker *wm = NULL; if (haveCount) wm = new WindowMaker(inputFile, idMethod, inputFileType, count); if (haveSize) wm = new WindowMaker(inputFile, idMethod, inputFileType, size, step); delete wm; } else { windowmaker_help(); } return 0; } void windowmaker_help(void) { cerr << "\nTool: bedtools makewindows" << endl; cerr << "Version: " << VERSION << "\n"; cerr << "Summary: Makes adjacent or sliding windows across a genome or BED file." << endl << endl; cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] [-g OR -b ]" << endl; cerr << " [ -w OR -n ]" << endl << endl; cerr << "Input Options: " << endl; cerr << "\t-g " << endl; cerr << "\t\tGenome file size (see notes below)." << endl; cerr << "\t\tWindows will be created for each chromosome in the file." << endl << endl; cerr << "\t-b " << endl; cerr << "\t\tBED file (with chrom,start,end fields)." << endl; cerr << "\t\tWindows will be created for each interval in the file." << endl << endl; cerr << "Windows Output Options: " << endl; cerr << "\t-w " << endl; cerr << "\t\tDivide each input interval (either a chromosome or a BED interval)" << endl; cerr << "\t\tto fixed-sized windows (i.e. same number of nucleotide in each window)." << endl; cerr << "\t\tCan be combined with -s " << endl << endl; cerr << "\t-s " << endl; cerr << "\t\tStep size: i.e., how many base pairs to step before" << endl; cerr << "\t\tcreating a new window. Used to create \"sliding\" windows." << endl; cerr << "\t\t- Defaults to window size (non-sliding windows)." << endl << endl; cerr << "\t-n " << endl; cerr << "\t\tDivide each input interval (either a chromosome or a BED interval)" << endl; cerr << "\t\tto fixed number of windows (i.e. same number of windows, with" << endl; cerr << "\t\tvarying window sizes)." << endl << endl; cerr << "ID Naming Options: " << endl; cerr << "\t-i src|winnum|srcwinnum" << endl; cerr << "\t\tThe default output is 3 columns: chrom, start, end ." << endl; cerr << "\t\tWith this option, a name column will be added." << endl; cerr << "\t\t \"-i src\" - use the source interval's name." << endl; cerr << "\t\t \"-i winnum\" - use the window number as the ID (e.g. 1,2,3,4...)." << endl; cerr << "\t\t \"-i srcwinnum\" - use the source interval's name with the window number." << endl; cerr << "\t\tSee below for usage examples." << endl << endl; cerr << "Notes: " << endl; cerr << "\t(1) The genome file should tab delimited and structured as follows:" << endl; cerr << "\t " << endl << endl; cerr << "\tFor example, Human (hg19):" << endl; cerr << "\tchr1\t249250621" << endl; cerr << "\tchr2\t243199373" << endl; cerr << "\t..." << endl; cerr << "\tchr18_gl000207_random\t4262" << endl << endl; cerr << "Tips: " << endl; 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 << "Examples: " << endl; cerr << " # Divide the human genome into windows of 1MB:" << endl; cerr << " $ " << PROGRAM_NAME << " -g hg19.txt -w 1000000" << endl; cerr << " chr1 0 1000000" << endl; cerr << " chr1 1000000 2000000" << endl; cerr << " chr1 2000000 3000000" << endl; cerr << " chr1 3000000 4000000" << endl; cerr << " chr1 4000000 5000000" << endl; cerr << " ..." << endl; cerr << endl; cerr << " # Divide the human genome into sliding (=overlapping) windows of 1MB, with 500KB overlap:" << endl; cerr << " $ " << PROGRAM_NAME << " -g hg19.txt -w 1000000 -s 500000" << endl; cerr << " chr1 0 1000000" << endl; cerr << " chr1 500000 1500000" << endl; cerr << " chr1 1000000 2000000" << endl; cerr << " chr1 1500000 2500000" << endl; cerr << " chr1 2000000 3000000" << endl; cerr << " ..." << endl; cerr << endl; cerr << " # Divide each chromosome in human genome to 1000 windows of equal size:" << endl; cerr << " $ " << PROGRAM_NAME << " -g hg19.txt -n 1000" << endl; cerr << " chr1 0 249251" << endl; cerr << " chr1 249251 498502" << endl; cerr << " chr1 498502 747753" << endl; cerr << " chr1 747753 997004" << endl; cerr << " chr1 997004 1246255" << endl; cerr << " ..." << endl; cerr << endl; cerr << " # Divide each interval in the given BED file into 10 equal-sized windows:" << endl; cerr << " $ cat input.bed" << endl; cerr << " chr5 60000 70000" << endl; cerr << " chr5 73000 90000" << endl; cerr << " chr5 100000 101000" << endl; cerr << " $ " << PROGRAM_NAME << " -b input.bed -n 10" << endl; cerr << " chr5 60000 61000" << endl; cerr << " chr5 61000 62000" << endl; cerr << " chr5 62000 63000" << endl; cerr << " chr5 63000 64000" << endl; cerr << " chr5 64000 65000" << endl; cerr << " ..." << endl; cerr << endl; cerr << " # Add a name column, based on the window number: "<< endl; cerr << " $ cat input.bed" << endl; cerr << " chr5 60000 70000 AAA" << endl; cerr << " chr5 73000 90000 BBB" << endl; cerr << " chr5 100000 101000 CCC" << endl; cerr << " $ " << PROGRAM_NAME << " -b input.bed -n 3 -i winnum" << endl; cerr << " chr5 60000 63334 1" << endl; cerr << " chr5 63334 66668 2" << endl; cerr << " chr5 66668 70000 3" << endl; cerr << " chr5 73000 78667 1" << endl; cerr << " chr5 78667 84334 2" << endl; cerr << " chr5 84334 90000 3" << endl; cerr << " chr5 100000 100334 1" << endl; cerr << " chr5 100334 100668 2" << endl; cerr << " chr5 100668 101000 3" << endl; cerr << " ..." << endl; cerr << endl; cerr << " # Add a name column, based on the source ID + window number: "<< endl; cerr << " $ cat input.bed" << endl; cerr << " chr5 60000 70000 AAA" << endl; cerr << " chr5 73000 90000 BBB" << endl; cerr << " chr5 100000 101000 CCC" << endl; cerr << " $ " << PROGRAM_NAME << " -b input.bed -n 3 -i srcwinnum" << endl; cerr << " chr5 60000 63334 AAA_1" << endl; cerr << " chr5 63334 66668 AAA_2" << endl; cerr << " chr5 66668 70000 AAA_3" << endl; cerr << " chr5 73000 78667 BBB_1" << endl; cerr << " chr5 78667 84334 BBB_2" << endl; cerr << " chr5 84334 90000 BBB_3" << endl; cerr << " chr5 100000 100334 CCC_1" << endl; cerr << " chr5 100334 100668 CCC_2" << endl; cerr << " chr5 100668 101000 CCC_3" << endl; cerr << " ..." << endl; cerr << endl; cerr << endl; exit(1); }