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2013-11-26some spacing changesCalvin Morrison
2013-11-26working single threaded multifasta with rarityCalvin Morrison
2013-11-13remove nbc:Calvin Morrison
2013-11-07add quikr.hCalvin Morrison
2013-11-07remove debuggingCalvin Morrison
2013-11-07update to work with kmer rarityCalvin Morrison
2013-11-07 don't cast the return of callocCalvin Morrison
2013-11-07fix memleakCalvin Morrison
2013-10-31say failname on failCalvin Morrison
2013-10-31fix variableCalvin Morrison
2013-10-31remove all references to sensing-fastaCalvin Morrison
2013-10-31add test.faCalvin Morrison
2013-10-31inital test system in placeCalvin Morrison
2013-10-31finish up removing OCaml Code and general code refactoringCalvin Morrison
2013-10-31fix memsetCalvin Morrison
2013-10-31formatting changes for quikrCalvin Morrison
2013-10-31return 0 instead of exit_failure in count_sequences, and remove the newline ↵Calvin Morrison
from our header
2013-10-31exit if no sequencesCalvin Morrison
2013-10-31fix a bug so we only read when the length is greater han the kmerCalvin Morrison
2013-10-29remove the fasta file requirement for multifasta, and no longer parse ↵Calvin Morrison
headers (we already do)
2013-10-29initial commit of multifasta_to_otu.c working with new formatCalvin Morrison
2013-10-29update tpyes for quikr_train.cCalvin Morrison
2013-10-29update types for quikr_functionsCalvin Morrison
2013-10-29update types and check mallocCalvin Morrison
2013-10-29append variables in makefile to reduce redundancyCalvin Morrison
2013-10-29use type in memset, add +1 to our matrix widthCalvin Morrison
2013-10-29update errors from load_sensing_matrixCalvin Morrison
2013-10-29update quikr to work with internally parsed sensing matrixCalvin Morrison
2013-10-29update headerCalvin Morrison
2013-10-29fix memset in quikr_train as weelCalvin Morrison
2013-10-29Fix a nasty bug in kmer-counting codeCalvin 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
2013-10-28update kmer utilsCalvin Morrison
2013-10-28New sensing matrix formatCalvin 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 ....
2013-10-28update Makefile to be more sane and use targets correctlyCalvin Morrison
2013-10-28Update quikr_functions to read our sensing formatCalvin Morrison
2013-10-18add kmercounting code from dna-utils. update our make file to support ↵Calvin Morrison
debugging, and update quikr to count-kmer code internally
2013-09-05last fixes for 1.0.4v1.0.4Calvin Morrison
2013-09-05bump to version v1.0.4Calvin Morrison
2013-09-05Merge branch 'master' of github.com:mutantturkey/quikrCalvin Morrison
2013-09-05build nbc and c before we install quikrCalvin Morrison
2013-09-05update cli.markdown to remove debugCalvin Morrison
2013-09-05Remove debugging versionCalvin 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
2013-09-05README formattingCalvin Morrison
- add two spaces after each section - add question marks to the question titles
2013-09-05Merge branch 'master' of github.com:EESI/quikrCalvin Morrison
2013-08-30Update cli.markdownCalvin Morrison
Fix markdown formatting, and add some details about the pre-requisites for multifasta
2013-08-29parse -h and --help and print out the help messageCalvin Morrison
2013-08-20Don't escape _'sCalvin Morrison
2013-08-16Merge branch 'master' of github.com:EESI/quikrCalvin Morrison
2013-08-16Merge branch 'master' of github.com:mutantturkey/quikrCalvin Morrison
2013-08-16remove unused caseCalvin Morrison
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