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public interface KMerCounter
Contains methods for counting kmers in sets of sequences.
| Method Summary | |
|---|---|
Pair<java.lang.Integer,java.lang.Integer> |
countOccurrences(Sequence pattern,
int beginIndex,
int endIndex,
int offset)
Counts the number of occurrences of the kmers pattern[beginIndex..endIndex-2] and pattern[beginIndex..endIndex-1] respectively, from a given position in a set of sequences. |
int |
sequenceCount()
Returns the number of sequences over which kmers are counted. |
| Method Detail |
|---|
int sequenceCount()
Pair<java.lang.Integer,java.lang.Integer> countOccurrences(Sequence pattern,
int beginIndex,
int endIndex,
int offset)
pattern - The base pattern.beginIndex - The start position of the subpattern to be counted.endIndex - The end position (not inclusive) of the subpattern to be counted.offset - The position at which the match must begin.
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