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Patch some bugs in writing files

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Former-commit-id: 612868a281dc0ecf4e6c5776973735e5c71bd517
This commit is contained in:
Eric Coissac
2024-06-19 13:15:30 +02:00
parent 73996bb0b7
commit 818ce87bab
8 changed files with 75 additions and 22 deletions
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27
pkg/obitools/obiconsensus/obiconsensus.go
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@@ -108,14 +108,12 @@ func BuildConsensus(seqs obiseq.BioSequenceSlice,
sumCount += s.Count()
}
log.Warnf("sumCount : %d", sumCount)
seq.SetCount(sumCount)
seq.SetAttribute("seq_length", seq.Len())
seq.SetAttribute("kmer_size", kmer_size)
seq.SetAttribute("kmer_max_occur", graph.MaxWeight())
seq.SetAttribute("filtered_graph_size", graph.Len())
seq.SetAttribute("full_graph_size", total_kmer)
seq.SetAttribute("obiconsensus_weight", sumCount)
seq.SetAttribute("obiconsensus_seq_length", seq.Len())
seq.SetAttribute("obiconsensus_kmer_size", kmer_size)
seq.SetAttribute("obiconsensus_kmer_max_occur", graph.MaxWeight())
seq.SetAttribute("obiconsensus_filtered_graph_size", graph.Len())
seq.SetAttribute("obiconsensus_full_graph_size", total_kmer)
}
return seq, err
}
@@ -280,19 +278,23 @@ func MinionDenoise(graph *obigraph.Graph[*obiseq.BioSequence, Mutation],
if err != nil {
log.Warning(err)
clean = (*graph.Vertices)[i]
clean.SetAttribute("obiminion_consensus", false)
clean.SetAttribute("obiconsensus_consensus", false)
} else {
clean.SetAttribute("obiminion_consensus", true)
clean.SetAttribute("obiconsensus_consensus", true)
}
pack.Recycle(false)
} else {
clean = obiseq.NewBioSequence(v.Id(), v.Sequence(), v.Definition())
clean.SetAttribute("obiminion_consensus", false)
clean.SetAttribute("obiconsensus_consensus", false)
}
// clean.SetCount(int(graph.VertexWeight(i)))
clean.SetCount(int(graph.VertexWeight(i)))
clean.SetAttribute(sample_key, graph.Name)
if !clean.HasAttribute("obiconsensus_weight") {
clean.SetAttribute("obiconsensus_weight", int(1))
}
denoised[i] = clean
}
@@ -376,6 +378,7 @@ func CLIOBIMinion(itertator obiiter.IBioSequence) obiiter.IBioSequence {
}()
obiuniq.AddStatsOn(CLISampleAttribute())
obiuniq.AddStatsOn("obiconsensus_weight")
obiuniq.SetUniqueInMemory(false)
obiuniq.SetNoSingleton(CLINoSingleton())
return obiuniq.CLIUnique(newIter).Pipe(obiiter.WorkerPipe(obiannotate.AddSeqLengthWorker(), false))