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correction of several small bugs

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This commit is contained in:
Eric Coissac
2024-09-03 06:08:07 -03:00
parent 373464cb06
commit 65ae82622e
22 changed files with 770 additions and 79 deletions
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36
pkg/obiseq/merge.go
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@@ -91,8 +91,7 @@ func (sequence *BioSequence) HasStatsOn(key string) bool {
// - StatsOnValues
func (sequence *BioSequence) StatsOn(desc StatsOnDescription, na string) StatsOnValues {
mkey := StatsOnSlotName(desc.Name)
annotations := sequence.Annotations()
istat, ok := annotations[mkey]
istat, ok := sequence.GetAttribute(mkey)
var stats StatsOnValues
var newstat bool
@@ -117,39 +116,40 @@ func (sequence *BioSequence) StatsOn(desc StatsOnDescription, na string) StatsOn
}
}
default:
stats = make(StatsOnValues, 10)
annotations[mkey] = stats
stats = make(StatsOnValues)
sequence.SetAttribute(mkey, stats)
newstat = true
}
} else {
stats = make(StatsOnValues, 10)
annotations[mkey] = stats
stats = make(StatsOnValues)
sequence.SetAttribute(mkey, stats)
newstat = true
}
if newstat && sequence.StatsPlusOne(desc, sequence, na) {
delete(sequence.Annotations(), desc.Key)
if newstat {
sequence.StatsPlusOne(desc, sequence, na)
}
return stats
}
// StatsPlusOne adds the count of the sequence toAdd to the count of the key in the stats.
// StatsPlusOne updates the statistics on the given attribute (desc) on the receiver BioSequence
// with the value of the attribute on the toAdd BioSequence.
//
// Parameters:
// - key: the attribute key (string) to be summarized
// - toAdd: the BioSequence to add to the stats
// - desc: StatsOnDescription of the attribute to be updated
// - toAdd: the BioSequence containing the attribute to be updated
// - na: the value to be used if the attribute is not present
//
// Return type:
// - bool
// - bool: true if the update was successful, false otherwise
func (sequence *BioSequence) StatsPlusOne(desc StatsOnDescription, toAdd *BioSequence, na string) bool {
sval := na
annotations := sequence.Annotations()
stats := sequence.StatsOn(desc, na)
retval := false
if toAdd.HasAnnotation() {
value, ok := toAdd.Annotations()[desc.Key]
value, ok := toAdd.GetAttribute(desc.Key)
if ok {
@@ -178,8 +178,9 @@ func (sequence *BioSequence) StatsPlusOne(desc StatsOnDescription, toAdd *BioSeq
if !ok {
old = 0
}
stats[sval] = old + desc.Weight(toAdd)
annotations[StatsOnSlotName(desc.Name)] = stats // TODO: check if this is necessary
sequence.SetAttribute(StatsOnSlotName(desc.Name), stats) // TODO: check if this is necessary
return retval
}
@@ -263,7 +264,7 @@ func (sequence *BioSequence) Merge(tomerge *BioSequence, na string, inplace bool
}
}
annotations["count"] = count
sequence.SetCount(count)
return sequence
}
@@ -282,7 +283,7 @@ func (sequences BioSequenceSlice) Merge(na string, statsOn StatsOnDescriptions)
seq.SetQualities(nil)
if len(sequences) == 1 {
seq.Annotations()["count"] = seq.Count()
seq.SetCount(seq.Count())
for _, desc := range statsOn {
seq.StatsOn(desc, na)
}
@@ -296,5 +297,4 @@ func (sequences BioSequenceSlice) Merge(na string, statsOn StatsOnDescriptions)
sequences.Recycle(false)
return seq
}