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Adjust the size of the genbank and embl buffer size

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This commit is contained in:
Eric Coissac
2024-08-05 11:32:37 +02:00
parent 886b5d9a96
commit 3f57935328
4 changed files with 6 additions and 8 deletions
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2
pkg/obiformats/embl_read.go
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@ -187,7 +187,7 @@ func _ParseEmblFile(
func ReadEMBL(reader io.Reader, options ...WithOption) (obiiter.IBioSequence, error) { func ReadEMBL(reader io.Reader, options ...WithOption) (obiiter.IBioSequence, error) {
opt := MakeOptions(options) opt := MakeOptions(options)
buff := make([]byte, 1024*1024*512) buff := make([]byte, 1024*1024*128) // 128 MB
entry_channel := ReadSeqFileChunk( entry_channel := ReadSeqFileChunk(
opt.Source(), opt.Source(),

2
pkg/obiformats/genbank_read.go
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@ -223,7 +223,7 @@ func ReadGenbank(reader io.Reader, options ...WithOption) (obiiter.IBioSequence,
opt := MakeOptions(options) opt := MakeOptions(options)
// entry_channel := make(chan _FileChunk) // entry_channel := make(chan _FileChunk)
buff := make([]byte, 1024*1024*512) buff := make([]byte, 1024*1024*128) // 128 MB
entry_channel := ReadSeqFileChunk( entry_channel := ReadSeqFileChunk(
opt.Source(), opt.Source(),

8
pkg/obiformats/seqfile_chunk_read.go
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@ -9,8 +9,6 @@ import (
log "github.com/sirupsen/logrus" log "github.com/sirupsen/logrus"
) )
var _FileChunkSize = 1024 * 1024 * 10
type SeqFileChunkParser func(string, io.Reader) (obiseq.BioSequenceSlice, error) type SeqFileChunkParser func(string, io.Reader) (obiseq.BioSequenceSlice, error)
type SeqFileChunk struct { type SeqFileChunk struct {
@ -46,7 +44,7 @@ func ReadSeqFileChunk(
chunk_channel := make(ChannelSeqFileChunk) chunk_channel := make(ChannelSeqFileChunk)
_FileChunkSize := len(buff) fileChunkSize := len(buff)
go func() { go func() {
size := 0 size := 0
@ -73,9 +71,9 @@ func ReadSeqFileChunk(
// Read from the reader in 1 MB increments until the end of the last entry is found // Read from the reader in 1 MB increments until the end of the last entry is found
for end = splitter(buff); err == nil && end < 0; end = splitter(buff) { for end = splitter(buff); err == nil && end < 0; end = splitter(buff) {
ic++ ic++
buff = slices.Grow(buff, _FileChunkSize) buff = slices.Grow(buff, fileChunkSize)
l := len(buff) l := len(buff)
extbuff := buff[l:(l + _FileChunkSize - 1)] extbuff := buff[l:(l + fileChunkSize - 1)]
size, err = io.ReadFull(reader, extbuff) size, err = io.ReadFull(reader, extbuff)
buff = buff[0:(l + size)] buff = buff[0:(l + size)]
} }

2
pkg/obioptions/version.go
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@ -7,7 +7,7 @@ import (
// TODO: The version number is extracted from git. This induces that the version // TODO: The version number is extracted from git. This induces that the version
// corresponds to the last commit, and not the one when the file will be // corresponds to the last commit, and not the one when the file will be
// commited // commited
var _Commit = "f83032e" var _Commit = "886b5d9"
var _Version = "Release 4.2.0" var _Version = "Release 4.2.0"
// Version returns the version of the obitools package. // Version returns the version of the obitools package.