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Correction on obiformat of bug leading to partial parsing and add godocs

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Former-commit-id: b27105355f1a330eedf6eaa72c8ac94f06806c28
This commit is contained in:
Eric Coissac
2024-05-07 10:54:12 +02:00
parent 5b98393a68
commit 9e63013bc2
6 changed files with 231 additions and 42 deletions
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73
pkg/obiseq/merge.go
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@ -11,14 +11,24 @@ import (
type StatsOnValues map[string]int
// StatsOnSlotName returns the name of the slot that summarizes statistics of occurrence for a given attribute.
//
// Parameters:
// - key: the attribute key (string)
//
// Return type:
// - string
func StatsOnSlotName(key string) string {
return "merged_" + key
}
/*
Tests if the sequence has already a slot summarizing statistics
of occurrence for a given attribute.
*/
// HasStatsOn tests if the sequence has already a slot summarizing statistics of occurrence for a given attribute.
//
// Parameters:
// - key: the attribute key (string)
//
// Return type:
// - bool
func (sequence *BioSequence) HasStatsOn(key string) bool {
if !sequence.HasAnnotation() {
return false
@ -31,7 +41,14 @@ func (sequence *BioSequence) HasStatsOn(key string) bool {
return ok
}
// A function that takes a BioSequence and a key and returns a StatsOnValues.
// StatsOn returns the slot summarizing statistics of occurrence for a given attribute.
//
// Parameters:
// - key: the attribute key (string) to be summarized
// - na: the value to be used if the attribute is not present
//
// Return type:
// - StatsOnValues
func (sequence *BioSequence) StatsOn(key string, na string) StatsOnValues {
mkey := StatsOnSlotName(key)
annotations := sequence.Annotations()
@ -77,7 +94,14 @@ func (sequence *BioSequence) StatsOn(key string, na string) StatsOnValues {
return stats
}
// Adding the count of the sequence to the count of the key in the stats.
// StatsPlusOne adds the count of the sequence toAdd to the count of the key in the stats.
//
// Parameters:
// - key: the attribute key (string) to be summarized
// - toAdd: the BioSequence to add to the stats
// - na: the value to be used if the attribute is not present
// Return type:
// - bool
func (sequence *BioSequence) StatsPlusOne(key string, toAdd *BioSequence, na string) bool {
sval := na
annotations := sequence.Annotations()
@ -109,10 +133,14 @@ func (sequence *BioSequence) StatsPlusOne(key string, toAdd *BioSequence, na str
old = 0
}
stats[sval] = old + toAdd.Count()
annotations[StatsOnSlotName(key)] = stats
annotations[StatsOnSlotName(key)] = stats // TODO: check if this is necessary
return retval
}
// Merge merges the given StatsOnValues with the current StatsOnValues.
//
// It takes a parameter `toMerged` of type StatsOnValues, which represents the StatsOnValues to be merged.
// It returns a value of type StatsOnValues, which represents the merged StatsOnValues.
func (stats StatsOnValues) Merge(toMerged StatsOnValues) StatsOnValues {
for k, val := range toMerged {
old, ok := stats[k]
@ -125,7 +153,16 @@ func (stats StatsOnValues) Merge(toMerged StatsOnValues) StatsOnValues {
return stats
}
// Merging two sequences.
// Merge merges two sequences into a single sequence.
//
// Parameters:
// - tomerge: the sequence to be merged (BioSequence)
// - na: the value to be used if the attribute is not present (string)
// - inplace: a boolean indicating whether to merge in place or not (bool)
// - statsOn: a variadic string parameter representing the attributes to be summarized (string)
//
// Return type:
// - *BioSequence: the merged sequence (BioSequence)
func (sequence *BioSequence) Merge(tomerge *BioSequence, na string, inplace bool, statsOn ...string) *BioSequence {
if !inplace {
sequence = sequence.Copy()
@ -184,17 +221,15 @@ func (sequence *BioSequence) Merge(tomerge *BioSequence, na string, inplace bool
return sequence
}
/*
*
Merges a set of sequence into a single sequence.
The function assumes that every sequence in the batch is
identical in term of sequence. Actually the function only
aggregates the annotations of the different sequences to be merged
Quality information is lost during the merge procedure.
*/
// Merge merges the given sequences into a single sequence.
//
// Parameters:
// - sequences: a slice of BioSequence objects to be merged (BioSequenceSlice)
// - na: the value to be used if the attribute is not present (string)
// - statsOn: a slice of strings representing the attributes to be summarized ([]string)
//
// Return type:
// - *BioSequence: the merged sequence (BioSequence)
func (sequences BioSequenceSlice) Merge(na string, statsOn []string) *BioSequence {
seq := sequences[0]
//sequences[0] = nil