Dysgu

Minor release
------------------
Fixes for the following issues:

107
90

Minor release
--------------
Addresses the following issues with dysgu filter command:
- Fixes a regression bug which caused `dysgu filter` to drop intra-chromosomal SVs for paired-end reads 100
- Fixes 99 `--keep-all` now works for dysgu filter kdm9
- Fixes a zero division error for long-reads using dysgu filter

====

Minor update adding following features and fixes
- Faster --cohort-update option for dysgu merge
- Returns an empty vcf file (with header) when no events called
- Merged 89 thanks to JMencius checks for sorted input where possible
- Small speed increase

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