File: sequenceUtils.h

package info (click to toggle)
bedtools 2.27.1%2Bdfsg-4
  • links: PTS, VCS
  • area: main
  • in suites: buster
  • size: 54,804 kB
  • sloc: cpp: 38,072; sh: 7,307; makefile: 2,241; python: 163
file content (27 lines) | stat: -rw-r--r-- 725 bytes parent folder | download | duplicates (6)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
#ifndef SEQUENCEUTILS_H
#define SEQUENCEUTILS_H

#include <string>
#include <algorithm>
#include <cctype>

using namespace std;

// Performs an in-place sequence reversal
void reverseSequence(string &seq);

// Performs an in-place reverse complement conversion
void reverseComplement(string &seq);

// Converts every character in a string to lowercase
void toLowerCase(string &seq);

// Converts every character in a string to uppercase
void toUpperCase(string &seq);

// Calculates the number of a, c, g, t, n, and other bases found in a sequence
void getDnaContent(const string &seq, int &a, int &c, int &g, int &t, int &n, int &other);

int countPattern(const string &seq, const string &pattern, bool ignoreCase);

#endif