--- a/BEDTools-Version-2.14.3/src/utils/bedFilePE/bedFilePE.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,530 +0,0 @@
-//
-//  bedFilePE.cpp
-//  BEDTools
-//
-//  Created by Aaron Quinlan Spring 2009.
-//  Copyright 2009 Aaron Quinlan. All rights reserved.
-//
-//  Summary:  Contains common functions for finding BED overlaps.
-//
-//  Acknowledgments: Much of the code herein is taken from Jim Kent's
-//                   BED processing code.  I am grateful for his elegant
-//                   genome binning algorithm and therefore use it extensively.
-
-
-#include "bedFilePE.h"
-
-
-// Constructor
-BedFilePE::BedFilePE(string &bedFile) {
-    this->bedFile = bedFile;
-}
-
-// Destructor
-BedFilePE::~BedFilePE(void) {
-}
-
-void BedFilePE::Open(void) {
-    if (bedFile == "stdin" || bedFile == "-") {
-        _bedStream = &cin;
-    }
-    else {
-        _bedStream = new ifstream(bedFile.c_str(), ios::in);
-
-        if (isGzipFile(_bedStream) == true) {
-            delete _bedStream;
-            _bedStream = new igzstream(bedFile.c_str(), ios::in);
-        }
-        // can we open the file?
-        if ( !(_bedStream->good()) ) {
-            cerr << "Error: The requested bed file (" << bedFile << ") could not be opened. Exiting!" << endl;
-            exit (1);
-        }
-    }
-}
-
-
-
-// Close the BEDPE file
-void BedFilePE::Close(void) {
-    if (bedFile != "stdin" && bedFile != "-") delete _bedStream;
-}
-
-
-BedLineStatus BedFilePE::GetNextBedPE (BEDPE &bedpe, int &lineNum) {
-
-    // make sure there are still lines to process.
-    // if so, tokenize, validate and return the BEDPE entry.
-    if (_bedStream->good()) {
-        string bedPELine;
-        vector<string> bedPEFields;
-        bedPEFields.reserve(10);
-
-        // parse the bedStream pointer
-        getline(*_bedStream, bedPELine);
-        lineNum++;
-
-        // split into a string vector.
-        Tokenize(bedPELine,bedPEFields);
-
-        // load the BEDPE struct as long as it's a valid BEDPE entry.
-        return parseLine(bedpe, bedPEFields, lineNum);
-    }
-    // default if file is closed or EOF
-    return BED_INVALID;
-}
-
-
-/*
-    reportBedPETab
-
-    Writes the _original_ BED entry for A.
-    Works for BEDPE only.
-*/
-void BedFilePE::reportBedPETab(const BEDPE &a) {
-
-    if (this->bedType == 6) {
-        printf("%s\t%d\t%d\t%s\t%d\t%d\t", a.chrom1.c_str(), a.start1, a.end1,
-                                            a.chrom2.c_str(), a.start2, a.end2);
-    }
-    else if (this->bedType == 7) {
-        printf("%s\t%d\t%d\t%s\t%d\t%d\t%s\t", a.chrom1.c_str(), a.start1, a.end1,
-                                            a.chrom2.c_str(), a.start2, a.end2,
-                                            a.name.c_str());
-    }
-    else if (this->bedType == 8) {
-        printf("%s\t%d\t%d\t%s\t%d\t%d\t%s\t%s\t", a.chrom1.c_str(), a.start1, a.end1,
-                                            a.chrom2.c_str(), a.start2, a.end2,
-                                            a.name.c_str(), a.score.c_str());
-    }
-    else if (this->bedType == 10) {
-        printf("%s\t%d\t%d\t%s\t%d\t%d\t%s\t%s\t%s\t%s\t", a.chrom1.c_str(), a.start1, a.end1,
-                                            a.chrom2.c_str(), a.start2, a.end2,
-                                            a.name.c_str(), a.score.c_str(), a.strand1.c_str(), a.strand2.c_str());
-    }
-    else if (this->bedType > 10) {
-        printf("%s\t%d\t%d\t%s\t%d\t%d\t%s\t%s\t%s\t%s", a.chrom1.c_str(), a.start1, a.end1,
-                                            a.chrom2.c_str(), a.start2, a.end2,
-                                            a.name.c_str(), a.score.c_str(), a.strand1.c_str(), a.strand2.c_str());
-
-        vector<string>::const_iterator othIt = a.otherFields.begin();
-        vector<string>::const_iterator othEnd = a.otherFields.end();
-        for ( ; othIt != othEnd; ++othIt) {
-            printf("\t%s", othIt->c_str());
-        }
-        printf("\t");
-    }
-}
-
-
-
-/*
-    reportBedPENewLine
-
-    Writes the _original_ BED entry for A.
