Fix #76 - revert to output unannotated loci

[dnil]

Description

Fixed

• Fix Different output for repeats with missing info  #76 - revert to allow output of unannotated loci

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
• 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 ...

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 91.18%. Comparing base (24bc966) to head (c17692c).

Additional details and impacted files

@@           Coverage Diff           @@
##             main      #78   +/-   ##
=======================================
  Coverage   91.18%   91.18%           
=======================================
  Files           8        8           
  Lines         397      397           
=======================================
  Hits          362      362           
  Misses         35       35           

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[dnil]

With mildly modified ExHu demo variants.json (from @Stikus in issue #76).

(stranger) ➜  output git:(pass_through_unannotated) ✗ stranger repeats.vcf --repeats-file variants.stranger.json > repeats.stranger.vcf
2024-09-26 10:21:14 MacBook-Pro-4 stranger.cli[88173] INFO Running stranger version 0.9.1
2024-09-26 10:21:14 MacBook-Pro-4 stranger.cli[88173] INFO Parsing repeats file variants.stranger.json
2024-09-26 10:21:14 MacBook-Pro-4 stranger.utils[88173] WARNING Repeat number 1 (SNV_AND_STR) has multiple 'ReferenceRegion' but no 'PathologicRegion'. Skipping..
2024-09-26 10:21:14 MacBook-Pro-4 stranger.utils[88173] WARNING No info for repeat id None
2024-09-26 10:21:14 MacBook-Pro-4 stranger.utils[88173] WARNING No info for repeat id SNV_AND_STR_chr1:2005-2008
(stranger) ➜  output git:(pass_through_unannotated) ✗ cat repeats.stranger.vcf
##fileformat=VCFv4.1
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant">
##INFO=<ID=REF,Number=1,Type=Integer,Description="Reference copy number">
##INFO=<ID=REPID,Number=1,Type=String,Description="Repeat identifier as specified in the variant catalog">
##INFO=<ID=RL,Number=1,Type=Integer,Description="Reference length in bp">
##INFO=<ID=RU,Number=1,Type=String,Description="Repeat unit in the reference orientation">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=VARID,Number=1,Type=String,Description="Variant identifier as specified in the variant catalog">
##FILTER=<ID=LowDepth,Description="The overall locus depth is below 10x or number of reads spanning one or both breakends is below 5">
##FILTER=<ID=PASS,Description="All filters passed">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=ADFL,Number=1,Type=String,Description="Number of flanking reads consistent with the allele">
##FORMAT=<ID=ADIR,Number=1,Type=String,Description="Number of in-repeat reads consistent with the allele">
##FORMAT=<ID=ADSP,Number=1,Type=String,Description="Number of spanning reads consistent with the allele">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=LC,Number=1,Type=Float,Description="Locus coverage">
##FORMAT=<ID=REPCI,Number=1,Type=String,Description="Confidence interval for REPCN">
##FORMAT=<ID=REPCN,Number=1,Type=String,Description="Number of repeat units spanned by the allele">
##FORMAT=<ID=SO,Number=1,Type=String,Description="Type of reads that support the allele; can be SPANNING, FLANKING, or INREPEAT meaning that the reads span, flank, or are fully contained in the repeat">
##ALT=<ID=STR10,Description="Allele comprised of 10 repeat units">
##ALT=<ID=STR2,Description="Allele comprised of 2 repeat units">
##INFO=<ID=STR_STATUS,Number=A,Type=String,Description="Repeat expansion status. Alternatives in [normal, pre_mutation, full_mutation]">
##INFO=<ID=STR_NORMAL_MAX,Number=1,Type=Integer,Description="Max number of repeats allowed to call as normal">
##INFO=<ID=STR_PATHOLOGIC_MIN,Number=1,Type=Integer,Description="Min number of repeats required to call as pathologic">
##INFO=<ID=SourceDisplay,Number=1,Type=String,Description="Source for variant definition, display">
##INFO=<ID=Source,Number=1,Type=String,Description="Source collection for variant definition">
##INFO=<ID=SourceId,Number=1,Type=String,Description="Source id for variant definition">
##INFO=<ID=SweGenMean,Number=1,Type=Float,Description="Average number of repeat unit copies in population">
##INFO=<ID=SweGenStd,Number=1,Type=Float,Description="Standard deviation of number of repeat unit copies in population">
##INFO=<ID=DisplayRU,Number=1,Type=String,Description="Display repeat unit familiar to clinician">
##INFO=<ID=InheritanceMode,Number=1,Type=String,Description="Main mode of inheritance for disorder">
##INFO=<ID=HGNCId,Number=1,Type=Integer,Description="HGNC gene id for associated disease gene">
##INFO=<ID=RankScore,Number=1,Type=String,Description="RankScore for variant in this family as family(str):score(int)">
##INFO=<ID=Disease,Number=1,Type=String,Description="Associated disorder">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	variants
chr1	2001	.	A	T	.	PASS	VARID=SNV_AND_STR_chr1:2000-2001	GT:AD:LC	0/1:47,39:99.648649
chr1	2005	.	C	<STR2>,<STR10>	.	PASS	END=2008;REF=1;RL=3;RU=CAG;VARID=SNV_AND_STR_chr1:2005-2008;REPID=SNV_AND_STR_chr1:2005-2008	GT:SO:REPCN:REPCI:ADSP:ADFL:ADIR:LC	1/2:SPANNING/SPANNING:2/10:2-2/10-10:47/35:5/20:0/0:99.648649