Ont-spectre

Fixed
- Remove extra character in hg19 metadata file

Added
- System tests of hg002 real variation with hg19 reference

Changed
- This is a housekeeping release to update the ont-spectre conda package requirements.

Added
- Karyotype detection for XXX and XYY
- Output karyotype to .vcf file
- Numpy >= 2 support
- Ont-spectre description to README
- Blacklists v1 and metadata for hg19/hg38/chm13 in package resources

Fixed
- Installation from source instructions
- threshold_quantile parameter name typo

Removed
- Plotting charts per every chromosome

Added
- System tests based on single chromosome subsample

Changed
- Match default parameters with wf-human-variation
- Copy CN from INFO field to sample column in vcf output
- Metadata and blacklist can be parsed from package resources
- Metadata and blacklist duplicated with omitting "chr" from chromosome names

Fixed
- Missing dependencies
- Parsing mosdepth with number/string chromosome names

Changed
- Forked from upstread spectre project.
- Reworked package to be packaged.