findRepeats

Function

findRepeats

Search for repeats in a text.

findRepeats(repeatString, text, minRepeatLength[, maxPeriod])

Include Headers

seqan/index.h

Parameters

repeatString	A String of Repeat objects.
text	The text to search repeats in. Types: String, StringSet
minRepeatLength	The minimum length each reported repeat must have.
maxPeriod	Optionally, the maximal period that reported repeats can have. Default: 1

Remarks

Subsequences of undefined values/Ns will always be reported.

Examples

The following demonstrates finding repeats of period 1.

String<Repeat<unsigned, unsigned> > repeats;
Dna5String text = "CGATAAAACTNN";
// repeat 0            AAAA
// repeat 1                  NN

findRepeats(repeats, text, 3);
// ==> length(repeats) == 2
// ==> repeats[0] == {beginPosition:  4, endPosition:  8, period: 1}
// ==> repeats[1] == {beginPosition: 11, endPosition: 13, period: 1}