bcftools view unnecessarily modifies genotype column with trailing missing values (".")
Nobody has claimed this yet.
Assessment
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Newbie friendliness
- 35/100
Research direction
Start by reproducing the shown record with the bcftools view entry point and compare its input and output genotype columns. Trace how trailing missing values are handled, then verify that view preserves the original genotype fields while still processing the record correctly.
Written by the indexing model from the issue text.
Description
This:
chr1 125179503 . A AT . PASS . GT:GQ:GQX:DPI:AD:ADF:ADR:PL . 1/1:24:60:9:0,9:0,7:0,2:204,27,0 .
gets modified to:
chr1 125179503 . A AT . PASS . GT:GQ:GQX:DPI:AD:ADF:ADR:PL .:.:.:.:.:.:.:. 1/1:24:60:9:0,9:0,7:0,2:204,27,0 .:.:.:.:.:.:.:.
- Dominant language
- C
- Stars
- 950
- Forks
- 475
- Avg merge
- 3d 13h
- Merged PRs (30d)
- 11
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
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- Open a pull request that references the issue number.
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