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

Age	Commit message (Collapse)	Author
2014-01-18	Add initial, non working version	orbitz

2014-01-18	Fix compiler warnings	orbitz

2014-01-17	add in pointer fix	Calvin Morrison

2014-01-17	fix pointer	Calvin Morrison

2014-01-16	update translate function	Calvin Morrison

2014-01-16	add a fread_save_n_bytes function	Calvin Morrison

2014-01-15	fix spacing	Calvin Morrison

2014-01-15	start using fread, still not working	Calvin Morrison

2014-01-15	add 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
2014-01-15	add a fix for skip char	Calvin Morrison

2014-01-15	fix 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
2013-12-31	Remove need for strnstrip	orbitz

2013-12-31	Make functions static, move inner loop out to a function	orbitz

2013-12-31	Refactor out translation and error checking	orbitz

2013-12-31	Iterate in other direction	orbitz

2013-12-31	Remove fclose of file handle	orbitz

2013-12-29	Remove this shared thing...	orbitz

2013-12-29	Flip impossible ordering	orbitz

2013-12-29	Clneaup some whitespace, change how calloc called	orbitz

2013-12-29	Namespace all the functions and make private ones static	orbitz

2013-12-29	Clean up signed comparison warnings	orbitz

2013-12-29	Remove useless inline decorator	orbitz

2013-12-29	Align and label lookup map	orbitz

2013-12-29	Refactor to pull opening the file out of the count function	orbitz

2013-12-29	Cleanup indentation and whitespace	orbitz

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	index to kmerfunction	Calvin Morrison

2013-10-17	update kmer utils	Calvin Morrison

2013-10-16	added new functions	Calvin Morrison

2013-10-04	no more branching	Calvin Morrison

2013-10-02	use an external iterator so that we can skip over anything in range of an errorw	Calvin Morrison

2013-10-02	remove unused headers	Calvin Morrison

2013-10-01	update headers, use const for better performance (.500ms on ~2gb file), ↵	Calvin Morrison
	update comments for functions
2013-09-28	idea	Calvin Morrison

2013-09-14	improve 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
2013-09-12	don't use strtol	Calvin Morrison

2013-09-11	update convert_kmer_to_index for brevity and clarity	Calvin Morrison

2013-09-11	add headers	Calvin Morrison

2013-09-10	Initial 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