--- a/BEDTools-Version-2.14.3/src/utils/Fasta/Fasta.h	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,78 +0,0 @@
-// ***************************************************************************
-// FastaIndex.h (c) 2010 Erik Garrison <erik.garrison@bc.edu>
-// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
-// ---------------------------------------------------------------------------
-// Last modified: 5 February 2010 (EG)
-// ---------------------------------------------------------------------------
-
-#ifndef _FASTA_H
-#define _FASTA_H
-
-#include <map>
-#include <iostream>
-#include <fstream>
-#include <vector>
-#include <stdint.h>
-#include <stdio.h>
-#include <algorithm>
-#include "LargeFileSupport.h"
-#include <sys/stat.h>
-#include <sys/mman.h>
-#include "split.h"
-#include <stdlib.h>
-#include <ctype.h>
-#include <unistd.h>
-
-using namespace std;
-
-class FastaIndexEntry {
-    friend ostream& operator<<(ostream& output, const FastaIndexEntry& e);
-    public:
-        FastaIndexEntry(string name, int length, long long offset, int line_blen, int line_len);
-        FastaIndexEntry(void);
-        ~FastaIndexEntry(void);
-        string name;  // sequence name
-        int length;  // length of sequence
-        long long offset;  // bytes offset of sequence from start of file
-        int line_blen;  // line length in bytes, sequence characters
-        int line_len;  // line length including newline
-        void clear(void);
-};
-
-class FastaIndex : public map<string, FastaIndexEntry> {
-    friend ostream& operator<<(ostream& output, FastaIndex& i);
-    public:
-        FastaIndex(void);
-        ~FastaIndex(void);
-        vector<string> sequenceNames;
-        void indexReference(string refName);
-        void readIndexFile(string fname);
-        void writeIndexFile(string fname);
-        ifstream indexFile;
-        FastaIndexEntry entry(string key);
-        void flushEntryToIndex(FastaIndexEntry& entry);
-        string indexFileExtension(void);
-};
-
-class FastaReference {
-    public:
-        void open(string reffilename, bool usemmap = false);
-        bool usingmmap;
-        string filename;
-        FastaReference(void) : usingmmap(false) { }
-        ~FastaReference(void);
-        FILE* file;
-        void* filemm;
-        size_t filesize;
-        FastaIndex* index;
-        vector<FastaIndexEntry> findSequencesStartingWith(string seqnameStart);
-        string getSequence(string seqname);
-        // potentially useful for performance, investigate
-        // void getSequence(string seqname, string& sequence);
-        string getSubSequence(string seqname, int start, int length);
-        string sequenceNameStartingWith(string seqnameStart);
-        long unsigned int sequenceLength(string seqname);
-};
-
-#endif