-    Works for BEDPE only.
-*/
-void BedFilePE::reportBedPENewLine(const BEDPE &a) {
-
-    if (this->bedType == 6) {
-        printf("%s\t%d\t%d\t%s\t%d\t%d\n", a.chrom1.c_str(), a.start1, a.end1,
-                                            a.chrom2.c_str(), a.start2, a.end2);
-    }
-    else if (this->bedType == 7) {
-        printf("%s\t%d\t%d\t%s\t%d\t%d\t%s\n", a.chrom1.c_str(), a.start1, a.end1,
-                                            a.chrom2.c_str(), a.start2, a.end2,
-                                            a.name.c_str());
-    }
-    else if (this->bedType == 8) {
-        printf("%s\t%d\t%d\t%s\t%d\t%d\t%s\t%s\n", a.chrom1.c_str(), a.start1, a.end1,
-                                            a.chrom2.c_str(), a.start2, a.end2,
-                                            a.name.c_str(), a.score.c_str());
-    }
-    else if (this->bedType == 10) {
-        printf("%s\t%d\t%d\t%s\t%d\t%d\t%s\t%s\t%s\t%s\n", a.chrom1.c_str(), a.start1, a.end1,
-                                            a.chrom2.c_str(), a.start2, a.end2,
-                                            a.name.c_str(), a.score.c_str(), a.strand1.c_str(), a.strand2.c_str());
-    }
-    else if (this->bedType > 10) {
-        printf("%s\t%d\t%d\t%s\t%d\t%d\t%s\t%s\t%s\t%s", a.chrom1.c_str(), a.start1, a.end1,
-                                            a.chrom2.c_str(), a.start2, a.end2,
-                                            a.name.c_str(), a.score.c_str(), a.strand1.c_str(), a.strand2.c_str());
-
-        vector<string>::const_iterator othIt  = a.otherFields.begin();
-        vector<string>::const_iterator othEnd = a.otherFields.end();
-        for ( ; othIt != othEnd; ++othIt) {
-            printf("\t%s", othIt->c_str());
-        }
-        printf("\n");
-    }
-}
-
-
-BedLineStatus BedFilePE::parseLine (BEDPE &bedpe, const vector<string> &lineVector, int &lineNum) {
-
-    // bail out if we have a blank line
-    if (lineVector.empty())
-        return BED_BLANK;
-
-    if ((lineVector[0].find("track") == string::npos) && (lineVector[0].find("browser") == string::npos) && (lineVector[0].find("#") == string::npos) ) {
-        // we need at least 6 columns
-        if (lineVector.size() >= 6) {
-            if (parseBedPELine(bedpe, lineVector, lineNum) == true)
-                return BED_VALID;
-            else return BED_INVALID;
-        }
-        else  {
-            cerr << "It looks as though you have less than 6 columns.  Are you sure your files are tab-delimited?" << endl;
-            exit(1);
-        }
-    }
-    else {
-        lineNum--;
-        return BED_HEADER;
-    }
-
-    // default
-    return BED_INVALID;
-}
-
-
-bool BedFilePE::parseBedPELine (BEDPE &bed, const vector<string> &lineVector, const int &lineNum) {
-
-    if ((lineNum == 1) && (lineVector.size() >= 6)) {
-
-        this->bedType = lineVector.size();
-
-        if (this->bedType == 6) {
-            bed.chrom1 = lineVector[0];
-            bed.start1 = atoi(lineVector[1].c_str());
-            bed.end1 = atoi(lineVector[2].c_str());
-
-            bed.chrom2 = lineVector[3];
-            bed.start2 = atoi(lineVector[4].c_str());
-            bed.end2 = atoi(lineVector[5].c_str());
-
-            return true;
-        }
-        else if (this->bedType == 7) {
-            bed.chrom1 = lineVector[0];
-            bed.start1 = atoi(lineVector[1].c_str());
-            bed.end1 = atoi(lineVector[2].c_str());
-
-            bed.chrom2 = lineVector[3];
-            bed.start2 = atoi(lineVector[4].c_str());
-            bed.end2 = atoi(lineVector[5].c_str());
-
-            bed.name = lineVector[6];
-            return true;
-        }
-        else if (this->bedType == 8) {
-            bed.chrom1 = lineVector[0];
-            bed.start1 = atoi(lineVector[1].c_str());
-            bed.end1 = atoi(lineVector[2].c_str());
-
-            bed.chrom2 = lineVector[3];
-            bed.start2 = atoi(lineVector[4].c_str());
-            bed.end2 = atoi(lineVector[5].c_str());
-
-            bed.name = lineVector[6];
-            bed.score = lineVector[7].c_str();
-            return true;
-        }
