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path: root/kmer_utils.c
AgeCommit message (Collapse)Author
2013-11-15instead of bitshift, use a equality operatorCalvin Morrison
2013-11-11index to kmerfunctionCalvin Morrison
2013-10-17update kmer utilsCalvin Morrison
2013-10-16added new functionsCalvin Morrison
2013-10-04no more branchingCalvin Morrison
2013-10-02use an external iterator so that we can skip over anything in range of an errorwCalvin Morrison
2013-10-02remove unused headersCalvin Morrison
2013-10-01update headers, use const for better performance (.500ms on ~2gb file), ↵Calvin Morrison
update comments for functions
2013-09-28ideaCalvin Morrison
2013-09-14improve performance of convert_kmer_to_index by using a bitwise OR to ↵Calvin Morrison
convert our characters to lowercare: str[i] | Ox20, and reduce the number of switches as a result
2013-09-12don't use strtolCalvin Morrison
2013-09-11update convert_kmer_to_index for brevity and clarityCalvin Morrison
2013-09-11add headersCalvin Morrison
2013-09-10Initial commit of some kmer utilities.Calvin Morrison
there are two utilties included. one is kmer_frequency_per_sequence, which outputs a (m x n) matrix where m is the sequence, and n is the frequency of that nmer to occur in the given sequence. the other tool is kmer_total_count, which counts kmers for the total file, not just one sequence