func (s *RegrSuite) SetUpTest(c *C) {
s.h = vcfgo.NewHeader()
s.h.Infos["DOCM_DISEASE"] = &vcfgo.Info{Id: "DOCM_DISEASE", Description: "DOCM_DISEASE", Type: "String", Number: "."}
s.h.Infos["DOCM_PMIDS"] = &vcfgo.Info{Id: "DOCM_PMIDS", Description: "DOCM_PMIDS", Type: "String", Number: "."}
s.v1 = makeVariant("1", 22, "A", []string{"T"}, "query", "", s.h)
s.v1.SetSource(0)
s.v2 = makeVariant("1", 22, "A", []string{"T"}, "docm", "DOCM_DISEASE=chronic_myeloid_leukemia,acute_myeloid_leukemia;DOCM_PMIDS=23634996,23656643", s.h)
s.v2.SetSource(1)
s.src_disease = Source{
File: "docm.vcf.gz",
Op: "concat",
Field: "DOCM_DISEASE",
Name: "docm_disease",
Index: 0,
}
s.src_pmids = Source{
File: "docm.vcf.gz",
Op: "uniq",
Field: "DOCM_PMIDS",
Name: "docm_pmids",
Index: 0,
}
s.v1.AddRelated(s.v2)
empty := make([]PostAnnotation, 0)
s.annotator = NewAnnotator([]*Source{&s.src_disease, &s.src_pmids}, "", true, false, empty)
}
// vFromB makes a variant from an interval. this helps avoid code duplication.
func vFromB(b *parsers.Interval) *parsers.Variant {
h := vcfgo.NewHeader()
h.Infos["SVLEN"] = &vcfgo.Info{Id: "SVLEN", Type: "Integer", Description: "", Number: "1"}
m := vcfgo.NewInfoByte([]byte(fmt.Sprintf("SVLEN=%d", int(b.End()-b.Start())-1)), h)
v := parsers.NewVariant(&vcfgo.Variant{Chromosome: b.Chrom(), Pos: uint64(b.Start() + 1),
Reference: "A", Alternate: []string{"<DEL>"}, Info_: m}, 0, b.Related())
return v
}
type APISuite struct {
sv1 *parsers.Variant
v1 *parsers.Variant
v2 *parsers.Variant
v3 *parsers.Variant
bed *parsers.Interval
src Source
src0 Source
annotator *Annotator
}
var _ = Suite(&APISuite{})
var h = vcfgo.NewHeader()
var v1 = &vcfgo.Variant{
Chromosome: "chr1",
Pos: uint64(234),
Id_: "id",
Reference: "A",
Alternate: []string{"T", "G"},
Quality: float32(555.5),
Filter: "PASS",
Info_: vcfgo.NewInfoByte([]byte("DP=35"), h),
}
var sv1 = &vcfgo.Variant{
Chromosome: "chr1",
Pos: uint64(230),
Id_: "id",