Readme clarifications, minor bug fixes #37
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Contributor
ebattistella
commented
Oct 3, 2025
ebattistella
commented
- Clarification order of length_ranges for dispersion.
- InsilicoSV version will now be written in the output VCF.
- documentation on min_intersv_dist
- clarification of contained overlap
- clarification of blacklist regions
- fix stats code that was failing when running insilicosv from inside the folder of the config file.
- fix edge case of SV placement with blacklist regions when looking to available regions after random assignment failed.
Clarification order of length_ranges for dispersion fix stats code
* documenation on min_intersv_dist
* clarification of conatined overlap
* source=InsilicoSV_v{version will now be written in the output VCF header
* clarification of blacklist regions
ebattistella
changed the title
viq854
reviewed
Oct 3, 2025
| * If blacklist_regions is provided in BED format, an optional fourth column (type) can be used to categorize | ||
| regions and filter them per variant set. | ||
| * If blacklist_regions is provided in VCF format, the REGION_TYPE INFO field can be used instead. | ||
| If this field is missing, the default region type will be DEFAULT. Only the CHROM, POS, and END fields are considered from each record. |
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is DEFAULT different from "all"?
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If two blacklist files are provided and one has a region_type field, then DEFAULT regions will only be the regions from the file without a region_type field.
…g to report non novel adjacencies
END = START + LENGTH - 1 TARGET is before the insertion
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