--- a/BEDTools-Version-2.14.3/src/bedToIgv/bedToIgv.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,269 +0,0 @@
-/*****************************************************************************
-  bedToIgv.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 "lineFileUtilities.h"
-#include "bedFile.h"
-#include "genomeFile.h"
-#include "version.h"
-
-#include <vector>
-#include <iostream>
-#include <fstream>
-#include <stdlib.h>
-
-using namespace std;
-
-// define our program name
-#define PROGRAM_NAME "bedToIgv"
-
-// 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);
-
-void DetermineBedInput(BedFile *bed, string path, string sortType, string session,
-                        bool collapse, bool useNames, string imageType, int slop);
-void ProcessBed(istream &bedInput, BedFile *bed, string path, string sortType, string session,
-                        bool collapse, bool useNames, string imageType, int slop);
-
-
-int main(int argc, char* argv[]) {
-
-    // our configuration variables
-    bool showHelp = false;
-
-    // input files
-    string bedFile   = "stdin";
-    string imagePath = "./";
-    string sortType  = "none";
-    string session   = "none";
-    int slop         = 0;
-    string imageType = "png";
-
-    bool haveBed         = true;
-    bool collapse        = false;
-    bool useNames        = false;
-
-    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("-i", 2, parameterLength)) {
-            if ((i+1) < argc) {
-                bedFile = argv[i + 1];
-                i++;
-            }
-        }
-        else if(PARAMETER_CHECK("-path", 5, parameterLength)) {
-            if ((i+1) < argc) {
-                imagePath = argv[i + 1];
-                i++;
-            }
-        }
-        else if(PARAMETER_CHECK("-sort", 5, parameterLength)) {
-            if ((i+1) < argc) {
-                sortType = argv[i + 1];
-                i++;
-            }
-        }
-        else if(PARAMETER_CHECK("-sess", 5, parameterLength)) {
-            if ((i+1) < argc) {
-                session = argv[i + 1];
-                i++;
-            }
-        }
-        else if(PARAMETER_CHECK("-clps", 5, parameterLength)) {
-            collapse = true;
-        }
-        else if(PARAMETER_CHECK("-name", 5, parameterLength)) {
-            useNames = true;
-        }
-        else if(PARAMETER_CHECK("-slop", 5, parameterLength)) {
-            if ((i+1) < argc) {
-                slop = atoi(argv[i + 1]);
-                i++;
-            }
-        }
-        else if(PARAMETER_CHECK("-img", 4, parameterLength)) {
-            if ((i+1) < argc) {
-                imageType = argv[i + 1];
-                i++;
-            }
-        }
-        else {
-            cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
-            showHelp = true;
-        }
-    }
-
-    // make sure we have an input files
-    if (!haveBed ) {
-        cerr << endl << "*****" << endl << "*****ERROR: Need -i (BED) file. " << endl << "*****" << endl;
-        showHelp = true;
-    }
-    if (sortType != "none") {
-        if ((sortType != "base")    && (sortType != "position") && (sortType != "strand") &&
-            (sortType != "quality") && (sortType != "sample")   && (sortType != "readGroup")) {
-                cerr << endl << "*****" << endl << "*****ERROR: Invalid sort option. " << endl << "*****" << endl;
-                showHelp = true;
-            }
-    }
-    if (slop < 0) {
-        cerr << endl << "*****" << endl << "*****ERROR: Slop must be >= 0. " << endl << "*****" << endl;
-        showHelp = true;
-    }
-
-    if (!showHelp) {
-        BedFile *bed       = new BedFile(bedFile);
-        DetermineBedInput(bed, imagePath, sortType, session, collapse, useNames, imageType, slop);
-    }
-    else {
-        ShowHelp();
-    }
-}
-
-
-void ShowHelp(void) {
-
-    cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
-
-    cerr << "Author:  Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
-
-    cerr << "Summary: Creates a batch script to create IGV images " << endl;
-    cerr << "         at each interval defined in a BED/GFF/VCF file." << endl << endl;
-
-    cerr << "Usage:   " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf>" << endl << endl;
-
-    cerr << "Options: " << endl;
-
-    cerr << "\t-path\t"     << "The full path to which the IGV snapshots should be written." << endl;
-    cerr                    << "\t\t(STRING) Default: ./" << endl << endl;
