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2014-04-10use object for utilsCalvin Morrison
2014-04-09MERGE sparse trunk into masterCalvin Morrison
2014-03-12bump versionCalvin Morrison
2014-03-06add continuous to install pathCalvin Morrison
2014-03-06add kmer_continuous_countCalvin Morrison
this tool will count continuously, instead of line by line. The way that this works out is something like this: test.fa > header 1 AAAAATTTTT > header 2 GGGGGAAAAA counting 6 mers, the program will count TTTGGG, TTGGGG, TGGGGG, like there was no header seperating them. This can be useful for certain tyeps of processing, like when the sequences are continuous from a genome. initial commit
2014-02-02add install sectionCalvin Morrison
2014-02-01add help functionCalvin Morrison
2014-02-01simplify makefileCalvin Morrison
2013-11-07update makefileCalvin Morrison
2013-11-07rename to counts per sequence, don't provide frequencies only countsCalvin Morrison
2013-10-17update makefile with dependencies and proper static linkingCalvin Morrison
2013-10-17add a static library to our makefileCalvin Morrison
2013-10-16update makefileCalvin Morrison
2013-10-10 don't use the num_to_index function for more speeeeedCalvin Morrison
2013-10-10update makefileCalvin Morrison
2013-10-02use an external iterator so that we can skip over anything in range of an errorwCalvin Morrison
2013-10-02add so support for makfileCalvin Morrison
2013-09-11fix binary name, and add -WextraCalvin 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