[BUFIX] fail when passed fastas with duplicate sequence ids #555
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skothenhill-nv
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malcolmgreaves,
jstjohn,
edawson and
cspades
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…o hillst/nvfaidx-restrictions
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/build-ci |
cspades
approved these changes
Dec 24, 2024
edawson
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Dec 25, 2024
nvdreidenbach
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this pull request
Jan 2, 2025
When NvFaidx was used on Fasta files containing duplicate sequence ids, which violates the FASTA spec, it would silently fail and use the last-seen sequence as an entry. This PR fails by default and exposes a parameter to ignore sequence_ids and use integer indexing instead. Signed-off-by: Danny <[email protected]>
nvdreidenbach
pushed a commit
to nvdreidenbach/bionemo-framework
that referenced
this pull request
Jan 2, 2025
When NvFaidx was used on Fasta files containing duplicate sequence ids, which violates the FASTA spec, it would silently fail and use the last-seen sequence as an entry. This PR fails by default and exposes a parameter to ignore sequence_ids and use integer indexing instead. Signed-off-by: Danny <[email protected]>
nvdreidenbach
pushed a commit
to nvdreidenbach/bionemo-framework
that referenced
this pull request
Jan 2, 2025
When NvFaidx was used on Fasta files containing duplicate sequence ids, which violates the FASTA spec, it would silently fail and use the last-seen sequence as an entry. This PR fails by default and exposes a parameter to ignore sequence_ids and use integer indexing instead. Signed-off-by: Danny <[email protected]>
nvdreidenbach
pushed a commit
to nvdreidenbach/bionemo-framework
that referenced
this pull request
Jan 2, 2025
When NvFaidx was used on Fasta files containing duplicate sequence ids, which violates the FASTA spec, it would silently fail and use the last-seen sequence as an entry. This PR fails by default and exposes a parameter to ignore sequence_ids and use integer indexing instead. Signed-off-by: Danny <[email protected]>
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When NvFaidx was used on Fasta files containing duplicate sequence ids, which violates the FASTA spec, it would silently fail and use the last-seen sequence as an entry.
This PR fails by default and exposes a parameter to ignore sequence_ids and use integer indexing instead.