[khmer] khmer v1.2 has been released

Michael R. Crusoe mcrusoe at msu.edu
Mon Dec 8 08:46:20 PST 2014 

This is the v1.2 release of khmer: minor new features and bug fixes. The
start of this release cycle coincided with the Mozilla Science Lab Global
Sprint 2014. We honor and thank the 19 new contributors (including four
Michigan State University undergraduates) who volunteered their time to
contribute!

Docs at: https://khmer.readthedocs.org/en/v1.2/
New items of note:

@mr-c <https://github.com/mr-c> and @ctb <https://github.com/ctb> are proud
to announce khmer's code of conduct
http://khmer.readthedocs.org/en/v1.2/dev/CODE_OF_CONDUCT.html #664
<https://github.com/ged-lab/khmer/pull/664>
All scripts list which files have been created during their execution #477
<https://github.com/ged-lab/khmer/issues/477> @bocajnotnef
<https://github.com/bocajnotnef>
All scripts now only output status messages to STDERR instead of STDOUT #626
<https://github.com/ged-lab/khmer/pull/626> @b-wyss
<https://github.com/b-wyss>
docs/ a fairly major re-organization and brand new developer docs @ctb
<https://github.com/ctb> @mr-c <https://github.com/mr-c>
load-into-counting.py: --summary-info: machine readable summary in JSON or
TSV format#649 <https://github.com/ged-lab/khmer/pull/649> @kdmurray91
<https://github.com/kdmurray91>
scripts/extract-partitions.py: added documentation for .dist columns #516
<https://github.com/ged-lab/khmer/pull/516> @chuckpr
<https://github.com/chuckpr>
Makefile: a new target make install-dependencies is useful for developers
#539 <https://github.com/ged-lab/khmer/pull/539> @mr-c
<https://github.com/mr-c>
Sandbox scripts have been cleaned up, or removed (see the
sandbox/README.rst for details)#589
<https://github.com/ged-lab/khmer/pull/589> @ctb <https://github.com/ctb>
Notable bugs fixed/issues closed:

do-partition.py's excessive spawning of threads fixed. #637
<https://github.com/ged-lab/khmer/pull/637> @camillescott
<https://github.com/camillescott>
Fixed unique k-mer count reporting in load-graph, load-into-counting, and
normalize-by-median.#562 <https://github.com/ged-lab/khmer/issues/562> @mr-c
<https://github.com/mr-c>
Clarified and test the requirement for a 64-bit operating system #529
<https://github.com/ged-lab/khmer/issues/529> @Echelon9
<https://github.com/Echelon9>
Removed some of the broken multi-threading options #511
<https://github.com/ged-lab/khmer/pull/511> @majoras-masque
<https://github.com/majoras-masque>
Fix table.get("wrong_length_string") gives core dump #585
<https://github.com/ged-lab/khmer/pull/585> @Echelon9
<https://github.com/Echelon9>
filter-abund lists parameters that it doesn't use #524
<https://github.com/ged-lab/khmer/issues/524> @jstapleton
<https://github.com/jstapleton>
Reduction of memory required to run the test suite #542
<https://github.com/ged-lab/khmer/pull/542> @leogargu
<https://github.com/leogargu>
BibTeX included in CITATIONS #541
<https://github.com/ged-lab/khmer/pull/541> @HLWiencko
<https://github.com/HLWiencko>
Additional fixes/features

