/***************************************************************************** pairToBedMain.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 "pairToBed.h" #include "version.h" using namespace std; // define our program name #define PROGRAM_NAME "bedtools pairtobed" // define our parameter checking macro #define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen) // function declarations void pairtobed_help(void); int pairtobed_main(int argc, char* argv[]) { // our configuration variables bool showHelp = false; // input files string bedAFile; string bedBFile; // input arguments float overlapFraction = 1E-9; string searchType = "either"; // flags to track parameters bool haveBedA = false; bool haveBedB = false; bool haveSearchType = false; bool haveFraction = false; bool sameStrand = false; bool diffStrand = false; bool useEditDistance = false; bool inputIsBam = false; bool outputIsBam = true; bool uncompressedBam = 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) pairtobed_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("-a", 2, parameterLength)) { if ((i+1) < argc) { haveBedA = true; outputIsBam = false; bedAFile = argv[i + 1]; 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("-bedpe", 6, parameterLength)) { outputIsBam = false; } else if(PARAMETER_CHECK("-ed", 3, parameterLength)) { useEditDistance = true; } else if(PARAMETER_CHECK("-type", 5, parameterLength)) { if ((i+1) < argc) { haveSearchType = true; searchType = argv[i + 1]; i++; } } else if(PARAMETER_CHECK("-f", 2, parameterLength)) { if ((i+1) < argc) { haveFraction = true; overlapFraction = atof(argv[i + 1]); i++; } } else if (PARAMETER_CHECK("-s", 2, parameterLength)) { sameStrand = true; } else if (PARAMETER_CHECK("-S", 2, parameterLength)) { diffStrand = true; } else if(PARAMETER_CHECK("-ubam", 5, parameterLength)) { uncompressedBam = true; } else { cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl; showHelp = true; } } // make sure we have both input files if (!haveBedA || !haveBedB) { cerr << endl << "*****" << endl << "*****ERROR: Need -a and -b files. " << endl << "*****" << endl; showHelp = true; } if (haveSearchType && (searchType != "either") && (searchType != "neither") && (searchType != "both") && (searchType != "xor") && (searchType != "notboth") && (searchType != "ispan") && (searchType != "ospan") && (searchType != "notispan") && (searchType != "notospan")) { cerr << endl << "*****" << endl << "*****ERROR: Request \"either\" or \"both\" or \"neither\" or \"xor\" or \"notboth\" or \"ispan\" or \"ospan\" or \"notispan\" or \"notospan\"" << endl << "*****" << endl; showHelp = true; } if ( ((searchType == "ispan") || (searchType == "ospan") || (searchType == "notispan") || (searchType == "notospan")) && (sameStrand || diffStrand) ) { cerr << endl << "*****" << endl << "*****ERROR: Cannot enforce strandedness with selected searchtype" << endl << "*****" << endl; showHelp = true; } if (useEditDistance && (inputIsBam == false || outputIsBam == true)) { cerr << endl << "*****" << endl << "*****ERROR: -ed must be used with -bedpe and -abam." << endl << "*****" << endl; showHelp = true; } if (sameStrand && diffStrand) { cerr << endl << "*****" << endl << "*****ERROR: Request either -s OR -S, not both." << endl << "*****" << endl; showHelp = true; } if (!showHelp) { BedIntersectPE *bi = new BedIntersectPE(bedAFile, bedBFile, overlapFraction, searchType, sameStrand, diffStrand, inputIsBam, outputIsBam, uncompressedBam, useEditDistance); delete bi; } else { pairtobed_help(); } return 0; } void pairtobed_help(void) { cerr << "\nTool: bedtools pairtobed (aka pairToBed)" << endl; cerr << "Version: " << VERSION << "\n"; cerr << "Summary: Report overlaps between a BEDPE file and a BED/GFF/VCF file." << endl << endl; cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -a -b " << endl << endl; cerr << "Options: " << endl; cerr << "\t-abam\t" << "The A input file is in BAM format. Output will be BAM as well. Replaces -a." << endl; cerr << "\t\t- Requires BAM to be grouped or sorted by query." << endl << endl; cerr << "\t-ubam\t" << "Write uncompressed BAM output. Default writes compressed BAM." << endl << endl; cerr << "\t\tis to write output in BAM when using -abam." << endl << endl; cerr << "\t-bedpe\t" << "When using BAM input (-abam), write output as BEDPE. The default" << endl; cerr << "\t\tis to write output in BAM when using -abam." << endl << endl; cerr << "\t-ed\t" << "Use BAM total edit distance (NM tag) for BEDPE score." << 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- When -ed is used the total edit distance" << endl; cerr << "\t\t from the two mates is reported as the score." << endl << endl; cerr << "\t-f\t" << "Minimum overlap required as fraction of A (e.g. 0.05)." << endl; cerr << "\t\tDefault is 1E-9 (effectively 1bp)." << endl << endl; cerr << "\t-s\t" << "Require same strandedness when finding overlaps." << endl; cerr << "\t\tDefault is to ignore stand." << endl; cerr << "\t\tNot applicable with -type inspan or -type outspan." << endl << endl; cerr << "\t-S\t" << "Require different strandedness when finding overlaps." << endl; cerr << "\t\tDefault is to ignore stand." << endl; cerr << "\t\tNot applicable with -type inspan or -type outspan." << endl << endl; cerr << "\t-type \t" << "Approach to reporting overlaps between BEDPE and BED." << endl << endl; cerr << "\t\teither\tReport overlaps if either end of A overlaps B." << endl; cerr << "\t\t\t- Default." << endl; cerr << "\t\tneither\tReport A if neither end of A overlaps B." << endl; cerr << "\t\tboth\tReport overlaps if both ends of A overlap B." << endl; cerr << "\t\txor\tReport overlaps if one and only one end of A overlaps B." << endl; cerr << "\t\tnotboth\tReport overlaps if neither end or one and only one " << endl; cerr << "\t\t\tend of A overlap B. That is, xor + neither." << endl << endl; cerr << "\t\tispan\tReport overlaps between [end1, start2] of A and B." << endl; cerr << "\t\t\t- Note: If chrom1 <> chrom2, entry is ignored." << endl << endl; cerr << "\t\tospan\tReport overlaps between [start1, end2] of A and B." << endl; cerr << "\t\t\t- Note: If chrom1 <> chrom2, entry is ignored." << endl << endl; cerr << "\t\tnotispan\tReport A if ispan of A doesn't overlap B." << endl; cerr << "\t\t\t\t- Note: If chrom1 <> chrom2, entry is ignored." << endl << endl; cerr << "\t\tnotospan\tReport A if ospan of A doesn't overlap B." << endl; cerr << "\t\t\t\t- Note: If chrom1 <> chrom2, entry is ignored." << endl << endl; cerr << "Refer to the BEDTools manual for BEDPE format." << endl << endl; exit(1); }