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Cleaning of obiminion

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Former-commit-id: 75148afd70e5006cc6855bcddc86506b099761a1
This commit is contained in:
Eric Coissac
2024-05-14 11:45:46 +02:00
parent 017030bcce
commit 7fcb0538a3
5 changed files with 11 additions and 219 deletions
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6
pkg/obikmer/debruijn.go
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@ -9,6 +9,7 @@ import (
"slices"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
"github.com/daichi-m/go18ds/sets/linkedhashset"
"github.com/daichi-m/go18ds/stacks/arraystack"
log "github.com/sirupsen/logrus"
@ -294,7 +295,7 @@ func (g *DeBruijnGraph) LongestPath(max_length int) []uint64 {
return path
}
func (g *DeBruijnGraph) LongestConsensus(id string, max_length int) (*obiseq.BioSequence, error) {
func (g *DeBruijnGraph) LongestConsensus(id string) (*obiseq.BioSequence, error) {
//path := g.LongestPath(max_length)
path := g.HaviestPath()
s := g.DecodePath(path)
@ -464,11 +465,12 @@ func (graph *DeBruijnGraph) Gml() string {
for idx := range graph.graph {
srcid := nodeidx[idx]
weight := graph.Weight(idx)
n := graph.Nexts(idx)
for _, dst := range n {
dstid := nodeidx[dst]
weight := obiutils.Min(graph.Weight(dst), weight)
label := decode[dst&3]
weight := graph.Weight(dst)
buffer.WriteString(
fmt.Sprintf(`edge [ source "%d"
target "%d"