We are pleased to announce release version 2.1 of khmer! This release includes several new features, bug fixes, and internal changes. CHANGELOG.md includes a complete description of changes made since the previous release. A concise summary of the most relevant changes is provided below.
The latest version of the khmer documentation is available at https://khmer.readthedocs.org/en/v2.1/.
New storage class using half a byte per entry. Exposed as SmallCounttable and SmallCountgraph.
New Counttable, SmallCounttable, and Nodetable classes to support non-reversible hashing functionality and k > 32.
Support for human-friendly memory requests (2G) in addition to the previous style of requests (2000000000 or 2e9).
Support for variable-coverage trimming in the
filter-abund-single.py
script.
khmer package version now included in .info
files.
Several simple examples of the Python API and the C++ API in
examples/python-api
and examples/c++-api
, respectively.
Support for assembling directly from k-mer graphs, and a new JunctionCountAssembler class.
New sandbox script extract-compact-dbg.py
for computing a compact
de Bruijn graph from sequence data.
Streaming gzip-compressed output from scripts now works correctly.
The load-graph.py
script now calculates required graph space
correctly.
The broken_paired_reader
no longer drops short reads when
require_paired
is set.
Command-line options -x
and -N
now suppressed by default in
script help messages.
Renamed core data structures: CountingHash –> Countgraph, Hashbits –> Nodegraph.
Replaced the IParser
and FastxParser
classes with a single
ReadParser
class. Different input formats are supported by
templating ReadParser
with a reader class.
Renamed consume_fasta
and related functions to
consume_seqfile
, with support for reading sequences from
additional formats pending.
load-graph.py
in multithreaded mode will find slightly different
number of unique kmers. This is being investigated in
https://github.com/dib-lab/khmer/issues/1248
Any scripts that consume FASTA or FASTQ data are unresponsive to
attempts to terminate the program with ctrl-c
. Eventually khmer
should handle this properly, but for now it should be possible to
halt a script using ctrl-\
. This is being tracked in
https://github.com/dib-lab/khmer/issues/1618.
‡@aaliyari, @ctb, ‡@caitsydney, @camillescott, @standage, @kdmurray91, @ljcohen, @luizirber, @mr-c, ‡@NBKingsley, ‡@ryneches, ‡@rcs333, ‡@satta, ‡@shannonekj, ‡@betatim
‡ Indicates new contributors