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Unaligned Sequences #255

Merged
merged 2 commits into from
Jan 24, 2024
Merged

Unaligned Sequences #255

merged 2 commits into from
Jan 24, 2024

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Taepper
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@Taepper Taepper commented Jan 23, 2024

feat: introduce storage of unaligned sequences from either ndjson file or fasta file and make them queryable via the Fasta action

The last required action

#112 is now very easy (for unaligned), where we can stream the sequences almost directly from the backing file

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@JonasKellerer JonasKellerer left a comment

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Thank you. Nice addition.

My comments are mostly for small refactors. However, the add_sequences_to_results_for_partition function was quite hard to read. If possible, splitting into smaller function would help.

src/silo/query_engine/actions/fasta.cpp Outdated Show resolved Hide resolved
src/silo/query_engine/actions/fasta.cpp Outdated Show resolved Hide resolved
src/silo/query_engine/actions/fasta.cpp Outdated Show resolved Hide resolved
src/silo/query_engine/actions/fasta.cpp Outdated Show resolved Hide resolved
.github/workflows/ci.yml Outdated Show resolved Hide resolved
.run/silo--preprocessing.run.xml Outdated Show resolved Hide resolved
endToEndTests/test/queries/manySequences.json Outdated Show resolved Hide resolved
endToEndTests/test/queries/oneSequenceUnaligned.json Outdated Show resolved Hide resolved
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@JonasKellerer JonasKellerer linked an issue Jan 24, 2024 that may be closed by this pull request
@Taepper Taepper force-pushed the unaligned-sequences branch 3 times, most recently from b326e04 to 92c3278 Compare January 24, 2024 09:16
…e or fasta file and make them queryable via the Fasta action
@Taepper Taepper force-pushed the unaligned-sequences branch from 92c3278 to 44df849 Compare January 24, 2024 12:29
# Conflicts:
#	src/silo/preprocessing/preprocessor.cpp
@Taepper Taepper merged commit 66bd0fe into main Jan 24, 2024
4 of 6 checks passed
@Taepper Taepper deleted the unaligned-sequences branch January 24, 2024 13:10
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Download fasta files
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