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Accelerate the speed of very long fasta sequences, and more generaly of every format

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This commit is contained in:
Eric Coissac
2025-03-12 13:29:41 +01:00
parent 83926c91e1
commit 3a1cf4fe97
8 changed files with 185 additions and 54 deletions
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5
pkg/obiformats/genbank_read.go
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@ -223,13 +223,12 @@ func ReadGenbank(reader io.Reader, options ...WithOption) (obiiter.IBioSequence,
opt := MakeOptions(options)
// entry_channel := make(chan _FileChunk)
buff := make([]byte, 1024*1024*128) // 128 MB
entry_channel := ReadFileChunk(
opt.Source(),
reader,
buff,
1024*1024*128,
EndOfLastFlatFileEntry,
"\nLOCUS ",
)
newIter := obiiter.MakeIBioSequence()