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Figure 2 | BMC Bioinformatics

Figure 2

From: Querying large read collections in main memory: a versatile data structure

Figure 2

Accessing the occurrences of a k -mer in the index. Accessing the index to get the occurrences of a k-mer starting at position j in the concatenation of the reads (i.e., C R ). Accessing GkIFA, GkCFPS and GkSA: (a) From C R to GkIFA: g(j) is the renumbered position of the P-position j. (b) From GkIFA to GkCFPS: GkIFA[g(j)] is the lexicographic rank of the P k -factor starting at P-position j in C R , and GkCFPS[GkIFA[g(j)]] is the number of occurrences in C R of the P k -factors of rank less than GkIFA[g(j)]. (c) From GkCFPS to GkSA: The positions of the occurrences of the P k -factor starting at position j are in GkSA in the range [GkCFPS[GkIFA[g(j)] -1], GkCFPS[GkIFA[g(j)]]].

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