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vcfRead_test.go
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vcfRead_test.go
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package vcfio
import (
"fmt"
"log"
"testing"
)
type Target struct {
Filename string
Variants []TargetVariant
}
type TargetVariant struct {
VariantInfo
Quality
Samples []SampleSpecific
}
func TestReadNewVcf(t *testing.T) {
testedVcfs := []Target{
{
Filename: "snv.vcf.gz",
Variants: []TargetVariant{
{
VariantInfo: VariantInfo{
VariantKey: "1-979847-A-G",
VariantKey37: "",
Chr: "chr1",
Start: 979846,
End: 979847,
Ref: "A",
Alt: "G",
SVtype: "",
IsSV: false,
},
Quality: Quality{
QualScore: 1098.8,
Filter: "PASS",
ReadDepth: nil,
ReadDepthRef: nil,
ReadDepthAlt: nil,
Platform: "",
SnpCount: 0,
},
Samples: []SampleSpecific{
{
SampleName: "EXOME_EXAMPLE",
NumAlts: 2,
IsPhased: false,
PhaseID: "",
ReadDepthRef: 0,
ReadDepthAlt: 33,
},
},
},
{
VariantInfo: VariantInfo{
VariantKey: "2-174824521-G-GA",
VariantKey37: "",
Chr: "chr2",
Start: 174824520,
End: 174824521,
Ref: "G",
Alt: "GA",
SVtype: "",
IsSV: false,
},
Quality: Quality{
QualScore: 84.7,
Filter: "DPhigh;ABlow",
ReadDepth: nil,
ReadDepthRef: nil,
ReadDepthAlt: nil,
Platform: "",
SnpCount: 0,
},
Samples: []SampleSpecific{
{
SampleName: "EXOME_EXAMPLE",
NumAlts: 1,
IsPhased: false,
PhaseID: "",
ReadDepthRef: 74,
ReadDepthAlt: 16,
},
},
},
{
VariantInfo: VariantInfo{
VariantKey: "X-156007627-A-C",
VariantKey37: "",
Chr: "chrX",
Start: 156007626,
End: 156007627,
Ref: "A",
Alt: "C",
SVtype: "",
IsSV: false,
},
Quality: Quality{
QualScore: 146.8,
Filter: "ABlow",
ReadDepth: nil,
ReadDepthRef: nil,
ReadDepthAlt: nil,
Platform: "",
SnpCount: 0,
},
Samples: []SampleSpecific{
{
SampleName: "EXOME_EXAMPLE",
NumAlts: 1,
IsPhased: false,
PhaseID: "",
ReadDepthRef: 47,
ReadDepthAlt: 10,
},
},
},
{
VariantInfo: VariantInfo{
VariantKey: "Y-5100327-G-T",
VariantKey37: "",
Chr: "chrY",
Start: 5100326,
End: 5100327,
Ref: "G",
Alt: "T",
SVtype: "",
IsSV: false,
},
Quality: Quality{
QualScore: 1206.8,
Filter: "PASS",
ReadDepth: nil,
ReadDepthRef: nil,
ReadDepthAlt: nil,
Platform: "",
SnpCount: 0,
},
Samples: []SampleSpecific{
{
SampleName: "EXOME_EXAMPLE",
NumAlts: 2,
IsPhased: false,
PhaseID: "",
ReadDepthRef: 0,
ReadDepthAlt: 39,
},
},
},
{
VariantInfo: VariantInfo{
VariantKey: "M-185-G-A",
VariantKey37: "",
Chr: "chrM",
Start: 184,
End: 185,
Ref: "G",
Alt: "A",
SVtype: "",
IsSV: false,
},
Quality: Quality{
QualScore: 829.8,
Filter: "PASS",
ReadDepth: nil,
ReadDepthRef: nil,
ReadDepthAlt: nil,
Platform: "",
SnpCount: 0,
},
Samples: []SampleSpecific{
{
SampleName: "EXOME_EXAMPLE",
NumAlts: 2,
IsPhased: false,
PhaseID: "",
ReadDepthRef: 0,
ReadDepthAlt: 17,
},
},
},
},
},
{
Filename: "cnv.vcf.gz",
Variants: []TargetVariant{
{
VariantInfo: VariantInfo{
VariantKey: "2-165959843-166169412-DEL",
VariantKey37: "",
Chr: "chr2",
Start: 165959842,
End: 166169412,
Ref: "",
Alt: "",
SVtype: "DEL",
IsSV: true,
},
Quality: Quality{
QualScore: 23.0,
Filter: "PASS",
ReadDepth: nil,
ReadDepthRef: nil,
ReadDepthAlt: nil,
Platform: "",
SnpCount: 0,
},
Samples: []SampleSpecific{
{