-
-    cerr << "\t-sess\t"     << "The full path to an existing IGV session file to be " << endl;
-    cerr                    << "\t\tloaded prior to taking snapshots." << endl << endl;
-    cerr                    << "\t\t(STRING) Default is for no session to be loaded." << endl << endl;
-
-    cerr << "\t-sort\t"     << "The type of BAM sorting you would like to apply to each image. " << endl;
-    cerr                    << "\t\tOptions: base, position, strand, quality, sample, and readGroup" << endl;
-    cerr                    << "\t\tDefault is to apply no sorting at all." << endl << endl;
-
-    cerr << "\t-clps\t"     << "Collapse the aligned reads prior to taking a snapshot. " << endl;
-    cerr                    << "\t\tDefault is to no collapse." << endl << endl;
-
-    cerr << "\t-name\t"     << "Use the \"name\" field (column 4) for each image's filename. " << endl;
-    cerr                    << "\t\tDefault is to use the \"chr:start-pos.ext\"." << endl << endl;
-
-    cerr << "\t-slop\t"     << "Number of flanking base pairs on the left & right of the image." << endl;
-    cerr                    << "\t\t- (INT) Default = 0." << endl << endl;
-
-    cerr << "\t-img\t"      << "The type of image to be created. " << endl;
-    cerr                    << "\t\tOptions: png, eps, svg" << endl;
-    cerr                    << "\t\tDefault is png." << endl << endl;
-
-    cerr << "Notes: " << endl;
-    cerr << "\t(1)  The resulting script is meant to be run from within the IGV GUI version 1.5 or later." << endl;
-    cerr << "\t(2)  Unless you use the -sess option, it is assumed that prior to running the script, " << endl;
-    cerr << "\t\tyou have loaded the proper genome, tracks and data files." << endl << endl;
-
-
-    // end the program here
-    exit(1);
-}
-
-
-void DetermineBedInput(BedFile *bed, string path, string sortType, string session,
-                       bool collapse, bool useNames, string imageType, int slop) {
-
-    // dealing with a proper file
-    if (bed->bedFile != "stdin") {
-
-        ifstream bedStream(bed->bedFile.c_str(), ios::in);
-        if ( !bedStream ) {
-            cerr << "Error: The requested bed file (" << bed->bedFile << ") could not be opened. Exiting!" << endl;
-            exit (1);
-        }
-        ProcessBed(bedStream, bed, path, sortType, session, collapse, useNames, imageType, slop);
-    }
-    // reading from stdin
-    else {
-        ProcessBed(cin, bed, path, sortType, session, collapse, useNames, imageType, slop);
-    }
-}
-
-
-void ProcessBed(istream &bedInput, BedFile *bed, string path, string sortType, string session,
-                bool collapse, bool useNames, string imageType, int slop) {
-
-    // set the image path
-    cout << "snapshotDirectory " << path << endl;
-
-    // should we load a session
-    if (session != "none")
-        cout << "load " << session << endl;
-
-
-    BED bedEntry, nullBed;
-    int lineNum = 0;
-    BedLineStatus bedStatus;
-
-    bed->Open();
-    // process each BED entry and convert to an IGV request
-    while ((bedStatus = bed->GetNextBed(bedEntry, lineNum)) != BED_INVALID) {
-        if (bedStatus == BED_VALID) {
-
-            string filename = bedEntry.chrom + "_" + ToString(bedEntry.start) + "_" + ToString(bedEntry.end);
-            string locus    = bedEntry.chrom + ":" + ToString(bedEntry.start - slop) + "-" + ToString(bedEntry.end + slop);
-
-            if (useNames == true) {
-                if (bedEntry.name.empty() == false)
-                    filename = filename + "_" + bedEntry.name;
-                else {
-                    cerr << "Error: You requested that filenames be based upon the name field.  However, it appears to be empty. Exiting!" << endl;
-                    exit (1);
-                }
-            }
-            if (slop > 0) {
-                filename = filename + "_" + "slop" + ToString(slop);
-            }
-            // goto
-            cout << "goto " << locus << endl;
-
-            // sort
-            if (sortType != "none")
-                cout << "sort " << sortType << endl;
-
-            // collapse
-            if (collapse == true)
-                cout << "collapse" << endl;
-
-            // snapshot
-            cout << "snapshot " << filename << "." << imageType << endl;
-
-            // reset
-            bedEntry = nullBed;
-        }
-    }
-    // close up
-    bed->Close();
-}