NSCCN/varlociraptor：基于概率模型的变异检测工具，用于体细胞或胚系变异调用与置信度评估。

fix: correct borders for vaf splitting (#545)

Description

This PR fixes the splitting logic for VAFRanges.

Previously, when an interval was split at a specific VAF value, the interval boundaries were not computed correctly if the split position is exactly equal to one of the existing borders.

The fix ensures that boundary conditions are handled properly when the split point lies exactly on an interval border.

QC

The PR contains a test case for the changes or the changes are already covered by an existing test case.
The documentation at https://github.com/varlociraptor/varlociraptor.github.io is updated in a separate PR to reflect the changes or this is not necessary (e.g. if the change does neither modify the calling grammar nor the behavior or functionalities of Varlociraptor).

Summary by CodeRabbit

Bug Fixes
Enhanced range boundary handling during split operations to correctly propagate exclusivity when splitting at specific boundary values. Updated singleton condition determination to be properly based on the actual updated range boundaries instead of the original range boundaries, thereby improving the overall accuracy of range calculations, especially in complex boundary scenarios.

Varlociraptor

Varlociraptor implements a novel, unified fully uncertainty-aware approach to genomic variant calling in arbitrary scenarios.

Key features

Calls SNVs, MNVs, indels, inversions, duplications, replacements and breakends in all length ranges (from small to structural) with a unified statistical model.

The statistical model encompasses all possible sources of uncertainty and biases.

Resulting variant calls can be filtered by false discovery rate. No parameter tuning necessary.

Unbiased, maximum a posteriori allele frequency estimates are provided with each call.

Calling modes

Generic, grammar based configuration of the statistical model, allowing to classify arbitrary scenarios, from population genetics, to pedigrees, complex tumor scenarios and arbitrary combinations thereof.

Tumor-normal-calling, classifying variants as somatic in tumor, somatic in normal, germline, or absent.

GitHub Workflow Status

Calls SNVs, MNVs, indels, inversions, duplications, replacements and breakends in all length ranges (from small to structural) with a unified statistical model.
The statistical model encompasses all possible sources of uncertainty and biases.
Resulting variant calls can be filtered by false discovery rate. No parameter tuning necessary.
Unbiased, maximum a posteriori allele frequency estimates are provided with each call.

Generic, grammar based configuration of the statistical model, allowing to classify arbitrary scenarios, from population genetics, to pedigrees, complex tumor scenarios and arbitrary combinations thereof.
Tumor-normal-calling, classifying variants as somatic in tumor, somatic in normal, germline, or absent.

For details, see the homepage: https://varlociraptor.github.io