SampleName: "TEST-001",
NumAlts: 1,
IsPhased: false,
PhaseID: "",
ReadDepthRef: 0,
ReadDepthAlt: 0,
},
},
},
{
VariantInfo: VariantInfo{
VariantKey: "7-117469210-117679939-DEL",
VariantKey37: "",
Chr: "chr7",
Start: 117469209,
End: 117679939,
Ref: "",
Alt: "",
SVtype: "DEL",
IsSV: true,
},
Quality: Quality{
QualScore: 23.0,
Filter: "PASS",
ReadDepth: nil,
ReadDepthRef: nil,
ReadDepthAlt: nil,
Platform: "",
SnpCount: 0,
},
Samples: []SampleSpecific{
{
SampleName: "TEST-001",
NumAlts: 2,
IsPhased: false,
PhaseID: "",
ReadDepthRef: 0,
ReadDepthAlt: 0,
},
},
},
{
VariantInfo: VariantInfo{
VariantKey: "17-15229777-15265357-DUP",
VariantKey37: "",
Chr: "chr17",
Start: 15229776,
End: 15265357,
Ref: "",
Alt: "",
SVtype: "DUP",
IsSV: true,
},
Quality: Quality{
QualScore: 9.97,
Filter: "PASS",
ReadDepth: nil,
ReadDepthRef: nil,
ReadDepthAlt: nil,
Platform: "",
SnpCount: 0,
},
Samples: []SampleSpecific{
{
SampleName: "TEST-001",
NumAlts: 1,
IsPhased: false,
PhaseID: "",
ReadDepthRef: 0,
ReadDepthAlt: 0,
},
},
},
{
VariantInfo: VariantInfo{
VariantKey: "X-154021013-154101781-DEL",
VariantKey37: "",
Chr: "chrX",
Start: 154021012,
End: 154101781,
Ref: "",
Alt: "",
SVtype: "DEL",
IsSV: true,
},
Quality: Quality{
QualScore: 11.7,
Filter: "PASS",
ReadDepth: nil,
ReadDepthRef: nil,
ReadDepthAlt: nil,
Platform: "",
SnpCount: 0,
},
Samples: []SampleSpecific{
{
SampleName: "TEST-001",
NumAlts: 1,
IsPhased: false,
PhaseID: "",
ReadDepthRef: 0,
ReadDepthAlt: 0,
},
},
},
},
},
{
Filename: "array.vcf.gz",
Variants: []TargetVariant{
{
VariantInfo: VariantInfo{
VariantKey: "1-109685814-109686073-DEL",
VariantKey37: "",
Chr: "chr1",
Start: 109685813,
End: 109686073,
Ref: "",
Alt: "",
SVtype: "DEL",
IsSV: true,
},
Quality: Quality{
QualScore: 55.722500,
Filter: "PASS",
ReadDepth: nil,
ReadDepthRef: nil,
ReadDepthAlt: nil,
Platform: "",
SnpCount: 0,
},
Samples: []SampleSpecific{
{
SampleName: "EXAMPLE_ARRAY",
NumAlts: 2,
IsPhased: false,
PhaseID: "",
ReadDepthRef: 0,
ReadDepthAlt: 0,
},
},
},
{
VariantInfo: VariantInfo{
VariantKey: "11-54567878-56860610-LOH",
VariantKey37: "",
Chr: "chr11",
Start: 54567877,
End: 56860610,
Ref: "",
Alt: "",
SVtype: "LOH",
IsSV: true,
},
Quality: Quality{
QualScore: 25.215500,
Filter: "PASS",
ReadDepth: nil,
ReadDepthRef: nil,
ReadDepthAlt: nil,
Platform: "",
SnpCount: 0,
},
Samples: []SampleSpecific{
{
SampleName: "EXAMPLE_ARRAY",
NumAlts: 1,
IsPhased: false,
PhaseID: "",
ReadDepthRef: 0,
ReadDepthAlt: 0,
},
},
},
{
VariantInfo: VariantInfo{
VariantKey: "11-67582790-67583970-DUP",
VariantKey37: "",
Chr: "chr11",
Start: 67582789,
End: 67583970,
Ref: "",
Alt: "",
SVtype: "DUP",
IsSV: true,
},
Quality: Quality{
QualScore: 43.181801,
Filter: "PASS",
ReadDepth: nil,
ReadDepthRef: nil,
ReadDepthAlt: nil,
Platform: "",
SnpCount: 0,
},
Samples: []SampleSpecific{
{
SampleName: "EXAMPLE_ARRAY",
NumAlts: 1,
IsPhased: false,
PhaseID: "",
ReadDepthRef: 0,
ReadDepthAlt: 0,
},
},
},
{
VariantInfo: VariantInfo{
VariantKey: "17-43093444-43093454-DEL",
VariantKey37: "",
Chr: "chr17",
Start: 43093443,
End: 43093454,
Ref: "",
Alt: "",
SVtype: "DEL",
IsSV: true,
},
Quality: Quality{
QualScore: 65.200798,
