khmer v1.0.1 release notes¶
This is bugfix release. Note: the installation instructions have been slightly simplified.
https://khmer.readthedocs.org/en/v1.0.1/
New items of note:¶
This release successfully installs and passes its unit tests on Debian 6.0 "Squeeze", Debian 7.0 "Wheezy", Fedora 19, OS X 7 "Lion", OS X 8 "Mountain Lion", Red Hat Enterprise Linux 6, Scientific Linux 6, Ubuntu 10.04 LTS, and Ubuntu 12.04 LTS. Thanks to the UW-Madison Build and Test Lab for their testing infrastructure.
Notable bugs fixed/issues closed:¶
fixed thread hanging issue #406 @ctb Explicit python2 invocation #404 @mr-c MANIFEST.in,setup.py: fix to correct zlib packaging #365 @mr-c fixed check_space_for_hashtable to use args.n_tables #382 @ctb Bug fix: make-initial-stoptags.py error on missing .ht input file, actual input file is .pt #391 @mr-c
Minor updates¶
include calc-best-assembly.py in v1.0.1 #409 @ctb updated normalize-by-median documentation for loadtable #378 @ctb updated diginorm for new FP rate info; corrected spelling error #398 @ctb Add spellcheck to code review checklist. #397 @ctb
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 https://github.com/dib-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 https://github.com/dib-lab/khmer/issues/249
If your k-mer table (hashfile) gets truncated, perhaps from a full filesystem, then our tools currently will get stuck. This is being tracked in https://github.com/dib-lab/khmer/issues/247 and https://github.com/dib-lab/khmer/issues/246
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 https://github.com/dib-lab/khmer/issues/23
annotate-partitions.py only outputs FASTA even if given a FASTQ file. This issue is being tracked in https://github.com/dib-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 https://github.com/dib-lab/khmer/issues/75
Contributors¶
@mr-c, @ctb, @luizirber, @RamRS, @ctSkennerton