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comparison BEDTools-Version-2.14.3/src/utils/Fasta/Fasta.h @ 0:dfcd8b6c1bda

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author aaronquinlan
date Thu, 03 Nov 2011 10:25:04 -0400
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1 // ***************************************************************************
2 // FastaIndex.h (c) 2010 Erik Garrison <erik.garrison@bc.edu>
3 // Marth Lab, Department of Biology, Boston College
4 // All rights reserved.
5 // ---------------------------------------------------------------------------
6 // Last modified: 5 February 2010 (EG)
7 // ---------------------------------------------------------------------------
8
9 #ifndef _FASTA_H
10 #define _FASTA_H
11
12 #include <map>
13 #include <iostream>
14 #include <fstream>
15 #include <vector>
16 #include <stdint.h>
17 #include <stdio.h>
18 #include <algorithm>
19 #include "LargeFileSupport.h"
20 #include <sys/stat.h>
21 #include <sys/mman.h>
22 #include "split.h"
23 #include <stdlib.h>
24 #include <ctype.h>
25 #include <unistd.h>
26
27 using namespace std;
28
29 class FastaIndexEntry {
30 friend ostream& operator<<(ostream& output, const FastaIndexEntry& e);
31 public:
32 FastaIndexEntry(string name, int length, long long offset, int line_blen, int line_len);
33 FastaIndexEntry(void);
34 ~FastaIndexEntry(void);
35 string name; // sequence name
36 int length; // length of sequence
37 long long offset; // bytes offset of sequence from start of file
38 int line_blen; // line length in bytes, sequence characters
39 int line_len; // line length including newline
40 void clear(void);
41 };
42
43 class FastaIndex : public map<string, FastaIndexEntry> {
44 friend ostream& operator<<(ostream& output, FastaIndex& i);
45 public:
46 FastaIndex(void);
47 ~FastaIndex(void);
48 vector<string> sequenceNames;
49 void indexReference(string refName);
50 void readIndexFile(string fname);
51 void writeIndexFile(string fname);
52 ifstream indexFile;
53 FastaIndexEntry entry(string key);
54 void flushEntryToIndex(FastaIndexEntry& entry);
55 string indexFileExtension(void);
56 };
57
58 class FastaReference {
59 public:
60 void open(string reffilename, bool usemmap = false);
61 bool usingmmap;
62 string filename;
63 FastaReference(void) : usingmmap(false) { }
64 ~FastaReference(void);
65 FILE* file;
66 void* filemm;
67 size_t filesize;
68 FastaIndex* index;
69 vector<FastaIndexEntry> findSequencesStartingWith(string seqnameStart);
70 string getSequence(string seqname);
71 // potentially useful for performance, investigate
72 // void getSequence(string seqname, string& sequence);
73 string getSubSequence(string seqname, int start, int length);
74 string sequenceNameStartingWith(string seqnameStart);
75 long unsigned int sequenceLength(string seqname);
76 };
77
78 #endif