Dysgu

New features
---------------

More options to tune sensitivity using `--sd` (span-distance, used for insertion clustering) and `--search-depth` options
Ability to filter on mapq when using dysgu-filter
`--cohort-update` option for dysgu merge, allowing regenotyped calls to be updated in a cohort file
More efficient merging of large cohorts - option for limiting number of local SV comparisons using dysgu-merge via `--max-comparisons`
Improved somatic filtering
Slightly improved runtime and memory footprint
Support for python 3.12
`--verbose` option for dysgu test
Added `MAPQS` to format line (mapq supplementary-reads)
Added `NMB` to format line (Edit distance, ignoring large gaps and soft-clips)


Bug Fixes
----------
Missing usage of bam file tell when using dysgu-call (improves sensitivity slightly)
Minor clustering bug (improves sensitivity slightly)
81 83

Minor release
==========
- Added option to use a file list for filtering normals using ``dysgu filter input.vcf list_of_normals.txt > output.vcf``
- Bug fix: using ``-o`` option with a ``/`` in file name, and combined with bam file stdin, now works again

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
------
- 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