Renumbering code was incorrectly reserving ranking spots for no-calls.
refs #17763
Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>
c.Assert(err, check.IsNil)
c.Check(npy.Shape, check.DeepEquals, []int{4, 4})
variants, err := npy.GetInt16()
c.Assert(err, check.IsNil)
c.Check(npy.Shape, check.DeepEquals, []int{4, 4})
variants, err := npy.GetInt16()
- c.Check(variants, check.DeepEquals, []int16{3, 2, 1, 2, -1, -1, 1, 1, 3, 2, 1, 2, -1, -1, 1, 1})
+ c.Check(variants, check.DeepEquals, []int16{2, 1, 1, 2, -1, -1, 1, 1, 2, 1, 1, 2, -1, -1, 1, 1})
annotations, err := ioutil.ReadFile(npydir + "/matrix.0000.annotations.csv")
c.Assert(err, check.IsNil)
annotations, err := ioutil.ReadFile(npydir + "/matrix.0000.annotations.csv")
c.Assert(err, check.IsNil)
defer throttleCPU.Release()
count := make(map[[blake2b.Size256]byte]int, len(variants))
for _, cg := range cgs {
defer throttleCPU.Release()
count := make(map[[blake2b.Size256]byte]int, len(variants))
for _, cg := range cgs {
- idx := (tag - tagstart) * 2
- if int(idx) < len(cg.Variants) {
- count[variants[cg.Variants[idx]].Blake2b]++
- count[variants[cg.Variants[idx+1]].Blake2b]++
+ idx := int(tag-tagstart) * 2
+ if idx < len(cg.Variants) {
+ for allele := 0; allele < 2; allele++ {
+ v := cg.Variants[idx+allele]
+ if v > 0 && len(variants[v].Sequence) > 0 {
+ count[variants[v].Blake2b]++
+ }
+ }
}
}
// hash[i] will be the hash of
}
}
// hash[i] will be the hash of