Version 1.2
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 and @ctb are proud to announce khmer's code of conduct http://khmer.readthedocs.org/en/v1.2/dev/CODE_OF_CONDUCT.html #664
All scripts list which files have been created during their execution #477 @bocajnotnef
All scripts now only output status messages to STDERR instead of STDOUT #626 @b-wyss
docs/ a fairly major re-organization and brand new developer docs @ctb @mr-c
load-into-counting.py: --summary-info: machine readable summary in JSON or TSV format #649 @kdmurray91
scripts/extract-partitions.py: added documentation for .dist columns #516 @chuckpr
Makefile: a new target make install-dependencies is useful for developers #539 @mr-c
Sandbox scripts have been cleaned up, or removed (see the sandbox/README.rst for details) #589 @ctb
Notable bugs fixed/issues closed:
do-partition.py's excessive spawning of threads fixed. #637 @camillescott
Fixed unique k-mer count reporting in load-graph, load-into-counting, and normalize-by-median. #562 @mr-c
Clarified and test the requirement for a 64-bit operating system #529 @Echelon9
Removed some of the broken multi-threading options #511 @majoras-masque
Fix table.get("wrong_length_string") gives core dump #585 @Echelon9
filter-abund lists parameters that it doesn't use #524 @jstapleton
Reduction of memory required to run the test suite #542 @leogargu
BibTeX included in CITATIONS #541 @HLWiencko
Additional fixes/features
delete ScoringMatrix::assign as it is unused #502 @RodPic
Root all of our C++ exceptions to a common base exception #508 @iglpdc
deleted KhmerError #503 @drlabratory
normalize-by-median reporting output after main loop exits, in case it hadn't been triggered #586 @ctb
Many issues discovered by cppcheck cleaned up #506 @brtaylor92
Developers have a new Makefile target to autofix formatting: make format #612 @brtaylor92
normalize-by-median.py test coverage increased #361 @SherineAwad
Several unused functions were removed #599 @brtaylor92
Developer docs now link to the stdc++ docs as appropriate #629 @mr-c
Added tests for non-sequential access to input files #644 @bocajnotnef
Removed khmer/theading_args.py #653 @bocajnotnef
Improved test for maximum k value #658 @pgarland
ReadParser no longer crashes if n_threads = 0 #86 @jiarong
Known issues:
All of these are pre-existing.
Multithreaded reading will drop reads. This major issue has been present for several khmer releases and was only found via a much larger test case that we had been previously using. Credit to @camillescott. Workaround: disable threading. The next release will fix this and the other FAST[AQ] parsing issues. #681
Some users have reported that normalize-by-median.py will utilize more memory than it was configured for. This is being investigated in #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
If your k-mer table is truncated on write, an error may not be reported; this is being tracked in #443. However, khmer will now (correctly) fail when trying to read a truncated file (See #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
Some scripts only output FASTA even if given a FASTQ file. This issue is being tracked in #46
A user reported that abundance-dist-single.py fails with small files and many threads. This issue is being tracked in #75
Contributors
@mr-c, @ctb, *@bocajnotnef, *@Echelon9, *@jlippi, *@kdmurray91, @qingpeng, *@leogargu, *@jiarong, *@brtaylor92, *@iglpdc, @camillescott, *@HLWiencko, *@cowguru2000, *@drlabratory, *@jstapleton, *@b-wyss, *@jgluck, @fishjord, *@SherineAwad, *@pgarland, *@majoras-masque, @chuckpr, *@RodPic, @luizirber, *@jrherr
* Denotes new contributor