-        else if (this->bedType == 10) {
-            bed.chrom1 = lineVector[0];
-            bed.start1 = atoi(lineVector[1].c_str());
-            bed.end1 = atoi(lineVector[2].c_str());
-
-            bed.chrom2 = lineVector[3];
-            bed.start2 = atoi(lineVector[4].c_str());
-            bed.end2 = atoi(lineVector[5].c_str());
-
-            bed.name = lineVector[6];
-            bed.score = lineVector[7].c_str();
-
-            bed.strand1 = lineVector[8];
-            bed.strand2 = lineVector[9];
-
-            return true;
-        }
-        else if (this->bedType > 10) {
-            bed.chrom1 = lineVector[0];
-            bed.start1 = atoi(lineVector[1].c_str());
-            bed.end1 = atoi(lineVector[2].c_str());
-
-            bed.chrom2 = lineVector[3];
-            bed.start2 = atoi(lineVector[4].c_str());
-            bed.end2 = atoi(lineVector[5].c_str());
-
-            bed.name = lineVector[6];
-            bed.score = lineVector[7].c_str();
-
-            bed.strand1 = lineVector[8];
-            bed.strand2 = lineVector[9];
-
-            for (unsigned int i = 10; i < lineVector.size(); ++i) {
-                bed.otherFields.push_back(lineVector[i]);
-            }
-            return true;
-        }
-        else {
-            cerr << "Unexpected number of fields: " << lineNum << ".  Verify that your files are TAB-delimited and that your BEDPE file has 6,7,8 or 10 fields.  Exiting..." << endl;
-            exit(1);
-        }
-
-        if (bed.start1 > bed.end1) {
-            cerr << "Error: malformed BEDPE entry at line " << lineNum << ". Start1 was greater than End1. Ignoring it and moving on." << endl;
-            return false;
-        }
-        else if (bed.start2 > bed.end2) {
-            cerr << "Error: malformed BEDPE entry at line " << lineNum << ". Start2 was greater than End2. Ignoring it and moving on." << endl;
-            return false;
-        }
-        else if ( (bed.start1 < 0) || (bed.end1 < 0) || (bed.start2 < 0) || (bed.end2 < 0) ) {
-            cerr << "Error: malformed BEDPE entry at line " << lineNum << ". Coordinate <= 0. Ignoring it and moving on." << endl;
-            return false;
-        }
-    }
-    else if ( (lineNum > 1) && (lineVector.size() == this->bedType)) {
-
-        if (this->bedType == 6) {
-            bed.chrom1 = lineVector[0];
-            bed.start1 = atoi(lineVector[1].c_str());
-            bed.end1 = atoi(lineVector[2].c_str());
-
-            bed.chrom2 = lineVector[3];
-            bed.start2 = atoi(lineVector[4].c_str());
-            bed.end2 = atoi(lineVector[5].c_str());
-
-            return true;
-        }
-        else if (this->bedType == 7) {
-            bed.chrom1 = lineVector[0];
-            bed.start1 = atoi(lineVector[1].c_str());
-            bed.end1 = atoi(lineVector[2].c_str());
-
-            bed.chrom2 = lineVector[3];
-            bed.start2 = atoi(lineVector[4].c_str());
-            bed.end2 = atoi(lineVector[5].c_str());
-
-            bed.name = lineVector[6];
-            return true;
-        }
-        else if (this->bedType == 8) {
-            bed.chrom1 = lineVector[0];
-            bed.start1 = atoi(lineVector[1].c_str());
-            bed.end1 = atoi(lineVector[2].c_str());
-
-            bed.chrom2 = lineVector[3];
-            bed.start2 = atoi(lineVector[4].c_str());
-            bed.end2 = atoi(lineVector[5].c_str());
-
-            bed.name = lineVector[6];
-            bed.score = lineVector[7].c_str();
-            return true;
-        }
-        else if (this->bedType == 10) {
-            bed.chrom1 = lineVector[0];
-            bed.start1 = atoi(lineVector[1].c_str());
-            bed.end1 = atoi(lineVector[2].c_str());
-
-            bed.chrom2 = lineVector[3];
-            bed.start2 = atoi(lineVector[4].c_str());
-            bed.end2 = atoi(lineVector[5].c_str());
-
-            bed.name = lineVector[6];
-            bed.score = lineVector[7].c_str();
-
-            bed.strand1 = lineVector[8];
-            bed.strand2 = lineVector[9];
-
-            return true;
-        }
-        else if (this->bedType > 10) {
-            bed.chrom1 = lineVector[0];
