obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2025-06-29 16:20:46 +00:00
Code Issues Packages Projects Releases Wiki Activity

Work on iterators and recycling of biosequences

Browse Source
This commit is contained in:
Eric Coissac
2022-01-14 23:11:36 +01:00
parent ef66ca4972
commit e8fff6477b
22 changed files with 350 additions and 111 deletions
Download Patch File Download Diff File Expand all files Collapse all files

9
pkg/obialign/pairedendalign.go
View File

@ -282,6 +282,11 @@ func PEAlign(seqA, seqB obiseq.BioSequence,
_InitDNAScoreMatrix()
}
// log.Println("==============")
// log.Println(seqA.String())
// log.Println(seqB.String())
// log.Println("--------------")
index := obikmer.Index4mer(seqA,
&arena.pointer.fastIndex,
&arena.pointer.fastBuffer)
@ -294,6 +299,10 @@ func PEAlign(seqA, seqB obiseq.BioSequence,
over = seqB.Length() + shift
}
// log.Println(seqA.String())
// log.Println(seqB.String())
// log.Printf("Shift : %d Score : %d Over : %d La : %d:%d Lb: %d:%d\n", shift, fastScore, over, seqA.Length(), len(seqA.Qualities()), seqB.Length(), len(seqB.Qualities()))
if fastScore+3 < over {
if shift > 0 {
startA = shift - delta