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First version of obisplit and patch a bug in the new workers API

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Former-commit-id: f28af9f104c08d68e29fd866739d8dd58241da63
This commit is contained in:
Eric Coissac
2024-03-03 11:16:24 -04:00
parent 0f3871d203
commit 7bd073ccd4
7 changed files with 507 additions and 37 deletions
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53
pkg/obiseq/worker.go
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@ -25,37 +25,27 @@ func AnnotatorToSeqWorker(function SeqAnnotator) SeqWorker {
}
func SeqToSliceWorker(worker SeqWorker,
inplace, breakOnError bool) SeqSliceWorker {
breakOnError bool) SeqSliceWorker {
var f SeqSliceWorker
if worker == nil {
if inplace {
f = func(input BioSequenceSlice) (BioSequenceSlice, error) {
return input, nil
}
} else {
f = func(input BioSequenceSlice) (BioSequenceSlice, error) {
output := MakeBioSequenceSlice(len(input))
copy(output, input)
return output, nil
}
f = func(input BioSequenceSlice) (BioSequenceSlice, error) {
return input, nil
}
} else {
f = func(input BioSequenceSlice) (BioSequenceSlice, error) {
output := input
if !inplace {
output = MakeBioSequenceSlice(len(input))
}
output := MakeBioSequenceSlice(len(input))
i := 0
for _, s := range input {
r, err := worker(s)
if err == nil {
for _, rs := range r {
if i == len(output) {
output = slices.Grow(output, cap(output))
output = output[:cap(output)]
}
output[i] = rs
i++
if i == cap(output) {
slices.Grow(output, cap(output))
}
}
} else {
@ -64,8 +54,8 @@ func SeqToSliceWorker(worker SeqWorker,
s.Id(), err)
return BioSequenceSlice{}, err
} else {
log.Warnf("got an error on sequence %s processing",
s.Id())
log.Warnf("got an error on sequence %s processing : %v",
s.Id(), err)
}
}
}
@ -80,18 +70,14 @@ func SeqToSliceWorker(worker SeqWorker,
func SeqToSliceConditionalWorker(
condition SequencePredicate,
worker SeqWorker,
inplace, breakOnError bool) SeqSliceWorker {
worker SeqWorker, breakOnError bool) SeqSliceWorker {
if condition == nil {
return SeqToSliceWorker(worker, inplace, breakOnError)
return SeqToSliceWorker(worker, breakOnError)
}
f := func(input BioSequenceSlice) (BioSequenceSlice, error) {
output := input
if !inplace {
output = MakeBioSequenceSlice(len(input))
}
output := MakeBioSequenceSlice(len(input))
i := 0
@ -100,11 +86,12 @@ func SeqToSliceConditionalWorker(
r, err := worker(s)
if err == nil {
for _, rs := range r {
if i == len(output) {
output = slices.Grow(output, cap(output))
output = output[:cap(output)]
}
output[i] = rs
i++
if i == cap(output) {
slices.Grow(output, cap(output))
}
}
} else {
if breakOnError {
@ -112,8 +99,8 @@ func SeqToSliceConditionalWorker(
s.Id(), err)
return BioSequenceSlice{}, err
} else {
log.Warnf("got an error on sequence %s processing",
s.Id())
log.Warnf("got an error on sequence %s processing : %v",
s.Id(), err)
}
}
}
@ -134,7 +121,7 @@ func (worker SeqWorker) ChainWorkers(next SeqWorker) SeqWorker {
}
}
sw := SeqToSliceWorker(next, true, false)
sw := SeqToSliceWorker(next, false)
f := func(seq *BioSequence) (BioSequenceSlice, error) {
if seq == nil {