delete ScoringMatrix::assign as it is unused #502
<https://github.com/ged-lab/khmer/issues/502> @RodPic
<https://github.com/RodPic>
Root all of our C++ exceptions to a common base exception #508
<https://github.com/ged-lab/khmer/issues/508> @iglpdc
<https://github.com/iglpdc>
deleted KhmerError #503 <https://github.com/ged-lab/khmer/issues/503>
@drlabratory <https://github.com/drlabratory>
normalize-by-median reporting output after main loop exits, in case it
hadn't been triggered #586 <https://github.com/ged-lab/khmer/pull/586>@ctb
<https://github.com/ctb>
Many issues discovered by cppcheck cleaned up #506
<https://github.com/ged-lab/khmer/issues/506> @brtaylor92
<https://github.com/brtaylor92>
Developers have a new Makefile target to autofix formatting: make format
#612 <https://github.com/ged-lab/khmer/pull/612> @brtaylor92
<https://github.com/brtaylor92>
normalize-by-median.py test coverage increased #361
<https://github.com/ged-lab/khmer/issues/361> @SherineAwad
<https://github.com/SherineAwad>
Several unused functions were removed #599
<https://github.com/ged-lab/khmer/issues/599> @brtaylor92
<https://github.com/brtaylor92>
Developer docs now link to the stdc++ docs as appropriate #629
<https://github.com/ged-lab/khmer/pull/629> @mr-c <https://github.com/mr-c>
Added tests for non-sequential access to input files #644
<https://github.com/ged-lab/khmer/pull/644> @bocajnotnef
<https://github.com/bocajnotnef>
Removed khmer/theading_args.py #653
<https://github.com/ged-lab/khmer/pull/653> @bocajnotnef
<https://github.com/bocajnotnef>
Improved test for maximum k value #658
<https://github.com/ged-lab/khmer/issues/658> @pgarland
<https://github.com/pgarland>
ReadParser no longer crashes if n_threads = 0 #86
<https://github.com/ged-lab/khmer/issues/86> @jiarong
<https://github.com/jiarong>
Known issues:

All of these are pre-existing.

Some users have reported that normalize-by-median.py will utilize more
memory than it was configured for. This is being investigated in
#266 <https://github.com/ged-lab/khmer/issues/266>

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
#249 <https://github.com/ged-lab/khmer/issues/249>

If your k-mer table is truncated on write, an error may not be reported;
this
is being tracked in #443 <https://github.com/ged-lab/khmer/issues/443>.
However, khmer will now (correctly) fail when trying to read a truncated
file
(See #333 <https://github.com/ged-lab/khmer/pull/333>).

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 #23
<https://github.com/ged-lab/khmer/issues/23>

Some scripts only output FASTA even if given a FASTQ file. This issue
is being tracked in #46 <https://github.com/ged-lab/khmer/issues/46>

A user reported that abundance-dist-single.py fails with small files and
many
threads. This issue is being tracked in #75
<https://github.com/ged-lab/khmer/issues/75>
Contributors

@mr-c <https://github.com/mr-c>, @ctb <https://github.com/ctb>, *
@bocajnotnef <https://github.com/bocajnotnef>, *@Echelon9
<https://github.com/Echelon9>, *@jlippi <https://github.com/jlippi>, *
@kdmurray91 <https://github.com/kdmurray91>, @qingpeng
<https://github.com/qingpeng>, *@leogargu <https://github.com/leogargu>, *
@jiarong <https://github.com/jiarong>, *@brtaylor92
<https://github.com/brtaylor92>, *@iglpdc <https://github.com/iglpdc>,
@camillescott <https://github.com/camillescott>, *@HLWiencko
<https://github.com/HLWiencko>, *@cowguru2000
<https://github.com/cowguru2000>, *@drlabratory
<https://github.com/drlabratory>, *@jstapleton
<https://github.com/jstapleton>, *@b-wyss <https://github.com/b-wyss>, *
@jgluck <https://github.com/jgluck>, @fishjord <https://github.com/fishjord>,
*@SherineAwad <https://github.com/SherineAwad>, *@pgarland
<https://github.com/pgarland>, *@majoras-masque
<https://github.com/majoras-masque>, @chuckpr <https://github.com/chuckpr>,
*@RodPic <https://github.com/RodPic>, @luizirber
<https://github.com/luizirber>, *@jrherr <https://github.com/jrherr>

* Denotes new contributor


-- 
Michael R. Crusoe:  Programmer & Bioinformatician   mcrusoe at msu.edu
 @ the Genomics, Evolution, and Development lab; Michigan State U
https://impactstory.org/MichaelRCrusoe http://twitter.com/biocrusoe
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