/*****************************************************************************
  slopBed.cpp

  (c) 2009 - Aaron Quinlan
  Hall Laboratory
  Department of Biochemistry and Molecular Genetics
  University of Virginia
  aaronquinlan@gmail.com

  Licensed under the GNU General Public License 2.0 license.
******************************************************************************/
#include "lineFileUtilities.h"
#include "slopBed.h"


  BedSlop::BedSlop(string &bedFile, string &genomeFile, bool forceStrand, 
   float leftSlop, float rightSlop, bool fractional,
   bool printHeader) {

    _bedFile     = bedFile;
    _genomeFile  = genomeFile;
    _forceStrand = forceStrand;
    _leftSlop    = leftSlop;
    _rightSlop   = rightSlop;
    _fractional  = fractional;
    _printHeader = printHeader;

    _bed    = new BedFile(bedFile);
    _genome = new GenomeFile(genomeFile);

    // get going, slop it up.
    SlopBed();
}


BedSlop::~BedSlop(void) {

}


void BedSlop::SlopBed() {

    BED bedEntry;     // used to store the current BED line from the BED file.
    float l, r;

    _bed->Open();
    // report header first if asked.
    if (_printHeader == true) {
        _bed->PrintHeader();
    }        
    while (_bed->GetNextBed(bedEntry)) {    
        if (_bed->_status == BED_VALID) {
            if (_fractional == false) {
                AddSlop(bedEntry);
            }
            else {
               l = _leftSlop;	
               _leftSlop  = _leftSlop * (float)bedEntry.size();
               r = _rightSlop;	
               _rightSlop = _rightSlop * (float)bedEntry.size();
               AddSlop(bedEntry);
               _rightSlop = r;
               _leftSlop = l;
           }
           _bed->reportBedNewLine(bedEntry);
       }
   }
   _bed->Close();
}


void BedSlop::AddSlop(BED &bed) {

    // special handling if the BED entry is on the negative
    // strand and the user cares about strandedness.
    CHRPOS chromSize = (CHRPOS)_genome->getChromSize(bed.chrom);

    if ( (_forceStrand) && (bed.strand == "-") ) {
        if ( ((int)bed.start - (long)_rightSlop) >= 0 ) {
          // if the _rightSlop is negative and pushes bed.start to be > chromSize 0, set to chromSize
            if (((int)bed.start - (long)_rightSlop) >= chromSize && _rightSlop < 0) {
                bed.start = chromSize;  
            }
            else {
              bed.start = bed.start - (long)_rightSlop;
            }
        }
        else {
            bed.start = 0;
        }
        if ( ((int)bed.end + (long)_leftSlop) <= chromSize ) {
            // if the _leftSlop is negative and pushes bed.end to be < 0, set to 0
            if((((int)bed.end + (int)_leftSlop) <= 0) && _leftSlop < 0) {
                bed.end = 0;
            }
            else {
              bed.end = bed.end + (int)_leftSlop;
            }
        }    
        else {
            
            bed.end = chromSize;
        }
    }
    else {
        if ( ((int)bed.start - (long)_leftSlop) >= 0 ) {
          // checking negative condition for _leftSlop
            if( ((int)bed.start - (long)_leftSlop) >= chromSize && _leftSlop < 0)
            {
              bed.start = chromSize;
            }
            else {
              bed.start = bed.start - (int)_leftSlop;
            }
        }
        else {
            bed.start = 0;
        }

        if ( ((int)bed.end + (long)_rightSlop) <= chromSize )
        {
          // checking negative _rightSlop condition
            if( ((int)bed.end + (long)_rightSlop) <= 0 && _rightSlop < 0) {
                bed.end = 0;
              }
              else {
                bed.end = bed.end + (int)_rightSlop;            
              }
        }
        else
        {
          
                bed.end = chromSize;                
        }
    }
    //checking edge case and adjusting
    if( bed.start == bed.end && bed.start == chromSize ){
      bed.start -= 1;
    }
    // Since bed files have 0 base system, the end is incremented by one
    else if ( bed.start == bed.end ){
      bed.end += 1;
    }
    else if(bed.start > bed.end){
      int temp = bed.start;
      bed.start = bed.end;
      bed.end = temp;
    }
}