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

Age	Commit message (Collapse)	Author
2014-04-10	use object for utils	Calvin Morrison

2014-04-09	MERGE sparse trunk into master	Calvin Morrison

2014-03-12	bump version	Calvin Morrison

2014-03-06	add continuous to install path	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
2014-02-02	add install section	Calvin Morrison

2014-02-01	add help function	Calvin Morrison

2014-02-01	simplify makefile	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

2013-10-17	update makefile with dependencies and proper static linking	Calvin Morrison

2013-10-17	add a static library to our makefile	Calvin Morrison

2013-10-16	update makefile	Calvin Morrison

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

2013-10-10	update makefile	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 so support for makfile	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