Dysgu

Bug fixes
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- Fixed zero division error
- 125, missing call when support is low
- Reference base issue causing issues with IGV

Improvements
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- SV phasing is now supported. Supply dysgu with a 'haplotagged' bam file (with HP and PS tags for reads) and dysgu will automatically phase output SVs. This results in a large increase in performance for long reads (see PacBio benchmark here: https://github.com/kcleal/SV_Benchmark_CMRG_GIAB)
- Added AF allele frequency to FORMAT column 117
- New `progressive` merge method when using `dysgu merge` that allows better scaling to large cohorts. This can be set using `--merge-method [ auto | all-vs-all | progressive ]`, default is `auto` 82
- Improvements to merging SVs during calling

Fixes
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- Fixed DUP sequences ending up in REF column 123

This release brings important improvements:

- Much improved sensitivity, especially for long-read data at multi-allelic sites, or clustered SVs on the same haplotype
- Faster runtime
- New preset modes for `pacbio-revio` and `nanopore-r10`

Issues fixed:

- Overriding presets works as expected
- 114, 109

CLI changes:
- `--no-gt` flag has been removed
- `--mode pacbio` and `--mode nanopore` presets have been changed to `--mode pacbio-sequel2` and `--mode nanopore-r9`
- Using run pipeline with long-reads (cram files) now applies compression to the temp bam file `wb3`

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

107
90

Minor release
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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

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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