khmer v1.4 release notes¶
This is the v1.4 release of khmer featuring the results of our March coding sprint; the use of the new v0.8 release of screed (the library we use for pure Python reading of nucleotide sequence files); and the addition of @luizirber's HyperLogLog counter for quick cardinality estimation.
Documentation is at https://khmer.readthedocs.org/en/v1.4/
New items of note:¶
Casava 1.8 read naming is now fully supported and in general the scripts
no longer mangle read names. Side benefits: split-paired-reads.py
will no longer drop reads with 'bad' names; count-median.py can
generate output in CSV format. #759 #818 @ctb
Most scripts now support a "broken" interleaved paired-read format for
FASTA/FASTQ nucleotide sequence files.
`trim-low-abund.py <http://khmer.readthedocs.org/en/v1.4/user/scripts.html#trim-low-abund-py>`__
has been promoted from the sandbox as well. #759 @ctb
The script to transform an interleaved paired-read nucleotide sequence file into two now allows one to name the output files which can be useful in combination with named pipes for streaming processing #762 @ctb
Streaming everywhere: thanks to screed v0.8 we now support streaming of almost all inputs and outputs. #830 @aditi9783 #812 @mr-c
Need a quick way to count total number of unique k-mers in very low
memory? the unique-kmers.py in the sandbox uses a HyperLogLog
counter to quickly (and with little memory) provide an estimate with a
controllable error rate. #257 #738 #895 #902 @luizirber
Notable bugs fixed/issues closed:¶
Paired-end reads from Casava 1.8 no longer require renaming for use in normalize-by-median and abund-filter when used in paired mode #818 @ctb
Python version support clarified. We do not (yet) support Python 3.x #741 @mr-c
If a single output file mode is chosen for normalize-by-median.py we now default to overwriting the output. Appending the output is available by using the append redirection operator from the shell. #843 @drtamermansour
Scripts that consume sequence data using C++ will now properly throw an error on truncated files. #897 @kdmurray91
Additional fixes/features¶
Of interest to users:¶
Misc documentation updates #782 @bocajnotnef, #845 @alameldin, #804 @ctb, #870 @SchwarzEM
The example script for the STAMPS database has been fixed to run correctly #781 @drtamermansour
split-paired-reads.py: added -o option to allow specification of an output directory #752 @bede
Fixed a string formatting glitch in sample-reads-randomly.py #773
@qingpeng
CSV output also added to abundance-dist.py,
abundance-dist-single.py, and count-overlap.py #831 #854 #855
@drtamermansour
interleave-reads.py now prints the output filename nicely #827 @kdmurray91
Cleaned up error for input file not existing #772 @jessicamizzi #851 @ctb
Fixed error in find-knots.py #860 @TheOneHyer
The help text for load-into-counting.py for the
--no-bigcounts/-b flag has been clarified #857 @kdmurray91
Of interest to developers:¶
Switched away from using --user install for developers #740 @mr-c
@drtamermansour & #883 @standage
Developers can now see a summary of important Makefile targets via
make help #783 @standage
The unused khmer.load_pe module has been removed #828 @kdmurray91
Versioneer bug due to new screed release was squashed #835 @mr-c
A Python 2.6 and 2.7.2 specific bug was worked around #869 @kdmurray91 @ctb
added functions hash_find_all_tags_list and hash_get_tags_and_positions to CountingHash objects #749 #765 @ctb
The make diff-cover and ChangeLog formatting requirements have been
added to checklist #766 @mr-c
A useful message is now presented if large tables fail to allocate enough memory #704 @mr-c
A checklist for developers adding new CPython types was added #727 @mr-c
Specific policies for sandbox/ and scripts/ content, and a process for adding new command line scripts into scripts/ have been added to the developer documentation #799 @ctb
Sandbox scripts update: corrected #! Python invocation #815 @Echelon9, executable bits, copyright headers, no underscores in filenames #823 #826 #850 @alameldin several scripts deleted, docs + requirements updated #852 @ctb
Avoid running big-memory tests on OS X #819 @ctb
Unused callback code was removed #698 @mr-c
The CPython code was updated to use the new checklist and follow additional best practices #785 #842 @luizirber
Added a read-only view of the raw counting tables #671 @camillescott #869 @kdmurray91
Added a Python method for quickly getting the number of underlying tables in a counting or presence table #879 #880 @kdmurray91
The C++ library can now be built separately for the brave and curious developer #788 @kdmurray91
The ReadParser object now keeps track of the number of reads processed #877 @kdmurray91
Documentation is now reproducible #886 @mr-c
Python future proofing: specify floor division #863 @mr-c
Miscellaneous spelling fixes; thanks codespell! #867 @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
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).
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, @b-wyss, @wrightmhw, @jsspencer
Issue reporters¶
@moorepants, @teshomem, @macmanes, @lexnederbragt, @r-gaia-cs