Add parameters for penalty and threshold

[Jakob37]

Description

This addresses two issues in Lund with using Genmod compounds.

1. We use different threshold and score from those hard-coded here.
2. For single cases, we do not want to apply a penalty (i.e. we would use --penalty 0 here).

Close #137

Further discussed with @dnil and @northwestwitch in: https://github.com/Clinical-Genomics/scout/issues/4823

Added

• Optional command line parameter to set threshold and penalty applied in compound scorer.

Changed

-

Fixed

-

How to prepare for test

• [ ] Ssh to relevant server (depending on type of change)
• [ ] Use stage: us
• [ ] Paxa the environment: paxa
• [ ] Install on stage (example for Hasta):

  bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_[TOOL]-t [TOOL] -b [THIS-BRANCH-NAME] -a

How to test

• [ ] Do ...

Expected test outcome

• [ ] Check that ...
• [ ] Take a screenshot and attach or copy/paste the output.

Review

• [ ] Tests executed by
• [ ] "Merge and deploy" approved by Thanks for filling in who performed the code review and the test!

This version is a

• [ ] MAJOR - when you make incompatible API changes
• [x] MINOR - when you add functionality in a backwards compatible manner
• [ ] PATCH - when you make backwards compatible bug fixes or documentation/instructions

Implementation Plan

• [ ] Document in ...
• [ ] Deploy this branch on ...
• [ ] Inform to ...

[Jakob37]

Parameters are tested such that they respond.

First no penalty is applied, yielding score -6 (which matches the RankResult).

Then a penalty of 5 is applied, changing the score to -6.

Finally, the threshold for penalty is lowered below the low scoring compound, thus avoiding the penalty by having a passing compound variant. Score going back to -6.

jakob@laptop:~/src/genmod$ /usr/bin/python3 -m genmod.commands.base compound -p 1 test/3_scored.vcf --penalty 0 | grep Compounds | tail -1 | cut -f8 | sed "s/.*;Compounds=/Compounds=/" | tr ";" "\n" | cat -n
     1  Compounds=SAMPLE_ID:21_46602317_C_G>-11.0
     2  GeneticModels=SAMPLE_ID:AD|AR_comp
     3  ModelScore=SAMPLE_ID:99
     4  RankScore=SAMPLE_ID:-6.0
     5  RankScoreNormalized=SAMPLE_ID:0.3037974683544304
     6  RankScoreMinMax=SAMPLE_ID:-30.0:49.0
     7  RankResult=-12|0|0|1|1|0|3|0|0|0|1
     8  CompoundsNormalized=SAMPLE_ID:21_46602317_C_G>0.620253164556962
jakob@laptop:~/src/genmod$ /usr/bin/python3 -m genmod.commands.base compound -p 1 test/3_scored.vcf --penalty 5 | grep Compounds | tail -1 | cut -f8 | sed "s/.*;Compounds=/Compounds=/" | tr ";" "\n" | cat -n
     1  Compounds=SAMPLE_ID:21_46602317_C_G>-16.0
     2  GeneticModels=SAMPLE_ID:AD|AR_comp
     3  ModelScore=SAMPLE_ID:99
     4  RankScore=SAMPLE_ID:-11.0
     5  RankScoreNormalized=SAMPLE_ID:0.24050632911392406
     6  RankScoreMinMax=SAMPLE_ID:-30.0:49.0
     7  RankResult=-12|0|0|1|1|0|3|0|0|0|1
     8  CompoundsNormalized=SAMPLE_ID:21_46602317_C_G>0.5569620253164558
jakob@laptop:~/src/genmod$ /usr/bin/python3 -m genmod.commands.base compound -p 1 test/3_scored.vcf --penalty 5 --threshold -20 | grep Compounds | tail -1 | cut -f8 | sed "s/.*;Compounds=/Compounds=/" | tr ";" "\n" | cat -n
     1  Compounds=SAMPLE_ID:21_46602317_C_G>-11.0
     2  GeneticModels=SAMPLE_ID:AD|AR_comp
     3  ModelScore=SAMPLE_ID:99
     4  RankScore=SAMPLE_ID:-6.0
     5  RankScoreNormalized=SAMPLE_ID:0.3037974683544304
     6  RankScoreMinMax=SAMPLE_ID:-30.0:49.0
     7  RankResult=-12|0|0|1|1|0|3|0|0|0|1
     8  CompoundsNormalized=SAMPLE_ID:21_46602317_C_G>0.620253164556962

[Jakob37]

Not sure how to turn to with reviewing here. Maybe @dnil , @northwestwitch or @torbjorgen could give this a look?

[Jakob37]

Thanks for the review @torbjorgen !

I don't have merge-access to the repo. Maybe someone else could help me merge this PR?

[Jakob37]

I don't have access to this repo, so I am unable to merge / release.

Not sure who to ask. Could maybe @torbjorgen or @dnil help me out here? With merging or giving me access to the repo so I can do it myself.

[dnil]

I would call this a minor, since it adds functionality in a completely backwards compatible manner. It does not correct a bug per se, but almost. ;)

[Jakob37]

Thanks for the review 🙏