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

Age	Commit message (Collapse)	Author
2014-04-09	MERGE sparse trunk into master	Calvin Morrison

2014-03-12	update cli for reverse-compliment counting	Calvin Morrison

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

2014-02-01	add --help	Calvin Morrison

2014-02-01	backport stdin reading	Calvin Morrison

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

2014-02-01	add help function	Calvin Morrison

2014-01-31	remove commas	Calvin Morrison

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

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

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

2013-10-23	output individual kmers if requested	Calvin Morrison

2013-10-16	reorder kmer_utils.h, actually take a kmer value as argv[2] for frequency, ↵	Calvin Morrison
	error check kmer
2013-10-16	works with multiline sequences, abstracted most code to kmer_utils.c	Calvin Morrison

2013-10-10	don't use the num_to_index function for more speeeeed	Calvin Morrison

2013-10-10	don't depend on math.h's POW by using a bitshift instead:	Calvin Morrison

2013-10-04	no more branching	Calvin Morrison

2013-10-02	provide errno error details	Calvin Morrison

2013-10-02	formatting	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	add check for line length. if read > kmer we are good to go	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
2013-09-13	don't use strlen(line) when we already have that in the read variable	Calvin Morrison

2013-09-11	use right types	Calvin Morrison

2013-09-11	move declarations to top, make sure to use the appropriate type	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