--- a/BEDTools-Version-2.14.3/src/fjoin/fjoinMain.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,271 +0,0 @@
-/*****************************************************************************
-  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);
-
-}