--- a/BEDTools-Version-2.14.3/src/pairToBed/pairToBedMain.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,237 +0,0 @@
-/*****************************************************************************
-  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 "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 ShowHelp(void);
-
-int 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) 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("-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;
-        return 0;
-    }
-    else {
-        ShowHelp();
-    }
-}
-
-
-void ShowHelp(void) {
-
-    cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
-
-    cerr << "Author:  Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
-
-    cerr << "Summary: Report overlaps between a BEDPE file and a BED/GFF/VCF file." << endl << endl;
-
-    cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -a <bedpe> -b <bed/gff/vcf>" << endl << endl;
-
-    cerr << "Options: " << endl;
-
-    cerr << "\t-abam\t"         << "The A input file is in BAM format.  Output will be BAM as well." << endl;
-    cerr                        << "\t\t- Requires BAM to be grouped or sorted by query." << endl << endl;
-
-    cerr << "\t-ubam\t"         << "Write uncompressed BAM output. Default is to write 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);
-}