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comparison BEDTools-Version-2.14.3/src/utils/sequenceUtilities/sequenceUtils.h @ 1:bec36315bd12 default tip

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author aaronquinlan
date Sat, 19 Nov 2011 14:17:03 -0500
parents dfcd8b6c1bda
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0:dfcd8b6c1bda 1:bec36315bd12
1 #ifndef SEQUENCEUTILS_H
2 #define SEQUENCEUTILS_H
3
4 #include <string>
5 #include <algorithm>
6 #include <cctype>
7
8 using namespace std;
9
10 // Performs an in-place sequence reversal
11 void reverseSequence(string &seq);
12
13 // Performs an in-place reverse complement conversion
14 void reverseComplement(string &seq);
15
16 // Converts every character in a string to lowercase
17 void toLowerCase(string &seq);
18
19 // Converts every character in a string to uppercase
20 void toUpperCase(string &seq);
21
22 // Calculates the number of a, c, g, t, n, and other bases found in a sequence
23 void getDnaContent(const string &seq, int &a, int &c, int &g, int &t, int &n, int &other);
24
25 int countPattern(const string &seq, const string &pattern);
26
27 #endif