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

Age	Commit message (Collapse)	Author
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

2013-10-02	update header	Calvin Morrison

2013-10-02	for kmer frequence per sequence as well	Calvin Morrison

2013-10-02	add check for line length. if read > kmer we are good to go	Calvin Morrison

2013-10-02	add so support for makfile	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

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

2013-09-11	update convert_kmer_to_index for brevity and clarity	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

2013-09-11	fix binary name, and add -Wextra	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