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Add a reading option on readers to convet U to T

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This commit is contained in:
Eric Coissac
2025-07-07 15:29:07 +02:00
parent 8c26fc9884
commit 8d53d253d4
4 changed files with 34 additions and 13 deletions
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13
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, with_quality bool) func(string, io.Reader) (obiseq.BioSequenceSlice, error) {
func FastqChunkParser(quality_shift byte, with_quality bool, UtoT bool) func(string, io.Reader) (obiseq.BioSequenceSlice, error) {
parser := func(source string, input io.Reader) (obiseq.BioSequenceSlice, error) {
var identifier string
@@ -209,6 +209,9 @@ func FastqChunkParser(quality_shift byte, with_quality bool) func(string, io.Rea
if C >= 'A' && C <= 'Z' {
C = C + 'a' - 'A'
}
if C == 'u' && UtoT {
C = 't'
}
seqBytes.Reset()
seqBytes.WriteByte(C)
state = 6
@@ -228,6 +231,9 @@ func FastqChunkParser(quality_shift byte, with_quality bool) func(string, io.Rea
if C >= 'A' && C <= 'Z' {
C = C + 'a' - 'A'
}
if C == 'u' && UtoT {
C = 't'
}
if (C >= 'a' && C <= 'z') || C == '-' || C == '.' || C == '[' || C == ']' {
seqBytes.WriteByte(C)
} else {
@@ -301,10 +307,10 @@ func _ParseFastqFile(
input ChannelFileChunk,
out obiiter.IBioSequence,
quality_shift byte,
with_quality bool,
with_quality, UtoT bool,
) {
parser := FastqChunkParser(quality_shift, with_quality)
parser := FastqChunkParser(quality_shift, with_quality, UtoT)
for chunks := range input {
sequences, err := parser(chunks.Source, chunks.Raw)
@@ -342,6 +348,7 @@ func ReadFastq(reader io.Reader, options ...WithOption) (obiiter.IBioSequence, e
out,
obidefault.ReadQualitiesShift(),
opt.ReadQualities(),
opt.UtoT(),
)
}