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fix: cnvpytor header float #1182

Merged
merged 7 commits into from
Sep 19, 2023
Merged

fix: cnvpytor header float #1182

merged 7 commits into from
Sep 19, 2023

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mathiasbio
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@mathiasbio mathiasbio commented Jun 21, 2023 •
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This PR:

Attempts to fix issues:

With the solution described here:

Added:

  • sed command to cnvpytor rule to convert CN description in header from integer to float.

Tests:

WGS tumor only cases previously failed with: [E::vcf_parse_format] Invalid character '.' in 'CN' FORMAT in bcftools_quality_filter_svdb.

petmantis: previously had this error, now this error should not appear. Case has variant with float CN at:

21	16700001	CNVpytor_dup20	.	<DUP>	.	PASS	END=44200000;IMPRECISE;SVLEN=27500000;SVTYPE=DUP;pytorRD=2.2524309640529316;pytorP1=0.0;pytorP2=0.0;pytorP3=0.0;pytorP4=0.0;pytorQ0=0.0015552215961759483;pytorPN=0.0018927272727272727;pytorDG=0.0;pytorCL=rd_mean_shift	GT:CN	./1:2.25
  • CN with float value exists
  • Analysis finishes successfully

awareraptor: as described in issue (#1157) has variant with float CN at:

21      22900001        CNVpytor_dup22  .       <DUP>   .       PASS    END=44200000;IMPRECISE;SVLEN=21300000;SVTYPE=DUP;pytorRD=3.70678765025364;pytorP1=0.0;pytorP2=0.0;pytorP3=0.0;pytorP4=0.0;pytorQ0=0.0011310821079172444;pytorPN=0.002443661971830986;pytorDG=0.0;pytorCL=rd_mean_shift;set=cnvpytor;FOUNDBY=1;cnvpytor_CHROM=CNVpytor_dup22|21;cnvpytor_POS=CNVpytor_dup22|22900001;cnvpytor_QUAL=CNVpytor_dup22|.;cnvpytor_FILTERS=CNVpytor_dup22|PASS;cnvpytor_SAMPLE=CNVpytor_dup22|TUMOR|GT:./1|CN:3.71;cnvpytor_INFO=CNVpytor_dup22|END:44200000|IMPRECISE|SVLEN:21300000|SVTYPE:DUP|pytorRD:3.70678765025364|pytorP1:0.0|pytorP2:0.0|pytorP3:0.0|pytorP4:0.0|pytorQ0:0.0011310821079172444|pytorPN:0.002443661971830986|pytorDG:0.0|pytorCL:rd_mean_shift;svdb_origin=cnvpytor;SUPP_VEC=10000     GT:CN   ./1:3.71
  • CN with float value exists
  • Analysis finishes successfully

Other integrity tests:

  • SV variants uploaded to Scout are unaffected by float header change
  • SV variants can still be uploaded as usual to LoqusDB

Review and tests:

  • Tests pass
  • Code review
  • New code is executed and covered by tests, and test approve

@sonarqubecloud
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Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 2 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication

@mathiasbio mathiasbio mentioned this pull request Jun 21, 2023
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codecov bot commented Jun 21, 2023 •
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Codecov Report

Patch coverage is 100.00% of modified lines.

Files Changed Coverage
BALSAMIC/constants/metrics.py ø
BALSAMIC/utils/scheduler.py ø
BALSAMIC/commands/base.py 100.00%
BALSAMIC/commands/config/base.py 100.00%
BALSAMIC/commands/config/case.py 100.00%
BALSAMIC/commands/config/pon.py 100.00%
BALSAMIC/commands/init/base.py 100.00%
BALSAMIC/commands/options.py 100.00%
BALSAMIC/commands/report/base.py 100.00%
BALSAMIC/commands/report/deliver.py 100.00%
... and 18 more

📢 Thoughts on this report? Let us know!.

@mathiasbio mathiasbio changed the base branch from master to develop June 21, 2023 08:06
@mathiasbio mathiasbio marked this pull request as ready for review September 12, 2023 15:30
@mathiasbio mathiasbio requested a review from a team as a code owner September 12, 2023 15:30
@mathiasbio mathiasbio linked an issue Sep 14, 2023 that may be closed by this pull request
fix cnvpytor CN integer-float conflict #1183
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ivadym
ivadym approved these changes Sep 14, 2023
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Well done 🧁

@sonarqubecloud
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Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
No Duplication information No Duplication information

@mathiasbio mathiasbio merged commit 9e5ad3c into develop Sep 19, 2023
@mathiasbio mathiasbio deleted the fix_cnvpytor_float branch September 19, 2023 13:16
@pbiology pbiology mentioned this pull request Nov 1, 2023
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@mathiasbio mathiasbio mentioned this pull request Nov 2, 2023
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mathiasbio added a commit that referenced this pull request Nov 4, 2023
@mathiasbio
fix: rename samplename in final vcf header (#1310)
66b049e 
This PR aims to change the name of the sample columns in the final VCFs to match the changes in the scout_load.yaml for sample-id, which will use LIMS-ID instead of TUMOR/NORMAL. (Clinical-Genomics/cg#2650)

Added:
- New rule to create namemap to translate sample type names in vcf header to sampleID

Changed:
- Renamed names of sample columns in final vcf (clinical.pass.vcf.gz) to sampleID

Removed:
- Removed sed command in CNVpytor rule introduced here (fix: cnvpytor header float #1182) as it has been fixed by updating CNVpytor and is no longer necessary ([ Failed Analysis ] CNVpytor float values not accepted by bcftools #1152)
@ivadym ivadym mentioned this pull request Nov 6, 2023
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fix cnvpytor CN integer-float conflict
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@mathiasbio @ivadym