Duplicate Sample IDs in VCF aborts

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
38/100
Issue type
Bug
Clarity
Mostly clear
Activity status
Stale
Tech stack
c
Domain
data

Research direction

Start by reproducing the crash with the duplicated-sampleid VCF in ga4gh/server/tests/faultydata/variants/duplicated_sampleid. Read the behavior described in ga4gh/server issue 521 and trace the htslib VCF parsing path involved. Done means the offending VCF no longer causes htslib to abort, with the resulting behavior checked against that report.

Written by the indexing model from the issue text.

Description

(via pysam) A VCF that has repeated sample names causes htslib to crash. An offending VCF can be found here: https://github.com/ga4gh/server/tree/master/tests/faultydata/variants/duplicated_sampleid .

As described here: https://github.com/ga4gh/server/issues/521

Dominant language
C
Stars
950
Forks
475
Avg merge
3d 13h
Merged PRs (30d)
11

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First steps

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  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

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