-            bed.start1 = atoi(lineVector[1].c_str());
-            bed.end1 = atoi(lineVector[2].c_str());
-
-            bed.chrom2 = lineVector[3];
-            bed.start2 = atoi(lineVector[4].c_str());
-            bed.end2 = atoi(lineVector[5].c_str());
-
-            bed.name = lineVector[6];
-            bed.score = lineVector[7].c_str();
-
-            bed.strand1 = lineVector[8];
-            bed.strand2 = lineVector[9];
-
-            for (unsigned int i = 10; i < lineVector.size(); ++i) {
-                bed.otherFields.push_back(lineVector[i]);
-            }
-            return true;
-        }
-        else {
-            cerr << "Unexpected number of fields: " << lineNum << ".  Verify that your files are TAB-delimited and that your BEDPE file has 6,7,8 or 10 fields.  Exiting..." << endl;
-            exit(1);
-        }
-
-        if (bed.start1 > bed.end1) {
-            cerr << "Error: malformed BED entry at line " << lineNum << ". Start1 was greater than End1. Ignoring it and moving on." << endl;
-            return false;
-        }
-        else if (bed.start2 > bed.end2) {
-            cerr << "Error: malformed BED entry at line " << lineNum << ". Start2 was greater than End2. Ignoring it and moving on." << endl;
-            return false;
-        }
-        else if ( (bed.start1 < 0) || (bed.end1 < 0) || (bed.start2 < 0) || (bed.end2 < 0) ) {
-            cerr << "Error: malformed BED entry at line " << lineNum << ". Coordinate <= 0. Ignoring it and moving on." << endl;
-            return false;
-        }
-    }
-    else if (lineVector.size() == 1) {
-        cerr << "Only one BED field detected: " << lineNum << ".  Verify that your files are TAB-delimited.  Exiting..." << endl;
-        exit(1);
-    }
-    else if ((lineVector.size() != this->bedType) && (lineVector.size() != 0)) {
-        cerr << "Differing number of BEDPE fields encountered at line: " << lineNum << ".  Exiting..." << endl;
-        exit(1);
-    }
-    else if ((lineVector.size() < 6) && (lineVector.size() != 0)) {
-        cerr << "TAB delimited BEDPE file with at least 6 fields (chrom1, start1, end1, chrom2, start2, end2) is required at line: "<< lineNum << ".  Exiting..." << endl;
-        exit(1);
-    }
-    return false;
-}
-
-
-/*
-    Adapted from kent source "binKeeperFind"
-*/
-void BedFilePE::FindOverlapsPerBin(int bEnd, string chrom, CHRPOS start, CHRPOS end, string name, string strand,
-                                   vector<MATE> &hits, float overlapFraction, bool forceStrand, bool enforceDiffNames) {
-
-    int startBin, endBin;
-    startBin = (start >> _binFirstShift);
-    endBin = ((end-1) >> _binFirstShift);
-
-    // loop through each bin "level" in the binning hierarchy
-    for (int i = 0; i < _binLevels; ++i) {
-
-        // loop through each bin at this level of the hierarchy
-        int offset = _binOffsetsExtended[i];
-        for (int j = (startBin+offset); j <= (endBin+offset); ++j)  {
-
-            // loop through each feature in this chrom/bin and see if it overlaps
-            // with the feature that was passed in.  if so, add the feature to
-            // the list of hits.
-            vector<MATE>::const_iterator bedItr;
-            vector<MATE>::const_iterator bedEnd;
-            if (bEnd == 1) {
-                bedItr = bedMapEnd1[chrom][j].begin();
-                bedEnd = bedMapEnd1[chrom][j].end();
-            }
-            else if (bEnd == 2) {
-                bedItr = bedMapEnd2[chrom][j].begin();
-                bedEnd = bedMapEnd2[chrom][j].end();
-            }
-            else {
-                cerr << "Unexpected end of B requested" << endl;
-            }
-            for (; bedItr != bedEnd; ++bedItr) {
-                float overlap = overlaps(bedItr->bed.start, bedItr->bed.end, start, end);
-                float size    = end - start;
-
-                if ( (overlap / size) >= overlapFraction ) {
-
-                    // skip the hit if not on the same strand (and we care)
-                    if ((forceStrand == false) && (enforceDiffNames == false)) {
-                        hits.push_back(*bedItr);    // it's a hit, add it.
