khmer v1.1 release notes¶
This is v1.1, a minor version release; this version adds several new scripts.
Docs at: https://khmer.readthedocs.org/en/v1.1/
Release notes w/links: https://github.com/ged-lab/khmer/releases/tag/v1.1
New items of note:¶
- removed unnecessary files from PyPI package; distribution is now under 2 MB (#419) @mr-c
- tests are now distributed with package and can be run after 'pip install' (#451) @mr-c
- complain properly on file read failures (#333) @ctb
- Sequence loading scripts will now report total numbers of k-mers if given --report_total_kmers (#491/#429) @mr-c
- added metagenome protocol to acceptance testing (#472) @SherineAwad @ctb
Notable bugs fixed/issues closed:¶
- removed sandbox/load-into-hashbits.py (superseded by scripts/load-graph.py --no-tagset) (#480, @wrightmhw)
- promoted extract-long-sequences.py to scripts (#461, @wrightmhw)
- promoted fastq-to-fasta.py to scripts (#436, @wrightmhw)
- remove incorrect filesystem space check from abundance-dist.py (#452, @chuckpr)
- when counting hash writes fail, produce error message (#411, @znruss)
- removed a number of memory leaks found by Coverity and valgrind (#451, @mr-c)
- updated reservoir sampling to produce multiple subsamples with -S (#197, @ctb)
- fixed pip2, python2 issues (#428 and #485, @accaldwell @mr-c)
- removed untested/unused code and scripts (#438, @mr-c)
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/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 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 https://github.com/ged-lab/khmer/issues/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 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 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 https://github.com/ged-lab/khmer/issues/75
Contributors¶
@mr-c, @ctb, @camillescott, @wrightmhw, @chuckpr, @luizirber, @accaldwell, @znruss