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Add logs to filtering #489

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Add logs to filtering #489

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4 changes: 4 additions & 0 deletions seqkit/cmd/seq.go
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Original file line number Diff line number Diff line change
Expand Up @@ -269,19 +269,23 @@ var seqCmd = &cobra.Command{
}

if filterMinLen && len(record.Seq.Seq) < minLen {
log.Info("sequence '%s' too short (%d < %d)", record.Seq.Id, len(record.Seq.Seq), minLen)
continue
}

if filterMaxLen && len(record.Seq.Seq) > maxLen {
log.Info("sequence '%s' too long (%d > %d)", record.Seq.Id, len(record.Seq.Seq), maxLen)
continue
}

if filterMinQual || filterMaxQual {
avgQual := record.Seq.AvgQual(qBase)
if filterMinQual && avgQual < minQual {
log.Info("average quality of sequence '%s' too low (%d < %d)", record.Seq.Id, avgQual, minQual)
continue
}
if filterMaxQual && avgQual >= maxQual {
log.Info("average quality of sequence '%s' too high (%d > %d)", record.Seq.Id, avgQual, maxQual)
continue
}
}
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