feat!: change arriba fusion detection algorithm input parameters

[jarbesfeld]

Closes #203

Notes: This translator includes a variable that tells us if a transcript segment starts or ends at breakpoint, so new logic was added to take this into account.

From Arriba:
direction1 and direction2 : These columns indicate the orientation of the fusion breakpoints. A value of downstream means that the fusion partner is fused downstream of the breakpoint, i.e., at a coordinate higher than the breakpoint.In other words, the supporting split reads are right-clipped. A value of upstream means the partner is fused at a coordinate lower than the breakpoint. In other words, the supporting split reads are left-clipped. When the prediction of the strands or of the 5' gene fails, this information gives insight into which parts of the fused genes are retained in the fusion.

This required the strand variable to be re-added as this indicates the direction of transcription and allows us to choose whether we should choose seg_start_genomic or seg_end_genomic for a breakpoint.

[jarbesfeld]

test_arriba failed for me when this is run:

pydantic_core._pydantic_core.ValidationError: 1 validation error for AssayedFusion
E         Value error, 5' TranscriptSegmentElement fusion partner must contain ending exon position
E       3' fusion partner junction must include starting position [type=value_error, input_value={'structure': [Transcript...ngFramePreserved': True}, input_type=dict]
E           For further information visit https://errors.pydantic.dev/2.4/v/value_error

I think this test should be changed as I don't believe the ending and start positions are needed to validate the fusion

[korikuzma]

I think we should talk about some cleanup work that could be done in the future. There is very similar code for these fusion callers that could be refactored to make maintenance easier