--- a/BEDTools-Version-2.14.3/src/windowBed/windowMain.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,263 +0,0 @@
-/*****************************************************************************
-  windowMain.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 "windowBed.h"
-#include "version.h"
-
-using namespace std;
-
-// define the version
-#define PROGRAM_NAME "windowBed"
-
-// 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
-    int leftSlop  = 1000;
-    int rightSlop = 1000;
-
-    bool haveBedA        = false;
-    bool haveBedB        = false;
-    bool noHit           = false;
-    bool anyHit          = false;
-    bool writeCount      = false;
-    bool haveSlop        = false;
-    bool haveLeft        = false;
-    bool haveRight       = false;
-    bool strandWindows   = false;
-    bool matchOnSameStrand   = false;
-    bool matchOnDiffStrand   = 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;
-                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("-c", 2, parameterLength)) {
-            writeCount = true;
-        }
-        else if (PARAMETER_CHECK("-v", 2, parameterLength)) {
-            noHit = true;
-        }
-        else if (PARAMETER_CHECK("-sw", 3, parameterLength)) {
-            strandWindows = true;
-        }
-        else if (PARAMETER_CHECK("-sm", 3, parameterLength)) {
-            matchOnSameStrand = true;
-        }
-        else if (PARAMETER_CHECK("-Sm", 3, parameterLength)) {
-            matchOnDiffStrand = true;
-        }
-        else if (PARAMETER_CHECK("-w", 2, parameterLength)) {
-            if ((i+1) < argc) {
-                haveSlop = true;
-                leftSlop = atoi(argv[i + 1]);
-                rightSlop = leftSlop;
-                i++;
-            }
-        }
-        else if (PARAMETER_CHECK("-l", 2, parameterLength)) {
-            if ((i+1) < argc) {
-                haveLeft = true;
-                leftSlop = atoi(argv[i + 1]);
-                i++;
-            }
-        }
-        else if (PARAMETER_CHECK("-r", 2, parameterLength)) {
-            if ((i+1) < argc) {
-                haveRight = true;
-                rightSlop = atoi(argv[i + 1]);
-                i++;
-            }
-        }
-        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 (anyHit && noHit) {
-        cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -v, not both." << endl << "*****" << endl;
-        showHelp = true;
-    }
-
-    if (anyHit && writeCount) {
-        cerr << endl << "*****" << endl << "*****ERROR: Request either -u OR -c, not both." << endl << "*****" << endl;
-        showHelp = true;
-    }
-
-    if (haveLeft && (leftSlop < 0)) {
-        cerr << endl << "*****" << endl << "*****ERROR: Upstream window (-l) must be positive." << endl << "*****" << endl;
-        showHelp = true;
-    }
-
-    if (haveRight && (rightSlop < 0)) {
-        cerr << endl << "*****" << endl << "*****ERROR: Downstream window (-r) must be positive." << endl << "*****" << endl;
-        showHelp = true;
-    }
-
-    if (haveSlop && (haveLeft || haveRight)) {
-        cerr << endl << "*****" << endl << "*****ERROR: Cannot choose -w with -l or -r.  Either specify -l and -r or specify solely -w" << endl << "*****" << endl;
-        showHelp = true;
-    }
-
-    if ((haveLeft && !haveRight) || (haveRight && !haveLeft)) {
-        cerr << endl << "*****" << endl << "*****ERROR: Please specify both -l and -r." << endl << "*****" << endl;
-        showHelp = true;
-    }
-
-    if (matchOnSameStrand && matchOnDiffStrand) {
-        cerr << endl << "*****" << endl << "*****ERROR: Use either -sm or -Sm, not both." << endl << "*****" << endl;
-        showHelp = true;
-    }
-
-    if (!showHelp) {
-        BedWindow *bi = new BedWindow(bedAFile, bedBFile, leftSlop, rightSlop, anyHit,
-                                      noHit, writeCount, strandWindows, matchOnSameStrand, matchOnDiffStrand,
-                                      inputIsBam, outputIsBam, uncompressedBam);
-        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: Examines a \"window\" around each feature in A and" << endl;
-    cerr << "\t reports all features in B that overlap the window. For each" << endl;
-    cerr << "\t overlap the entire entry in A and B are reported." << 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-ubam\t"         << "Write uncompressed BAM output. Default is to write compressed BAM." << 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-w\t"            << "Base pairs added upstream and downstream of each entry" << endl;
-    cerr                        << "\t\tin A when searching for overlaps in B." << endl;
-    cerr                        << "\t\t- Creates symterical \"windows\" around A." << endl;
-    cerr                        << "\t\t- Default is 1000 bp." << endl;
-    cerr                        << "\t\t- (INTEGER)" << endl << endl;
-
-    cerr << "\t-l\t"            << "Base pairs added upstream (left of) of each entry" << endl;
-    cerr                        << "\t\tin A when searching for overlaps in B." << endl;
-    cerr                        << "\t\t- Allows one to define assymterical \"windows\"." << endl;
-    cerr                        << "\t\t- Default is 1000 bp." << endl;
-    cerr                        << "\t\t- (INTEGER)" << endl << endl;
-
-    cerr << "\t-r\t"            << "Base pairs added downstream (right of) of each entry" << endl;
-    cerr                        << "\t\tin A when searching for overlaps in B." << endl;
-    cerr                        << "\t\t- Allows one to define assymterical \"windows\"." << endl;
-    cerr                        << "\t\t- Default is 1000 bp." << endl;
-    cerr                        << "\t\t- (INTEGER)" << endl << endl;
-
-    cerr << "\t-sw\t"           << "Define -l and -r based on strand.  For example if used, -l 500" << endl;
-    cerr                        << "\t\tfor a negative-stranded feature will add 500 bp downstream." << endl;
-    cerr                        << "\t\t- Default = disabled." << endl << endl;
-
-    cerr << "\t-sm\t"           << "Only report hits in B that overlap A on the _same_ strand." << endl;
-    cerr                        << "\t\t- By default, overlaps are reported without respect to strand." << endl << endl;
-
-    cerr << "\t-Sm\t"           << "Only report hits in B that overlap A on the _opposite_ strand." << endl;
-    cerr                        << "\t\t- By default, overlaps are reported without respect to strand." << 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 << 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." << 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.\"" << endl << endl;
-
-    // end the program here
-    exit(1);
-}