Filter: "PASS",
ReadDepth: nil,
ReadDepthRef: nil,
ReadDepthAlt: nil,
Platform: "",
SnpCount: 0,
},
Samples: []SampleSpecific{
{
SampleName: "EXAMPLE_ARRAY",
NumAlts: 1,
IsPhased: false,
PhaseID: "",
ReadDepthRef: 0,
ReadDepthAlt: 0,
},
},
},
{
VariantInfo: VariantInfo{
VariantKey: "M-16231-16288-DEL",
VariantKey37: "",
Chr: "chrM",
Start: 16230,
End: 16288,
Ref: "",
Alt: "",
SVtype: "DEL",
IsSV: true,
},
Quality: Quality{
QualScore: 193.455994,
Filter: "PASS",
ReadDepth: nil,
ReadDepthRef: nil,
ReadDepthAlt: nil,
Platform: "",
SnpCount: 0,
},
Samples: []SampleSpecific{
{
SampleName: "EXAMPLE_ARRAY",
NumAlts: 2,
IsPhased: false,
PhaseID: "",
ReadDepthRef: 0,
ReadDepthAlt: 0,
},
},
},
},
},
}
for _, f := range testedVcfs {
address := fmt.Sprintf("samples/%s", f.Filename)
scanner, header, err := ReadNewVcf(address)
if err != nil {
log.Fatalln("Failed reading VCF")
}
var count int
for scanner.Scan() {
line := scanner.Text()
v, q, s := ParseVariant(line, header)
if count+1 > len(f.Variants) {
t.Errorf("Variants: observed at least %d variants, expected %d variants", count+1, len(f.Variants))
}
if v.Chr != f.Variants[count].Chr {
t.Errorf("Chr: observed %s, expected %s", v.Chr, f.Variants[count].Chr)
}
if v.Start != f.Variants[count].Start {
t.Errorf("Start: observed %d, expected %d", v.Start, f.Variants[count].Start)
}
if v.End != f.Variants[count].End {
t.Errorf("End: observed %d, expected %d", v.End, f.Variants[count].End)
}
if v.Ref != f.Variants[count].Ref {
t.Errorf("Ref: observed %s, expected %s", v.Ref, f.Variants[count].Ref)
}
if v.Alt != f.Variants[count].Alt {
t.Errorf("Alt: observed %s, expected %s", v.Alt, f.Variants[count].Alt)
}
if v.SVtype != f.Variants[count].SVtype {
t.Errorf("SVtype: observed %s, expected %s", v.SVtype, f.Variants[count].SVtype)
}
if v.IsSV != f.Variants[count].IsSV {
t.Errorf("IsSV: observed %v, expected %v", v.IsSV, f.Variants[count].IsSV)
}
if q.Filter != f.Variants[count].Filter {
t.Errorf("Filter: observed %s, expected %s", q.Filter, f.Variants[count].Filter)
}
if q.QualScore < f.Variants[count].QualScore*0.99 || q.QualScore > f.Variants[count].QualScore*1.01 {
t.Errorf("QualScore: observed %f, expected %f", q.QualScore, f.Variants[count].QualScore)
}
if len(s) != len(f.Variants[count].Samples) {
t.Errorf("Samples: observed %d samples, expected %d samples", len(s), len(f.Variants[count].Samples))
}
for i, sample := range s {
if sample.NumAlts != f.Variants[count].Samples[i].NumAlts {
t.Errorf("Numalts: observed %d, expected %d", sample.NumAlts, f.Variants[count].Samples[i].NumAlts)
}
if sample.ReadDepthRef != f.Variants[count].Samples[i].ReadDepthRef {
t.Errorf("ReadDepthRef: observed %d, expected %d", sample.ReadDepthRef, f.Variants[count].Samples[i].ReadDepthRef)
}
if sample.ReadDepthAlt != f.Variants[count].Samples[i].ReadDepthAlt {
t.Errorf("ReadDepthAlt: observed %d, expected %d", sample.ReadDepthAlt, f.Variants[count].Samples[i].ReadDepthAlt)
}
if sample.SampleName != f.Variants[count].Samples[i].SampleName {
t.Errorf("SampleName: observed %s, expected %s", sample.SampleName, f.Variants[count].Samples[i].SampleName)
}
}
count++
}
}
}