-                    }
-                    else if ((forceStrand == true) && (enforceDiffNames == false)) {
-                        if (strand == bedItr->bed.strand)
-                            hits.push_back(*bedItr);    // it's a hit, add it.
-                    }
-                    else if ((forceStrand == true) && (enforceDiffNames == true)) {
-                        if ((strand == bedItr->bed.strand) && (name != bedItr->bed.name))
-                            hits.push_back(*bedItr);    // it's a hit, add it.
-                    }
-                    else if ((forceStrand == false) && (enforceDiffNames == true)) {
-                        if (name != bedItr->bed.name)
-                            hits.push_back(*bedItr);    // it's a hit, add it.
-                    }
-                }
-
-            }
-        }
-        startBin >>= _binNextShift;
-        endBin >>= _binNextShift;
-    }
-}
-
-
-void BedFilePE::loadBedPEFileIntoMap() {
-
-    int lineNum = 0;
-    int bin1, bin2;
-    BedLineStatus bedStatus;
-    BEDPE bedpeEntry, nullBedPE;
-
-    Open();
-    bedStatus = this->GetNextBedPE(bedpeEntry, lineNum);
-    while (bedStatus != BED_INVALID) {
-
-        if (bedStatus == BED_VALID) {
-            MATE *bedEntry1 = new MATE();
-            MATE *bedEntry2 = new MATE();
-            // separate the BEDPE entry into separate
-            // BED entries
-            splitBedPEIntoBeds(bedpeEntry, lineNum, bedEntry1, bedEntry2);
-
-            // load end1 into a UCSC bin map
-            bin1 = getBin(bedEntry1->bed.start, bedEntry1->bed.end);
-            this->bedMapEnd1[bedEntry1->bed.chrom][bin1].push_back(*bedEntry1);
-
-            // load end2 into a UCSC bin map
-            bin2 = getBin(bedEntry2->bed.start, bedEntry2->bed.end);
-            this->bedMapEnd2[bedEntry2->bed.chrom][bin2].push_back(*bedEntry2);
-
-            bedpeEntry = nullBedPE;
-        }
-        bedStatus = this->GetNextBedPE(bedpeEntry, lineNum);
-    }
-    Close();
-}
-
-
-void BedFilePE::splitBedPEIntoBeds(const BEDPE &bedpeEntry, const int &lineNum, MATE *bedEntry1, MATE *bedEntry2) {
-
-    /*
-       Split the BEDPE entry into separate BED entries
-
-       NOTE: I am using a trick here where I store
-       the lineNum of the BEDPE from the original file
-       in the "count" column.  This allows me to later
-       resolve whether the hits found on both ends of BEDPE A
-       came from the same entry in BEDPE B.  Tracking by "name"
-       alone with fail when there are multiple mappings for a given
-       read-pair.
-    */
-
-    bedEntry1->bed.chrom           = bedpeEntry.chrom1;
-    bedEntry1->bed.start           = bedpeEntry.start1;
-    bedEntry1->bed.end             = bedpeEntry.end1;
-    bedEntry1->bed.name            = bedpeEntry.name;
-    bedEntry1->bed.score           = bedpeEntry.score;        // only store the score in end1 to save memory
-    bedEntry1->bed.strand          = bedpeEntry.strand1;
-    bedEntry1->bed.otherFields     = bedpeEntry.otherFields;  // only store the otherFields in end1 to save memory
-    bedEntry1->lineNum             = lineNum;
-    bedEntry1->mate                = bedEntry2;               // keep a pointer to end2
-
-    bedEntry2->bed.chrom           = bedpeEntry.chrom2;
-    bedEntry2->bed.start           = bedpeEntry.start2;
-    bedEntry2->bed.end             = bedpeEntry.end2;
-    bedEntry2->bed.name            = bedpeEntry.name;
-    bedEntry2->bed.strand          = bedpeEntry.strand2;
-    bedEntry2->lineNum             = lineNum;
-    bedEntry2->mate                = bedEntry1;               // keep a pointer to end1
-}
-
-
-