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Ena 6648 fasta reader #76
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…ENA-6648-fasta-reader in\# the commit.
Rajkumar-D
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Dec 12, 2025
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| /** (4) count 'N'/'n' at the tail of the last sequence line only. */ | ||
| private long countTrailingNs(LineEntry line) throws IOException { |
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Should we read from the end of the line to get the trailing N's?
Rajkumar-D
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Dec 12, 2025
src/main/java/uk/ac/ebi/embl/gff3tools/fasta/sequenceutils/SequenceIndexBuilder.java
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src/main/java/uk/ac/ebi/embl/gff3tools/fasta/sequenceutils/SequenceIndexBuilder.java
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Had initial comments on this PR.
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A fasta reader that enables the user to read the sequences and stream/get as a string their slices.
Currently measured to process a 2GB single fasta entry with a large sequence in about 2.8 sec - so that's reading, parsing, indexing, complaining if the file is malformed etc etc.
Getting small slices of the sequence is almost instantaneous, while streaming the entire sequence will of course take longer, but around 3 sec is to be expected.
The user uses the reader through the interface in FastaFileService, the examples of usage are provided in FastaFileServiceIntegrationTest ("integration" because I am effectively testing the Fasta File Service together with the underlying SequentialFastaFileReader and the SequenceIndexBuilders and whatnot).
Requiring feedback on:
The spec for the file I am reading is provided here.
Currently I am aware of the following potential bugs: