CHANGELOG

Author: fellen31

CHANGELOG.md

@@ -8,8 +8,15 @@ Please add a new candidate release at the top after changing the latest one. Fee
 
 Try to use the following format:
 
+## [unreleased]
+### Changed
+- Changed to use PS-tag instead of intervals to check for variants in phase with `genmod models --phased` ([#197](https://github.com/Clinical-Genomics/genmod/pull/197))
+- Refactored the implementation of `check_compounds()` to improve maintainability ([#197](https://github.com/Clinical-Genomics/genmod/pull/197))
+### Fixed
+- KeyError when running `genmod models --phased` with multiple individuals ([#197](https://github.com/Clinical-Genomics/genmod/pull/197))
+
 ## [3.10.2]
-### Fixed 
+### Fixed
 - Add scoring normalisation for flag lookup mode ([#177](https://github.com/Clinical-Genomics/genmod/pull/177))
 - Fix crash on test for missing annotation key for phased mode ([#178](https://github.com/Clinical-Genomics/genmod/pull/178))
 - Bugfixes related to multiprocessing stability and error handling ([#183](https://github.com/Clinical-Genomics/genmod/pull/183) and [#186](https://github.com/Clinical-Genomics/genmod/pull/186))
@@ -33,7 +40,7 @@ Try to use the following format:
 - Fixed sorting of variants ([#152](https://github.com/Clinical-Genomics/genmod/pull/152))
 - genmod annotate for mitochondrial variants when using the `chrM` notation ([#157](https://github.com/Clinical-Genomics/genmod/pull/157))
 - Fix linting issues ([#154](https://github.com/Clinical-Genomics/genmod/issues/154))
-- genmod models adds headers to VCF even if it contains no variants ([#160](https://github.com/Clinical-Genomics/genmod/pull/160)) 
+- genmod models adds headers to VCF even if it contains no variants ([#160](https://github.com/Clinical-Genomics/genmod/pull/160))
 
 ## [3.9]
 - Fixed wrong models when chromosome X was named `chrX` and not `X` ([#135](https://github.com/Clinical-Genomics/genmod/pull/135))

genmod/annotate_models/models/compound_model.py

@@ -37,14 +37,12 @@ def check_compounds(variant_1: dict, variant_2: dict, family, phased: bool) -> b
     Args:
         variant_1, variant_2: Variants in a potential compound pair
         family: A family object with the individuals
-        intervals: A interval tree that describes the phased intervals
         phased: A bool that tells if the individuals are phased
 
     Returns:
         bool: depending on if the pair follow the rules stated above
 
     """
-    # Check in all individuals what genotypes that are in the trio based of the individual picked.
     logger = logging.getLogger(__name__)
     for individual_id, individual in family.individuals.items():
         logger.debug("Check compounds for individual {0}".format(individual_id))