func main() {
if len(util.FlagCpuProf) > 0 {
f := util.CreateFile(util.FlagCpuProf)
pprof.StartCPUProfile(f)
defer f.Close()
defer pprof.StopCPUProfile()
}
if len(flagGobIt) > 0 {
astralDir := util.Arg(0)
dists := readAlignmentDists(astralDir)
enc := gob.NewEncoder(util.CreateFile(flagGobIt))
util.Assert(enc.Encode(dists), "Could not GOB encode distances")
return
}
var dists *intern.Table
if util.IsDir(util.Arg(0)) {
dists = readAlignmentDists(util.Arg(0))
} else {
dec := gob.NewDecoder(util.OpenFile(util.Arg(0)))
util.Assert(dec.Decode(&dists), "Could not GOB decode distances")
}
treeFile := util.Arg(1)
outPath := util.Arg(2)
treeReader := newick.NewReader(util.OpenFile(treeFile))
tree, err := treeReader.ReadTree()
util.Assert(err, "Could not read newick tree")
csvw := csv.NewWriter(util.CreateFile(outPath))
clusters := treeClusters(flagThreshold, dists, tree)
util.Assert(csvw.WriteAll(clusters))
}
func ReadTree(r io.Reader) (*Tree, error) {
lx := newick.NewReader(r)
t, err := lx.ReadTree()
if err != nil {
return nil, err
}
if len(t.Children) == 0 {
err = fmt.Errorf("lineage tree only has a root node")
return nil, err
}
tree, err := treeFromNewick(t, 0)
return tree, err
}