Fix #73 - out format for multiindividuals decompose

[dnil]

Description

Fixed

• Fix Annotate multi-sample VCF #73 - output FORMAT incorrect for multiple individuals after (TRGT) decompose

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

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Expected test outcome

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Review

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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

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[dnil]

Before:

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG002_Revio_A_haplotagged	HG002_Revio_B_haplotagged
chr20	2652734	.	GGCCTGGGCCTGGGCCTGGGCCTGC	AGCCTGGGCCTGGGCCTGG	0	.	TRID=NOP56;END=2652775;MOTIFS=GGCCTG,CGCCTG;STRUC=(GGCCTG)n(CGCCTG)n;STR_STATUS=normal,normal;STR_NORMAL_MAX=14;STR_PATHOLOGIC_MIN=650;RankScore=1:10;HGNCId=15911;InheritanceMode=AD;DisplayRU=GGCCTG;SourceDisplay=GeneReviews Internet 2014-08-07;Source=GeneReviews;SourceId=NBK231880;Disease=SCA36	GT:AL:ALLR:SD:MC:MS:AP:AM	1/.:36:36-36:12:4_2:0(0-24)_1(24-36):0.972222:691/.:36:36-36:12:4_2:0(0-24)_1(24-36):0.972222:69:1/.:36:36-36:24:4_2:0(0-24)_1(24-36):0.972222:69
chr20	2652734	.	GGCCTGGGCCTGGGCCTGGGCCTGC	AGCCTGGGCCTGGGCCTGGGCCTGGGCCTGGGCCTGG	0	.	TRID=NOP56;END=2652775;MOTIFS=GGCCTG,CGCCTG;STRUC=(GGCCTG)n(CGCCTG)n;STR_STATUS=normal,normal;STR_NORMAL_MAX=14;STR_PATHOLOGIC_MIN=650;RankScore=1:10;HGNCId=15911;InheritanceMode=AD;DisplayRU=GGCCTG;SourceDisplay=GeneReviews Internet 2014-08-07;Source=GeneReviews;SourceId=NBK231880;Disease=SCA36	GT:AL:ALLR:SD:MC:MS:AP:AM	./1:54:52-54:18:7_2:0(0-42)_1(42-54):0.981481:118	./1:54:52-54:18:7_2:0(0-42)_1(42-54):0.981481:118:./1:54:52-54:36:7_2:0(0-42)_1(42-54):0.981481:118

After:

#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG002_Revio_A_haplotagged	HG002_Revio_B_haplotagged
chr20	2652734	.	GGCCTGGGCCTGGGCCTGGGCCTGC	AGCCTGGGCCTGGGCCTGG	0	.	TRID=NOP56;END=2652775;MOTIFS=GGCCTG,CGCCTG;STRUC=(GGCCTG)n(CGCCTG)n;STR_STATUS=normal,normal;STR_NORMAL_MAX=14;STR_PATHOLOGIC_MIN=650;RankScore=1:10;HGNCId=15911;InheritanceMode=AD;DisplayRU=GGCCTG;SourceDisplay=GeneReviews Internet 2014-08-07;Source=GeneReviews;SourceId=NBK231880;Disease=SCA36	GT:AL:ALLR:SD:MC:MS:AP:AM	1/.:36:36-36:12:4_2:0(0-24)_1(24-36):0.972222:691/.:36:36-36:24:4_2:0(0-24)_1(24-36):0.972222:69
chr20	2652734	.	GGCCTGGGCCTGGGCCTGGGCCTGC	AGCCTGGGCCTGGGCCTGGGCCTGGGCCTGGGCCTGG	0	.	TRID=NOP56;END=2652775;MOTIFS=GGCCTG,CGCCTG;STRUC=(GGCCTG)n(CGCCTG)n;STR_STATUS=normal,normal;STR_NORMAL_MAX=14;STR_PATHOLOGIC_MIN=650;RankScore=1:10;HGNCId=15911;InheritanceMode=AD;DisplayRU=GGCCTG;SourceDisplay=GeneReviews Internet 2014-08-07;Source=GeneReviews;SourceId=NBK231880;Disease=SCA36	GT:AL:ALLR:SD:MC:MS:AP:AM	./1:54:52-54:18:7_2:0(0-42)_1(42-54):0.981481:118	./1:54:52-54:36:7_2:0(0-42)_1(42-54):0.981481:118

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 91.18%. Comparing base (a7fcd76) to head (c80fe29).

Additional details and impacted files

@@           Coverage Diff           @@
##             main      #77   +/-   ##
=======================================
  Coverage   91.18%   91.18%           
=======================================
  Files           8        8           
  Lines         397      397           
=======================================
  Hits          362      362           
  Misses         35       35           

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