quikr.git - Quikr - a bio classifier based on NNLS

Age	Commit message (Collapse)	Author
2013-10-31	formatting changes for quikr	Calvin Morrison

2013-10-31	return 0 instead of exit_failure in count_sequences, and remove the newline ↵	Calvin Morrison
	from our header
2013-10-31	exit if no sequences	Calvin Morrison

2013-10-31	fix a bug so we only read when the length is greater han the kmer	Calvin Morrison

2013-10-29	remove the fasta file requirement for multifasta, and no longer parse ↵	Calvin Morrison
	headers (we already do)
2013-10-29	initial commit of multifasta_to_otu.c working with new format	Calvin Morrison

2013-10-29	update tpyes for quikr_train.c	Calvin Morrison

2013-10-29	update types for quikr_functions	Calvin Morrison

2013-10-29	update types and check malloc	Calvin Morrison

2013-10-29	append variables in makefile to reduce redundancy	Calvin Morrison

2013-10-29	use type in memset, add +1 to our matrix width	Calvin Morrison

2013-10-29	update errors from load_sensing_matrix	Calvin Morrison

2013-10-29	update quikr to work with internally parsed sensing matrix	Calvin Morrison

2013-10-29	update header	Calvin Morrison

2013-10-29	fix memset in quikr_train as weel	Calvin Morrison

2013-10-29	Fix a nasty bug in kmer-counting code	Calvin Morrison
	Memset of course does not deal properly with the unsigned long long type so we need to compensate by doing sizeof(unsigned long long) * width to fix the issue
2013-10-28	update kmer utils	Calvin Morrison

2013-10-28	New sensing matrix format	Calvin Morrison
	quikr_train now has a new format that should allow for a more sane approach in terms of usability. headers are now packed into the format, and counts, not probabilities are included as each row the header looks like quikr version of format sequences kmer >header 2 4 12 22 ... n-mers >header2 ....
2013-10-28	update Makefile to be more sane and use targets correctly	Calvin Morrison

2013-10-28	Update quikr_functions to read our sensing format	Calvin Morrison

2013-10-18	add kmercounting code from dna-utils. update our make file to support ↵	Calvin Morrison
	debugging, and update quikr to count-kmer code internally
2013-09-05	last fixes for 1.0.4v1.0.4	Calvin Morrison

2013-09-05	bump to version v1.0.4	Calvin Morrison

2013-09-05	Remove debugging version	Calvin Morrison
	remove the debugging option for quikr, since there is not a reason to keep it anymore, consider it cruft. Our users are unlikely to ever use it and the same for us - remove from manpage - remove from quikr.c
2013-08-29	parse -h and --help and print out the help message	Calvin Morrison

2013-08-16	Merge branch 'master' of github.com:mutantturkey/quikr	Calvin Morrison

2013-08-16	remove unused case	Calvin Morrison

2013-06-13	use readdir and #omp criticalv1.0.3	Calvin

2013-06-12	fix case	Calvin

2013-06-12	add --version and -V	Calvin

2013-06-12	use larger size for count_commmand, remove extra quotes, and fix a broken ↵	Calvin Morrison
	check in multifasta2otu
2013-06-11	remove file	Calvin Morrison

2013-06-11	remove extra word	Calvin

2013-06-11	updated functions with long	Calvin

2013-06-11	use int64_t for NNLS to avoid overflow issues	Calvin

2013-06-11	small edits to man page	Calvin

2013-06-11	use longs instead of ints, fix a mistake in the --help	Calvin

2013-06-10	finish gzip decoding, YOU MUST retrain your api	Calvin

2013-06-10	native zlib decoding for quikr/multifasta, was done earlier but never ↵	Calvin
	commited for some reason
2013-06-10	remove unused variable	Calvin

2013-06-07	free getline's calls	Calvin Morrison

2013-06-07	updated help text and manpages	Calvin

2013-06-06	fixed a malloc error, and fixed some strings	Calvin

2013-05-20	use nnn instead on n*n for nnls	Calvin

2013-05-20	updated documentation strings, add man page to be installed globally	Calvin

2013-05-19	native gzip decoding	Calvin Morrison

2013-05-15	added file checking for multifasta_to_otu	Calvin

2013-05-15	add some error checking	Calvin

2013-05-15	cleanup kmer/lambda default values	Calvin

2013-05-15	add -d flag for debugging so verbose doesn't take longer, use generate_kmers ↵	Calvin
	instead of a hacky awk