Mercurial > repos > aaronquinlan > multi_intersect
comparison BEDTools-Version-2.14.3/src/utils/sequenceUtilities/sequenceUtils.h @ 0:dfcd8b6c1bda
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| author | aaronquinlan |
|---|---|
| date | Thu, 03 Nov 2011 10:25:04 -0400 |
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| -1:000000000000 | 0:dfcd8b6c1bda |
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| 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 |