--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/fjoin/fjoinMain.cpp	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,271 @@
+/*****************************************************************************
+  intersectMain.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 "fjoin.h"
+#include "version.h"
+
+using namespace std;
+
+// define our program name
+#define PROGRAM_NAME "fjoin"
+
+
+// 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;
+
+    bool haveBedA           = false;
+    bool haveBedB           = false;
+    bool noHit              = false;
+    bool anyHit             = false;
+    bool writeA             = false;
+    bool writeB             = false;
+    bool writeCount         = false;
+    bool writeOverlap       = false;
+    bool writeAllOverlap    = false;
+    bool haveFraction       = false;
+    bool reciprocalFraction = false;
+    bool forceStrand        = false;
+    bool obeySplits         = false;
+    bool inputIsBam         = false;
+    bool outputIsBam        = true;
+
+    // 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("-bed", 4, parameterLength)) {
+            outputIsBam = false;
+        }
+        else if(PARAMETER_CHECK("-u", 2, parameterLength)) {
+            anyHit = true;
+        }
+        else if(PARAMETER_CHECK("-f", 2, parameterLength)) {
+            if ((i+1) < argc) {
+                haveFraction = true;
+                overlapFraction = atof(argv[i + 1]);
+                i++;
+            }
+        }
+        else if(PARAMETER_CHECK("-wa", 3, parameterLength)) {
+            writeA = true;
+        }
+        else if(PARAMETER_CHECK("-wb", 3, parameterLength)) {
+            writeB = true;
+        }
+        else if(PARAMETER_CHECK("-wo", 3, parameterLength)) {
+            writeOverlap = true;
+        }
+        else if(PARAMETER_CHECK("-wao", 4, parameterLength)) {
+            writeAllOverlap = true;
+            writeOverlap = true;
+        }
+        else if(PARAMETER_CHECK("-c", 2, parameterLength)) {
+            writeCount = true;
+        }
+        else if(PARAMETER_CHECK("-r", 2, parameterLength)) {
+            reciprocalFraction = true;
+        }
+        else if (PARAMETER_CHECK("-v", 2, parameterLength)) {
+            noHit = true;
+        }
+        else if (PARAMETER_CHECK("-s", 2, parameterLength)) {
+            forceStrand = true;
+        }
+        else if (PARAMETER_CHECK("-split", 6, parameterLength)) {
+            obeySplits = 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 (anyHit && noHit) {
+        cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -v, not both." << endl << "*****" << endl;
+        showHelp = true;
+    }
+
+    if (writeB && writeCount) {
+        cerr << endl << "*****" << endl << "*****ERROR: Request either -wb OR -c, not both." << endl << "*****" << endl;
+        showHelp = true;
+    }
+
+    if (writeCount && writeOverlap) {
+        cerr << endl << "*****" << endl << "*****ERROR: Request either -wb OR -wo, not both." << endl << "*****" << endl;
+        showHelp = true;
+    }
+
+    if (writeA && writeOverlap) {
+        cerr << endl << "*****" << endl << "*****ERROR: Request either -wa OR -wo, not both." << endl << "*****" << endl;
+        showHelp = true;
+    }
+
+    if (writeB && writeOverlap) {
+        cerr << endl << "*****" << endl << "*****ERROR: Request either -wb OR -wo, not both." << endl << "*****" << endl;
+        showHelp = true;
+    }
+
+    if (reciprocalFraction && !haveFraction) {
+        cerr << endl << "*****" << endl << "*****ERROR: If using -r, you need to define -f." << endl << "*****" << endl;
+        showHelp = true;
+    }
+
+    if (anyHit && writeCount) {
+        cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -c, not both." << endl << "*****" << endl;
+        showHelp = true;
+    }
+
+    if (anyHit && writeB) {
+        cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -wb, not both." << endl << "*****" << endl;
+        showHelp = true;
+    }
+
+    if (anyHit && writeOverlap) {
+        cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -wo, not both." << endl << "*****" << endl;
+        showHelp = true;
+    }
+
+
+    if (!showHelp) {
+
+        BedIntersect *bi = new BedIntersect(bedAFile, bedBFile, anyHit, writeA, writeB, writeOverlap,
+                                            writeAllOverlap, overlapFraction, noHit, writeCount, forceStrand,
+                                            reciprocalFraction, obeySplits, inputIsBam, outputIsBam);
+        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 two feature files." << endl << endl;
+
+    cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -a <bed/gff/vcf> -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 << endl;
+
+    cerr << "\t-bed\t"          << "When using BAM input (-abam), write output as BED. The default" << endl;
+    cerr                        << "\t\tis to write output in BAM when using -abam." << endl << endl;
+
+    cerr << "\t-wa\t"           << "Write the original entry in A for each overlap." << endl << endl;
+
+    cerr << "\t-wb\t"           << "Write the original entry in B for each overlap." << endl;
+    cerr                        << "\t\t- Useful for knowing _what_ A overlaps. Restricted by -f and -r." << endl << endl;
+
+    cerr << "\t-wo\t"           << "Write the original A and B entries plus the number of base" << endl;
+    cerr                        << "\t\tpairs of overlap between the two features." << endl;
+    cerr                        << "\t\t- Overlaps restricted by -f and -r." << endl;
+    cerr                        << "\t\t  Only A features with overlap are reported." << endl << endl;
+
+    cerr << "\t-wao\t"          << "Write the original A and B entries plus the number of base" << endl;
+    cerr                        << "\t\tpairs of overlap between the two features." << endl;
+    cerr                        << "\t\t- Overlapping features restricted by -f and -r." << endl;
+    cerr                        << "\t\t  However, A features w/o overlap are also reported" << endl;
+    cerr                        << "\t\t  with a NULL B feature and overlap = 0." << endl << endl;
+
+    cerr << "\t-u\t"            << "Write the original A entry _once_ if _any_ overlaps found in B." << endl;
+    cerr                        << "\t\t- In other words, just report the fact >=1 hit was found." << endl;
+    cerr                        << "\t\t- Overlaps restricted by -f and -r." << endl << endl;
+
+    cerr << "\t-c\t"            << "For each entry in A, report the number of overlaps with B." << endl;
+    cerr                        << "\t\t- Reports 0 for A entries that have no overlap with B." << endl;
+    cerr                        << "\t\t- Overlaps restricted by -f and -r." << endl << endl;
+
+    cerr << "\t-v\t"            << "Only report those entries in A that have _no overlaps_ with B." << endl;
+    cerr                        << "\t\t- Similar to \"grep -v\" (an homage)." << endl << endl;
+
+    cerr << "\t-f\t"            << "Minimum overlap required as a fraction of A." << endl;
+    cerr                        << "\t\t- Default is 1E-9 (i.e., 1bp)." << endl;
+    cerr                        << "\t\t- FLOAT (e.g. 0.50)" << endl << endl;
+
+    cerr << "\t-r\t"            << "Require that the fraction overlap be reciprocal for A and B." << endl;
+    cerr                        << "\t\t- In other words, if -f is 0.90 and -r is used, this requires" << endl;
+    cerr                        << "\t\t  that B overlap 90% of A and A _also_ overlaps 90% of B." << endl << endl;
+
+    cerr << "\t-s\t"            << "Force strandedness.  That is, only report hits in B that" << endl;
+    cerr                        << "\t\toverlap A on the same strand." << endl;
+    cerr                        << "\t\t- By default, overlaps are reported without respect to strand." << endl << endl;
+
+    cerr << "\t-split\t"        << "Treat \"split\" BAM or BED12 entries as distinct BED intervals." << endl << endl;
+
+
+    // end the program here
+    exit(1);
+
+}