--- a/BEDTools-Version-2.14.3/src/nucBed/nucBed.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,158 +0,0 @@
-/*****************************************************************************
-  nucBed.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 "nucBed.h"
-
-
-NucBed::NucBed(string &dbFile, string &bedFile, bool printSeq, 
-               bool hasPattern, const string &pattern, bool forceStrand) {
-
-    _dbFile       = dbFile;
-    _bedFile      = bedFile;
-    _printSeq     = printSeq;
-    _hasPattern   = hasPattern;
-    _pattern      = pattern;
-    _forceStrand  = forceStrand;
-    
-    _bed = new BedFile(_bedFile);
-
-    // Compute the DNA content in each BED/GFF/VCF interval
-    ProfileDNA();
-}
-
-
-NucBed::~NucBed(void) 
-{}
-
-
-void NucBed::ReportDnaProfile(const BED& bed, const string &sequence, int seqLength)
-{
-    int a,c,g,t,n,other,userPatternCount;
-    a = c = g = t = n = other = userPatternCount = 0;
-    
-    getDnaContent(sequence,a,c,g,t,n,other);
-    
-    if (_hasPattern)
-        userPatternCount = countPattern(sequence, _pattern);
-    
-    
-    // report the original interval
-    _bed->reportBedTab(bed);
-    // report AT and GC content
-    printf("%f\t%f\t",(float)(a+t)/seqLength, (float)(c+g)/seqLength);
-    // report raw nucleotide counts
-    printf("%d\t%d\t%d\t%d\t%d\t%d\t%d",a,c,g,t,n,other,seqLength);
-    // add the original sequence if requested.
-
-    if (_printSeq)
-        printf("\t%s",sequence.c_str());
-    if (_hasPattern)
-        printf("\t%d",userPatternCount);
-    printf("\n");
-
-}
-
-
-void NucBed::PrintHeader(void) {
-    printf("#");
-    
-    int numOrigColumns = (int) _bed->bedType;
-    for (int i = 1; i <= numOrigColumns; ++i) {
-        printf("%d_usercol\t", i);
-    }
-    printf("%d_pct_at\t", numOrigColumns + 1);
-    printf("%d_pct_gc\t", numOrigColumns + 2);
-    printf("%d_num_A\t", numOrigColumns + 3);
-    printf("%d_num_C\t", numOrigColumns + 4);
-    printf("%d_num_G\t", numOrigColumns + 5);
-    printf("%d_num_T\t", numOrigColumns + 6);
-    printf("%d_num_N\t", numOrigColumns + 7);
-    printf("%d_num_oth\t", numOrigColumns + 8);
-    printf("%d_seq_len\t", numOrigColumns + 9);
-    
-    if (_printSeq)
-        printf("%d_seq", numOrigColumns + 10);
-    if (_hasPattern && !_printSeq)
-        printf("%d_user_patt_count", numOrigColumns + 10);
-    else if (_hasPattern && _printSeq)
-        printf("\t%d_user_patt_count", numOrigColumns + 11);
-    printf("\n");
-
-}
-
-
-//******************************************************************************
-// ExtractDNA
-//******************************************************************************
-void NucBed::ProfileDNA() {
-
-    /* Make sure that we can oen all of the files successfully*/
-
-    // open the fasta database for reading
-    ifstream faDb(_dbFile.c_str(), ios::in);
-    if ( !faDb ) {
-        cerr << "Error: The requested fasta database file (" << _dbFile << ") could not be opened. Exiting!" << endl;
-        exit (1);
-    }
-
-    // open and memory-map genome file
-    FastaReference fr;
-    bool memmap = true;    
-    fr.open(_dbFile, memmap);
-
-    bool headerReported = false;
-    BED bed, nullBed;
-    int lineNum = 0;
-    BedLineStatus bedStatus;
-    string sequence;
-
-    _bed->Open();
-    while ((bedStatus = _bed->GetNextBed(bed, lineNum)) != BED_INVALID) {
-        if (bedStatus == BED_VALID) {
-            if (headerReported == false) {
-                PrintHeader();
-                headerReported = true;
-            }
-            // make sure we are extracting >= 1 bp
-            if (bed.zeroLength == false) {
-                size_t seqLength = fr.sequenceLength(bed.chrom);
-                // make sure this feature will not exceed the end of the chromosome.
-                if ( (bed.start <= seqLength) && (bed.end <= seqLength) ) 
-                {
-                    // grab the dna at this interval
-                    int length = bed.end - bed.start;
-                    // report the sequence's content
-                    string dna = fr.getSubSequence(bed.chrom, bed.start, length);
-                    // rev comp si necessaire
-                    if ((_forceStrand == true) && (bed.strand == "-"))
-                        reverseComplement(dna);
-                    ReportDnaProfile(bed, dna, length);
-                    bed = nullBed;
-                }
-                else
-                {
-                    cerr << "Feature (" << bed.chrom << ":" << bed.start << "-" << bed.end << ") beyond the length of "
-                        << bed.chrom << " size (" << seqLength << " bp).  Skipping." << endl;
-                }
-            }
-            // handle zeroLength 
-            else {
-                cerr << "Feature (" << bed.chrom << ":" << bed.start+1 << "-" << bed.end-1 << ") has length = 0, Skipping." << endl;
-            }
-            bed = nullBed;
-        }
-    }
-    _bed->Close();
-}
-
-
-