--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/windowBed/windowMain.cpp	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,263 @@
+/*****************************************************************************
+  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);
+}