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in-memory k-mer counting

Merge pull request #391 from RamRS/bugfix-htpt

Bug fix: make-initial-stoptags.py error on missing .ht input file, actual input file is .pt
latest commit f5428c5bdf
Michael R. Crusoe mr-c authored April 18, 2014
Octocat-spinner-32 data Correct test data for new FASTA{A,Q} name format. (Earlier conversion… February 20, 2013
Octocat-spinner-32 doc Hand merge of release/update_citations April 01, 2014
Octocat-spinner-32 examples Copyright headers corrected for all Python and shell scripts. March 25, 2014
Octocat-spinner-32 khmer Hand merge of release/update_citations April 01, 2014
Octocat-spinner-32 lib Fixes Coverity CID 1054804 & 1195088 April 01, 2014
Octocat-spinner-32 sandbox Copyright headers corrected for all Python and shell scripts. March 25, 2014
Octocat-spinner-32 scripts Bug fix: make-initial-stoptags.py error on missing .ht input file, ac… April 17, 2014
Octocat-spinner-32 tests Merge branch 'master' of github.com:ged-lab/khmer into bug/empty_dirpath April 01, 2014
Octocat-spinner-32 .gitattributes trying out versioneer October 22, 2013
Octocat-spinner-32 .gitignore properly clear zlib's Makefile March 26, 2014
Octocat-spinner-32 .landscape.yaml configure landscape.io service March 01, 2014
Octocat-spinner-32 .ycm_extra_conf.py work around for build_ext config #352 March 30, 2014
Octocat-spinner-32 CITATION Hand merge of release/update_citations April 01, 2014
Octocat-spinner-32 CONTRIBUTING.md Create CONTRIBUTING.md February 18, 2014
Octocat-spinner-32 ChangeLog Bug fix: make-initial-stoptags.py error on missing .ht input file, ac… April 17, 2014
Octocat-spinner-32 Doxyfile.in update to new Doxyfile format, make version number autoupdate March 04, 2014
Octocat-spinner-32 IDEAS remove outdated IDEAS October 03, 2013
Octocat-spinner-32 LICENSE Hand merge of release/update_citations April 01, 2014
Octocat-spinner-32 MANIFEST.in new version 0.10 of versioneer.py March 31, 2014
Octocat-spinner-32 Makefile Ensure that versioneer runs during an install. April 01, 2014
Octocat-spinner-32 README.rst updated README with CITATION information March 31, 2014
Octocat-spinner-32 TODO Add TODO item about hunting for more memory leaks. November 12, 2012
Octocat-spinner-32 bink.ipynb initial hacky implementation of streaming abundance binning September 01, 2013
Octocat-spinner-32 ez_setup.py new version 3.4.1 of ez_setup.py March 31, 2014
Octocat-spinner-32 jenkins-build.sh switch to autoprogram for all scripts March 31, 2014
Octocat-spinner-32 setup.cfg work around for build_ext config #352 March 30, 2014
Octocat-spinner-32 setup.py Hand merge of release/update_citations April 01, 2014
Octocat-spinner-32 versioneer.py new version 0.10 of versioneer.py March 31, 2014
README.rst

khmer

Welcome to khmer: k-mer counting, filtering and graph traversal FTW!

https://badge.fury.io/py/khmer.png https://pypip.in/d/khmer/badge.png License http://ci.ged.msu.edu/job/khmer/badge/icon Python Code Health Coverity Scan Build Status

The official repository is at

https://github.com/ged-lab/khmer

and you can read the docs online here:

http://khmer.readthedocs.org/

There are two mailing lists dedicated to khmer, an announcements-only list and a discussion list. To search their archives and sign-up for them, please visit the following URLs:

You can contact the current maintainers at khmer-project@idyll.org.

IMPORTANT NOTE: CITE US!

khmer is research software, so you should cite us when you use it in scientific publications! Please see the CITATION file for citation information.

INSTALL INSTRUCTIONS:

khmer requires Python 2.7+. Linux users will need the python development libraries and gcc. OS X users may need XCode installed. For more details see doc/install.txt

In short:

pip install khmer to download, build, and install the latest stable version.

The use of a virtualenv is recommended, see http://www.virtualenv.org/en/latest/#installation

khmer is under the BSD license; see doc/LICENSE.txt. Distribution, modification and redistribution, incorporation into other software, and pretty much everything else is allowed.

khmer project contributors also edit documents collaboratively at our wiki.

CTB 2014-03-31

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