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On development genome skim tools

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This commit is contained in:
Eric Coissac
2024-08-30 11:17:33 +02:00
parent cd330db672
commit 373464cb06
10 changed files with 144 additions and 50 deletions
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18
pkg/obialign/readalign.go
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@ -43,16 +43,25 @@ func ReadAlign(seqA, seqB *obiseq.BioSequence,
directAlignment = false
}
if shift > 0 {
// Compute the overlapping region length
switch {
case shift > 0:
over = seqA.Len() - shift
} else {
case shift < 0:
over = seqB.Len() + shift
default:
over = min(seqA.Len(), seqB.Len())
}
// log.Warnf("fw/fw: %v shift=%d fastCount=%d/over=%d fastScore=%f",
// directAlignment, shift, fastCount, over, fastScore)
// log.Warnf(("seqA: %s\nseqB: %s\n"), seqA.String(), seqB.String())
// At least one mismatch exists in the overlaping region
if fastCount+3 < over {
if shift > 0 {
if shift > 0 || (shift == 0 && seqB.Len() >= seqA.Len()) {
startA = shift - delta
if startA < 0 {
startA = 0
@ -105,7 +114,7 @@ func ReadAlign(seqA, seqB *obiseq.BioSequence,
// Both overlaping regions are identicals
if shift > 0 {
if shift > 0 || (shift == 0 && seqB.Len() >= seqA.Len()) {
startA = shift
startB = 0
extra5 = -startA
@ -123,6 +132,7 @@ func ReadAlign(seqA, seqB *obiseq.BioSequence,
extra3 = partLen - seqA.Len()
qualSeqA = seqA.Qualities()[:partLen]
}
score = 0
for i, qualA := range qualSeqA {
qualB := qualSeqB[i]