mirror of
https://github.com/metabarcoding/obitools4.git
synced 2026-04-30 12:00:39 +00:00
Eric Coissac
6d469bd711
[obiseq] Add length validation for qualities in SetQualities, Take Qualites and Subsequence - Panic if sequence/qualities length mismatch when setting or taking qualities in BioSequence. - Add same check before slicing Qualities() for Subsequence to ensure consistency.
111 lines
2.7 KiB
Go
111 lines
2.7 KiB
Go
package obiseq
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import (
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"fmt"
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log "github.com/sirupsen/logrus"
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)
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// Subsequence returns a subsequence of the BioSequence.
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//
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// Parameters:
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// - from: starting position of the subsequence.
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// - to: ending position of the subsequence.
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// - circular: indicates whether the subsequence should be circular.
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//
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// Return:
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// - *BioSequence: the subsequence of the BioSequence.
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// - error: an error if the subsequence parameters are invalid.
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func (sequence *BioSequence) Subsequence(from, to int, circular bool) (*BioSequence, error) {
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if from >= to && !circular {
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return nil, fmt.Errorf("from: %d greater than to: %d", from, to)
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}
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if from < 0 {
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return nil, fmt.Errorf("from out of bounds %d < 0", from)
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}
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if from >= sequence.Len() && !circular {
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return nil,
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fmt.Errorf("from out of bounds %d >= %d", from, sequence.Len())
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} else {
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log.Debugf("(%s) correcting from position from %d to %d", sequence.Id(), to, (to-1)%sequence.Len()+1)
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from = from % sequence.Len()
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}
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if to > sequence.Len() && !circular {
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return nil,
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fmt.Errorf("to out of bounds %d > %d", to, sequence.Len())
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} else {
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log.Debugf("(%s) correcting to position from %d to %d", sequence.Id(), to, (to-1)%sequence.Len()+1)
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to = ((to - 1) % sequence.Len()) + 1
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}
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var newSeq *BioSequence
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if from < to {
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newSeq = NewEmptyBioSequence(0)
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newSeq.sequence = CopySlice(sequence.Sequence()[from:to])
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if sequence.HasQualities() {
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qual := sequence.Qualities()
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if len(qual) != sequence.Len() {
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log.Panicf(
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"[BioSequence.Subsequence] Sequence %s has a length of %d and qualities a length of %d",
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sequence.Id(),
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sequence.Len(),
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len(qual),
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)
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}
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newSeq.qualities = CopySlice(qual[from:to])
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}
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newSeq.id = fmt.Sprintf("%s_sub[%d..%d]", sequence.Id(), from+1, to)
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// newSeq.definition = sequence.definition
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} else {
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newSeq, _ = sequence.Subsequence(from, sequence.Len(), false)
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newSeq.Write(sequence.Sequence()[0:to])
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if sequence.HasQualities() {
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qual := sequence.Qualities()
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if len(qual) != sequence.Len() {
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log.Panicf(
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"[BioSequence.Subsequence] Sequence %s has a length of %d and qualities a length of %d",
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sequence.Id(),
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sequence.Len(),
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len(qual),
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)
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}
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newSeq.WriteQualities(qual[0:to])
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}
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}
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if sequence.HasAnnotation() {
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newSeq.annotations = GetAnnotation(sequence.Annotations())
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}
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return newSeq._subseqMutation(from), nil
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}
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func (sequence *BioSequence) _subseqMutation(shift int) *BioSequence {
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lseq := sequence.Len()
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mut, ok := sequence.GetIntMap("pairing_mismatches")
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if ok && len(mut) > 0 {
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cmut := make(map[string]int, len(mut))
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for m, p := range mut {
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if p < lseq {
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cmut[m] = p - shift
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}
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}
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sequence.SetAttribute("pairing_mismatches", cmut)
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}
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return sequence
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}
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