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reduce the memory impact of obiuniq.

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This commit is contained in:
Eric Coissac
2024-11-27 13:30:16 +01:00
parent d29a56dcbf
commit 40fb4e9767
9 changed files with 145 additions and 8 deletions
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10
pkg/obiformats/fastqseq_read.go
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@ -131,7 +131,7 @@ func _storeSequenceQuality(bytes *bytes.Buffer, out *obiseq.BioSequence, quality
out.SetQualities(q)
}
func FastqChunkParser(quality_shift byte) func(string, io.Reader) (obiseq.BioSequenceSlice, error) {
func FastqChunkParser(quality_shift byte, with_quality bool) func(string, io.Reader) (obiseq.BioSequenceSlice, error) {
parser := func(source string, input io.Reader) (obiseq.BioSequenceSlice, error) {
var identifier string
@ -263,7 +263,9 @@ func FastqChunkParser(quality_shift byte) func(string, io.Reader) (obiseq.BioSeq
}
case 10:
if is_end_of_line {
_storeSequenceQuality(&qualBytes, sequences[len(sequences)-1], quality_shift)
if with_quality {
_storeSequenceQuality(&qualBytes, sequences[len(sequences)-1], quality_shift)
}
state = 11
} else {
qualBytes.WriteByte(C)
@ -299,9 +301,10 @@ func _ParseFastqFile(
input ChannelSeqFileChunk,
out obiiter.IBioSequence,
quality_shift byte,
with_quality bool,
) {
parser := FastqChunkParser(quality_shift)
parser := FastqChunkParser(quality_shift, with_quality)
for chunks := range input {
sequences, err := parser(chunks.Source, chunks.Raw)
@ -339,6 +342,7 @@ func ReadFastq(reader io.Reader, options ...WithOption) (obiiter.IBioSequence, e
chkchan,
out,
byte(obioptions.InputQualityShift()),
opt.ReadQualities(),
)
}