--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/pairToBed/pairToBedMain.cpp	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,237 @@
+/*****************************************************************************
+  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);
+}