khmer v2.1 release notes
========================

We are pleased to announce release version 2.1 of khmer! This release
includes several new features, bug fixes, and internal changes.
`CHANGELOG.md <https://github.com/dib-lab/khmer/blob/v2.1/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/.

Items of note
-------------

New features
~~~~~~~~~~~~

-  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.

Bug fixes
~~~~~~~~~

-  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.

Other changes
~~~~~~~~~~~~~

-  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.

Known issues:
-------------

-  ``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.

Contributors
------------

‡@aaliyari, @ctb, ‡@caitsydney, @camillescott, @standage, @kdmurray91,
@ljcohen, @luizirber, @mr-c, ‡@NBKingsley, ‡@ryneches, ‡@rcs333,
‡@satta, ‡@shannonekj, ‡@betatim

‡ Indicates new contributors