<div dir="ltr">Dear colleagues,<div><br></div><div>I am happy to announce version 0.8 of the khmer project.</div><div><br></div><div><div>89 changed files with 11,223 additions and 6,171 deletions.</div><div><br></div><div>
## New functionality</div><div><br></div><div>Sparse graph labeling @camillescott ( sweep-reads-by-partition-buffered.py )</div><div>Initial support for Galaxy integration (for normalize-by-median and abund-filter) @mr-c</div>
<div>Normalization of arguments across the scripts @camillescott</div><div><br></div><div>Note: The default branch on GitHub is now the 'master' branch. Our unmaintained tutorials that install khmer with a plain git clone have a warning added to them and potential user are directed to the khmer-protocols: <a href="http://khmer-protocols.readthedocs.org">http://khmer-protocols.readthedocs.org</a></div>
<div><br></div><div>## Notable bugs fixed</div><div><br></div><div>load-graph gives erroneous memory estimate #279 @camillescott </div><div>If loadhash is specified, do not complain about hashsize #278 @RamRS @humberto-ortiz</div>
<div>test_Hashbits case sensitivity #265 @luizirber </div><div>Installation fails: cannot find argparse >= 1.2.1 #258 @mr-c & @standage</div><div>Bugs found by coverity #256 @camillescott </div><div><br></div><div>
## Minor updates</div><div><br></div><div>abundance-dist-single.py, abundance-dist.py, do-partition.py, interleave-reads.py, load-graph.py, load-into-counting.py normalize-by-median.py now exit with return code 1 instead of 255 as is standard.</div>
<div>Program arguments that have default values are disclosed @mr-c</div><div>Developer documentation updates: contribution guidelines, coding standards, code review hints (with checklist). Release instruction completely rewritten.</div>
<div>Installation instructions tweaks including specific commands for Debian derivatives and RHEL6.</div><div>Update to the latest versioneer.py & ez_setup.py</div><div>The latest version of setuptools is no longer required: version 0.6c11 appears to be just fine.</div>
<div>Many code cleanups. Python namespace usage was tidied. Type safety was strengthened in the C++/Python integration.</div><div>Testing coverage measures the scripts properly.</div><div><br></div><div>## Known Issues</div>
<div><br></div><div>All of these are pre-existing.</div><div><br></div><div>Some users have reported that normalize-by-median.py will utilize more memory than it was configured for. This is being investigated in <a href="https://github.com/ged-lab/khmer/issues/266">https://github.com/ged-lab/khmer/issues/266</a></div>
<div><br></div><div>Some FASTQ files confuse our parser when running with more than one thread. For example, while using load-into-counting.py. If you experience this then add "--threads=1" to your command line. This issue is being tracked in <a href="https://github.com/ged-lab/khmer/issues/249">https://github.com/ged-lab/khmer/issues/249</a></div>
<div><br></div><div>If your hashfile gets truncated, perhaps from a full filesystem, then our tools currently will get stuck. This is being tracked in <a href="https://github.com/ged-lab/khmer/issues/247">https://github.com/ged-lab/khmer/issues/247</a></div>
<div><br></div><div>Paired-end reads from Casava 1.8 currently require renaming for use in normalize-by-median and abund-filter when used in paired mode. The integration of a fix for this is being tracked in <a href="https://github.com/ged-lab/khmer/issues/23">https://github.com/ged-lab/khmer/issues/23</a></div>
<div><br></div><div>A user has reported a floating point exception when running count-overlap.py. There is no workaround at this time. <a href="https://github.com/ged-lab/khmer/issues/282">https://github.com/ged-lab/khmer/issues/282</a></div>
<div><br></div><div>## Contributors</div><div><br></div><div>@camillescott, @mr-c, @ctb, @luizirber, @RamRS, @humberto-ortiz, and @standage</div><div>Special thanks to the new contributors!</div><br clear="all"><div><br>
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-- <br><div dir="ltr"><span style="font-family:'courier new',monospace;font-size:small">Michael R. Crusoe: Programmer & Bioinformatician </span><a href="mailto:mcrusoe@msu.edu" style="color:rgb(17,85,204);font-family:'courier new',monospace;font-size:small" target="_blank">mcrusoe@msu.edu</a><br style="font-family:'courier new',monospace;font-size:small">
<span style="font-family:'courier new',monospace;font-size:small"> @ the Genomics, Evolution, and Development lab; Michigan State U</span><br style="font-family:'courier new',monospace;font-size:small"><a href="http://ged.msu.edu/" style="color:rgb(17,85,204);font-family:'courier new',monospace;font-size:small" target="_blank">http://ged.msu.edu/</a><span style="font-family:'courier new',monospace;font-size:small"> </span><a href="http://orcid.org/0000-0002-2961-9670" style="color:rgb(17,85,204);font-family:'courier new',monospace;font-size:small" target="_blank">http://orcid.org/0000-0002-2961-9670</a><span style="font-family:'courier new',monospace;font-size:small"> </span><a href="http://twitter.com/biocrusoe" style="color:rgb(17,85,204);font-family:'courier new',monospace;font-size:small" target="_blank">@biocrusoe</a><br>
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