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/.
filter-abund-single.py
script..info
files.examples/python-api
and examples/c++-api
, respectively.extract-compact-dbg.py
for computing a compact
de Bruijn graph from sequence data.load-graph.py
script now calculates required graph space
correctly.broken_paired_reader
no longer drops short reads when
require_paired
is set.-x
and -N
now suppressed by default in
script help messages.IParser
and FastxParser
classes with a single
ReadParser
class. Different input formats are supported by
templating ReadParser
with a reader class.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/1248ctrl-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