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Adds possibility to provide the ngsfilter configuration as a CSV file

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Former-commit-id: f0fd2cb1a7b149ae2a330edc5087b21be2c4585b
This commit is contained in:
Eric Coissac
2024-05-31 11:08:20 +02:00
parent dbeb44bc79
commit 4487723d14
4 changed files with 160 additions and 12 deletions
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6
pkg/obiformats/fastseq_write_fastq.go
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@@ -11,7 +11,6 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
@@ -34,7 +33,7 @@ func FormatFastq(seq *obiseq.BioSequence, formater FormatHeader) string {
)
}
func FormatFastqBatch(batch obiiter.BioSequenceBatch, quality_shift int,
func FormatFastqBatch(batch obiiter.BioSequenceBatch,
formater FormatHeader, skipEmpty bool) []byte {
var bs bytes.Buffer
for _, seq := range batch.Slice() {
@@ -75,7 +74,6 @@ func WriteFastq(iterator obiiter.IBioSequence,
chunkchan := make(chan FileChunck)
header_format := opt.FormatFastSeqHeader()
quality := obioptions.OutputQualityShift()
newIter.Add(nwriters)
@@ -94,7 +92,7 @@ func WriteFastq(iterator obiiter.IBioSequence,
for iterator.Next() {
batch := iterator.Get()
chunk := FileChunck{
FormatFastqBatch(batch, quality, header_format, opt.SkipEmptySequence()),
FormatFastqBatch(batch, header_format, opt.SkipEmptySequence()),
batch.Order(),
}
chunkchan <- chunk