Dysgu

Improvements / changes

- Added ``--symbolic-sv-size`` option to switch between symbolic or sequence representation
- Added parallel processing for merge command
- Added ``--ignore-sample-sites`` option to ignore the input sample when using ``--sites``. This is set at True by default and addresses https://github.com/kcleal/dysgu/issues/37
- Minimum python version now 3.8

Bug fixes

- Fixed https://github.com/kcleal/dysgu/issues/69 https://github.com/kcleal/dysgu/issues/70
- Fixed minor issue resulting in dropping of paired-end INS SVs

Improvements / changes
----------------------
- Added 'auto' option for setting --min-support, this is set as default for long-reads
- Long-reads default mapq lowered to 1
- Improved sensitivity for large-insertions using long-reads
- Small numbers of BND events also now reported for long-reads
- Improved precision due to better SV merging and lower numbers of duplicated true-positive calls
- Coverage values now include reads < mapq threshold
- Around 10 % of insertions are now re-classified as DUP; occurs when split-read support is available

Bug fixes
---------
- Segfault for high coverage sample
- Exponential runtime for very large component in graph

v1.5.0
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- Significantly improved precision for long read SV calling
- Long-reads with poorly mapped ends are now ignored, controlled using `--divergence` option
- Nearby indels on the same read are now merged, controlled the `--length-extend` option
- CLI change: `filter-normal` command has been renamed `filter` and supports more options for filtering
- Improvements in runtime for long-reads

Improvements
---------------
- Better handling of supplementary reads - slight improvement in SV calling across the board, especially complex events and insertions (+1-2% F1 score)
- Improved 'filter-normal' command for long reads (tumor-normal SV calling), plus updated CLI

Fixes
-----
- Avoid over counting supplementary reads
- More error handling/checking

Improvements
---------------

- Added `filter-normal` command for somatic SV filtering.
- Support for Python 3.11 (linux)
- Run/call command added to vcf header

Bug fixes
---------
- Fixed over counting of within-read SVs from same read
- Prevent clustering of same-read events
- Fixed supplementary clustering issue

Minor release with features:
- `dysgu merge` now has a default `--collapse-nearby True` option for better merging of nearby SVs
- added support for building using conda htslib using `python setup.py install --conda-prefix $PREFIX` or setting PREFIX as an environment variable

Bug fix:
- py_call_code error