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path: root/kmer_utils.h
AgeCommit message (Collapse)Author
2014-03-03C++ version using unordered mapCalvin Morrison
2014-02-26update sparseCalvin Morrison
2014-02-18working sparse implementationCalvin Morrison
2014-02-02add a helper function for pythonCalvin Morrison
2014-02-01remove str alloc and replace inside s for strstrCalvin Morrison
2014-02-01change headers, organizeCalvin Morrison
2014-01-30kmer_count_per_sequence: add option to load specific mers from file, add ↵Calvin Morrison
multiline ecounting
2013-11-11fix warningsCalvin Morrison
2013-10-16reorder kmer_utils.h, actually take a kmer value as argv[2] for frequency, ↵Calvin Morrison
error check kmer
2013-10-16kmer utils.hCalvin Morrison
2013-10-02use an external iterator so that we can skip over anything in range of an errorwCalvin Morrison
2013-10-02update headerCalvin Morrison
2013-10-01update headers, use const for better performance (.500ms on ~2gb file), ↵Calvin Morrison
update comments for functions
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