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Patch a bug in fasta and fastq reading

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Former-commit-id: bcaa264b4c4a7c67617eb909b199176bf09913db
This commit is contained in:
Eric Coissac
2024-06-21 14:28:57 +02:00
parent 818ce87bab
commit 54a138196c
9 changed files with 85 additions and 44 deletions
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2
pkg/obitools/obiclean/obiclean.go
View File

@@ -34,7 +34,7 @@ func buildSamples(dataset obiseq.BioSequenceSlice,
samples := make(map[string]*([]*seqPCR))
for _, s := range dataset {
stats := s.StatsOn(tag, NAValue)
stats := s.StatsOn(obiseq.MakeStatsOnDescription(tag), NAValue)
for k, v := range stats {
pcr, ok := samples[k]

6
pkg/obitools/obiconsensus/obiconsensus.go
View File

@@ -129,7 +129,7 @@ func SampleWeight(seqs *obiseq.BioSequenceSlice, sample, sample_key string) func
f := func(i int) float64 {
stats := (*seqs)[i].StatsOn(sample_key, "NA")
stats := (*seqs)[i].StatsOn(obiseq.MakeStatsOnDescription(sample_key), "NA")
if value, ok := stats[sample]; ok {
return float64(value)
@@ -155,7 +155,7 @@ func SeqBySamples(seqs obiseq.BioSequenceSlice, sample_key string) map[string]*o
for _, s := range seqs {
if s.HasStatsOn(sample_key) {
stats := s.StatsOn(sample_key, "NA")
stats := s.StatsOn(obiseq.MakeStatsOnDescription(sample_key), "NA")
for k := range stats {
if seqset, ok := samples[k]; ok {
*seqset = append(*seqset, s)
@@ -378,7 +378,7 @@ func CLIOBIMinion(itertator obiiter.IBioSequence) obiiter.IBioSequence {
}()
obiuniq.AddStatsOn(CLISampleAttribute())
obiuniq.AddStatsOn("obiconsensus_weight")
obiuniq.AddStatsOn("sample:obiconsensus_weight")
obiuniq.SetUniqueInMemory(false)
obiuniq.SetNoSingleton(CLINoSingleton())
return obiuniq.CLIUnique(newIter).Pipe(obiiter.WorkerPipe(obiannotate.AddSeqLengthWorker(), false))