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

Age	Commit message (Collapse)	Author
2014-04-10	make sure arrays aer in utils.h	Calvin Morrison

2014-04-09	kmer utils too	Calvin Morrison

2014-03-12	reverse compliment	Calvin Morrison

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

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

2014-02-01	change headers, organize	Calvin Morrison

2014-01-30	kmer_count_per_sequence: add option to load specific mers from file, add ↵	Calvin Morrison
	multiline ecounting
2013-11-11	fix warnings	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	kmer utils.h	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	update header	Calvin Morrison

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