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path: root/kmer_utils.c
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2014-01-18Add initial, non working versionorbitz
2014-01-18Fix compiler warningsorbitz
2014-01-17add in pointer fixCalvin Morrison
2014-01-17fix pointerCalvin Morrison
2014-01-16update translate functionCalvin Morrison
2014-01-16add a fread_save_n_bytes functionCalvin Morrison
2014-01-15fix spacingCalvin Morrison
2014-01-15start using fread, still not workingCalvin Morrison
2014-01-15add handling for overrunning the string length, and if there's a skip char ↵Calvin Morrison
in the first position, also more smartly write (unsigned long long), and clean up our multiplier value
2014-01-15add a fix for skip charCalvin Morrison
2014-01-15fix counting to not be reversed, remove is_whitespace is_error_char and ↵Calvin Morrison
instead add values to lookup array, make lookup function more general for later use
2013-12-31Remove need for strnstriporbitz
2013-12-31Make functions static, move inner loop out to a functionorbitz
2013-12-31Refactor out translation and error checkingorbitz
2013-12-31Iterate in other directionorbitz
2013-12-31Remove fclose of file handleorbitz
2013-12-29Remove this shared thing...orbitz
2013-12-29Flip impossible orderingorbitz
2013-12-29Clneaup some whitespace, change how calloc calledorbitz
2013-12-29Namespace all the functions and make private ones staticorbitz
2013-12-29Clean up signed comparison warningsorbitz
2013-12-29Remove useless inline decoratororbitz
2013-12-29Align and label lookup maporbitz
2013-12-29Refactor to pull opening the file out of the count functionorbitz
2013-12-29Cleanup indentation and whitespaceorbitz
2013-11-24performance boost from skipping our first newline. It seems crazy, but this ↵Calvin Morrison
could be up to a 10-15% improvement because of our strstrip function. Each time we were copying the entire array, even if we didn't need to. There will be more of a benefit on a single line'd sequence file, but will see a speed up on all
2013-11-23fix labels, fix spelling of positionCalvin Morrison
2013-11-23better allocation of memory, make sure to free other memoryCalvin Morrison
2013-11-15Merge branch 'master' of github.com:mutantturkey/dna-utilsCalvin Morrison
2013-11-15instead of bitshift, use a equality operatorCalvin Morrison
2013-11-11fix memleakCalvin 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