- Option ``methylation --combine`` with which multiple analyses can be combined inside one plot (or text output)
Changed ~~~~~~~
- Speed up ``align`` and ``methylation`` commands - Replace IUPAC-pattern ``HCH`` by ``WCH`` for conversion rate calculation in NOMe-seq analyses
0.99.3
------------------------------
Fixed ~~~~~
- Revert removal of options in ``0.99.1`` and hide them in GUI instead - Update dependency to ``geniegui >=0.100``, which supports hidden options
0.99.2
------------------------------
Changed ~~~~~~~
- Set default dpi for methylation plots to 300
0.99.1
------------------------------
Changed ~~~~~~~
- Rename methylation analysis modes ``cpg, nome, cpg-nome, gcg-nome, wcg-nome`` to ``cg, gch, hcg, gcg, wcg`` with alias ``nome==gch``
Removed ~~~~~~~
- Remove alias options ``--showpositions`` and ``--badcpgs`` - Remove internal option ``--rngseed``
0.99
----------------------------
Added ~~~~~
- NOMe-seq methylation analysis support (via ``methylation --mode nome``) - Parallel execution option (``--parallel`` / ``-j``) for ``align`` and ``methylation`` commands - Option ``--includemode`` for ``methylation`` command allowing to include analysis mode in filenames - Option ``--show`` (taking one or more of ``index | position | c-index``) for ``methylation`` command; supercedes ``--showpositions``
Changed ~~~~~~~
- Speed up computations via using ``numba`` and ``numpy`` - Use all available cores for workers in ``analyze --parallel`` - Store sequence primers in analysis files; reuse them in methylation analysis to detect methylation sites at start / end of ROIs - Preserve order of input reads in analysis files for ``analyze --parallel`` - Replace option ``--badcpgs`` by ``--badmeth``
Deprecated ~~~~~~~~~~
- Make ``--badcpgs`` an alias for ``--badmeth`` and mark it as deprecated - Make ``--showpositions`` an alias for ``--show position`` and mark it as deprecated