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2013-11-07update makefileCalvin Morrison
2013-11-07rename to counts per sequence, don't provide frequencies only countsCalvin Morrison
2013-11-07rename to counts per sequence, don't provide frequencies only countsCalvin Morrison
2013-11-06fix freeCalvin Morrison
2013-10-31fix memset againCalvin Morrison
2013-10-31Revert "fix memset"Calvin Morrison
This reverts commit 8784d26bf275128935a1f682fab6cfff30d2e15b.
2013-10-31fix memsetCalvin Morrison
2013-10-23output individual kmers if requestedCalvin Morrison
2013-10-17update makefile with dependencies and proper static linkingCalvin Morrison
2013-10-17add a static library to our makefileCalvin Morrison
2013-10-17update kmer utilsCalvin 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
2013-10-16frequency_per_sequence still needs refactoringCalvin Morrison
2013-10-16works with multiline sequences, abstracted most code to kmer_utils.cCalvin Morrison
2013-10-16added new functionsCalvin Morrison
2013-10-16update makefileCalvin Morrison
2013-10-10 don't use the num_to_index function for more speeeeedCalvin Morrison
2013-10-10Merge branch 'master' of github.com:mutantturkey/dna-utils into HEADCalvin Morrison
2013-10-10update makefileCalvin Morrison
2013-10-10don't depend on math.h's POW by using a bitshift instead:Calvin Morrison
2013-10-06Update premature_optimization.mdCalvin Morrison
2013-10-06Update premature_optimization.mdCalvin Morrison
2013-10-06Update premature_optimization.mdCalvin Morrison
Adding the first attempt
2013-10-06Update premature_optimization.mdCalvin Morrison
Start fleshing it out
2013-10-06A story of my codeCalvin Morrison
2013-10-04Merge branch 'master' of github.com:mutantturkey/dna-utilsCalvin Morrison
2013-10-04no more branchingCalvin Morrison
2013-10-03Update README.mdCalvin Morrison
2013-10-03Create README.mdCalvin Morrison
Get a readme
2013-10-02provide errno error detailsCalvin Morrison
2013-10-02formattingCalvin 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
2013-10-02update headerCalvin Morrison
2013-10-02for kmer frequence per sequence as wellCalvin Morrison
2013-10-02add check for line length. if read > kmer we are good to goCalvin Morrison
2013-10-02add so support for makfileCalvin 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
2013-09-13don't use strlen(line) when we already have that in the read variableCalvin Morrison
2013-09-12don't use strtolCalvin Morrison
2013-09-11update convert_kmer_to_index for brevity and clarityCalvin Morrison
2013-09-11use right typesCalvin Morrison
2013-09-11move declarations to top, make sure to use the appropriate typeCalvin Morrison
2013-09-11add headersCalvin 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
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