dna-utils.git - Tools for parsing FASTA files very fast

Age	Commit message (Collapse)	Author
2014-03-06	update readme, add a check_null_ptr function to clear up clutter	Calvin Morrison

2014-03-06	add kmer_continuous_count	Calvin 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
2014-02-27	use sparse always if we use --mer	Calvin Morrison

2014-02-27	fixed sparse in combination with --mer-file	Calvin Morrison

2014-02-26	add gpl3 license	Calvin Morrison

2014-02-24	add more verbose error messages and add more memory checks	Calvin Morrison

2014-02-06	whoops, count even if it's zero	Calvin Morrison

2014-02-05	Merge branch 'master' of github.com:mutantturkey/dna-utils	Calvin Morrison

2014-02-05	add example, rename variables, rename function, improve error function, ↵	Calvin Morrison
	check for types
2014-02-04	add examples to readme.md	Calvin Morrison

2014-02-04	don't inline hint, breaks clang	Calvin Morrison

2014-02-02	somewhat working python module	Calvin Morrison

2014-02-02	nonworking commit of interface	Calvin Morrison

2014-02-02	add a helper function for python	Calvin Morrison

2014-02-02	add install section	Calvin Morrison

2014-02-02	add comment	Calvin Morrison

2014-02-01	remove str alloc and replace inside s for strstr	Calvin Morrison

2014-02-01	use pow_four instead	Calvin Morrison

2014-02-01	add getopts to kmer_counts_per_sequene and sparse output options	Calvin Morrison

2014-02-01	change headers, organize	Calvin Morrison

2014-02-01	use proper types, fix warnings, declare vars at top of section, take FILE ↵	Calvin Morrison
	instead of char
2014-02-01	fix spacing	Calvin Morrison

2014-02-01	update types of functions, remove non existant include and se size_t for ↵	Calvin Morrison
	strnstrip
2014-02-01	add --help	Calvin Morrison

2014-02-01	backport stdin reading	Calvin Morrison

2014-02-01	get rid of position, add help	Calvin Morrison

2014-02-01	use false instead of 0	Calvin Morrison

2014-02-01	add help function	Calvin Morrison

2014-02-01	simplify makefile	Calvin Morrison

2014-01-31	remove commas	Calvin Morrison

2014-01-31	update readme	Calvin Morrison

2014-01-31	add --help text for kmer_total_count	Calvin Morrison

2014-01-31	fix argv/c checking	Calvin Morrison

2014-01-30	kmer_count_per_sequence: add option to load specific mers from file, add ↵	Calvin Morrison
	multiline ecounting
2014-01-07	fix kmer_counts_per_sequence, make sure we convert the array fully, and ↵	Calvin Morrison
	update kmer_utils for str[i] == 5 instead of >> 2
2013-11-24	performance 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
2013-11-23	fix labels, fix spelling of position	Calvin Morrison

2013-11-23	better allocation of memory, make sure to free other memory	Calvin Morrison

2013-11-15	Merge branch 'master' of github.com:mutantturkey/dna-utils	Calvin Morrison

2013-11-15	instead of bitshift, use a equality operator	Calvin Morrison

2013-11-11	fix memleak	Calvin Morrison

2013-11-11	fix warnings	Calvin Morrison

2013-11-11	fix printf	Calvin Morrison

2013-11-11	added label and nonzero options	Calvin Morrison

2013-11-11	index to kmerfunction	Calvin Morrison

2013-11-07	update makefile	Calvin Morrison

2013-11-07	rename to counts per sequence, don't provide frequencies only counts	Calvin Morrison

2013-11-07	rename to counts per sequence, don't provide frequencies only counts	Calvin Morrison

2013-11-06	fix free	Calvin Morrison

2013-10-31	fix memset again	Calvin Morrison