Add support for inverting phase of genotypes with setGT plugin #2367
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pd3
reviewed
Feb 24, 2025
plugins/setGT.c
Outdated
| @@ -113,6 +114,7 @@ const char *usage(void) | |||
| " X .. allele with bigger read depth as determined from FMT/AD\n" | |||
| " p .. phase genotype (0/1 becomes 0|1)\n" | |||
| " u .. unphase genotype and sort by allele (1|0 becomes 0/1)\n" | |||
| " i .. inverse phase of genotype (0|1 becomes 1|0)\n" | |||
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I am not a native speaker, but I think a better description would be "invert the genotype phase"
pd3
reviewed
Feb 24, 2025
plugins/setGT.c
Outdated
| @@ -364,6 +367,21 @@ static inline int unphase_gt(int32_t *ptr, int ngts) | |||
| return changed; | |||
| } | |||
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| // inverse phase for a single sample, ngts is the ploidy | |||
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invert, not inverse, here and everywhere..
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Thank you for the pull request. Please add a test, see |
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@pd3 thank you for your response, I fixed the language and added a test case. Best regards, |
pd3
approved these changes
Mar 5, 2025
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Thank you |
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Hello,
I added an option to invert the phase of diploid genotypes in the setGT plugin.
So
0|1becomes1|0.This is useful when one wants to invert the whole phase of a file, or selected samples, or based on a filter.
The function only inverts the phase of diploid genotypes (checks
ngt==2and ifbcf_int32_vector_endis present).Phase flag is set correctly per BCF specs. Note unphased genotypes are also swapped so
0/1becomes1/0.I hope we can get this merged, let me know if there are any changes you would like me to make.
Best regards,
Rick