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2014-03-06update readme, add a check_null_ptr function to clear up clutterCalvin 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
2014-02-27use sparse always if we use --merCalvin Morrison
2014-02-27fixed sparse in combination with --mer-fileCalvin Morrison
2014-02-26add gpl3 licenseCalvin Morrison
2014-02-24add more verbose error messages and add more memory checksCalvin Morrison
2014-02-06whoops, count even if it's zeroCalvin Morrison
2014-02-05Merge branch 'master' of github.com:mutantturkey/dna-utilsCalvin Morrison
2014-02-05add example, rename variables, rename function, improve error function, ↵Calvin Morrison
check for types
2014-02-04add examples to readme.mdCalvin Morrison
2014-02-04don't inline hint, breaks clangCalvin Morrison
2014-02-02somewhat working python moduleCalvin Morrison
2014-02-02nonworking commit of interfaceCalvin Morrison
2014-02-02add a helper function for pythonCalvin Morrison
2014-02-02add install sectionCalvin Morrison
2014-02-02add commentCalvin Morrison
2014-02-01remove str alloc and replace inside s for strstrCalvin Morrison
2014-02-01use pow_four insteadCalvin Morrison
2014-02-01add getopts to kmer_counts_per_sequene and sparse output optionsCalvin Morrison
2014-02-01change headers, organizeCalvin Morrison
2014-02-01use proper types, fix warnings, declare vars at top of section, take FILE ↵Calvin Morrison
instead of char
2014-02-01fix spacingCalvin Morrison
2014-02-01update types of functions, remove non existant include and se size_t for ↵Calvin Morrison
strnstrip
2014-02-01add --helpCalvin Morrison
2014-02-01backport stdin readingCalvin Morrison
2014-02-01get rid of position, add helpCalvin Morrison
2014-02-01use false instead of 0Calvin Morrison
2014-02-01add help functionCalvin Morrison
2014-02-01simplify makefileCalvin Morrison
2014-01-31remove commasCalvin Morrison
2014-01-31update readmeCalvin Morrison
2014-01-31add --help text for kmer_total_countCalvin Morrison
2014-01-31fix argv/c checkingCalvin Morrison
2014-01-30kmer_count_per_sequence: add option to load specific mers from file, add ↵Calvin Morrison
multiline ecounting
2014-01-07fix kmer_counts_per_sequence, make sure we convert the array fully, and ↵Calvin Morrison
update kmer_utils for str[i] == 5 instead of >> 2
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
2013-11-11fix warningsCalvin Morrison
2013-11-11fix printfCalvin Morrison
2013-11-11added label and nonzero optionsCalvin Morrison
2013-11-11index to kmerfunctionCalvin Morrison
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