forked from mendelics/vcf
/
vcf_blackbox_test.go
405 lines (328 loc) · 17.6 KB
/
vcf_blackbox_test.go
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package vcf_test
import (
"fmt"
"strings"
"testing"
"github.com/mendelics/vcf"
"github.com/stretchr/testify/assert"
"github.com/stretchr/testify/suite"
)
type ChannelSuite struct {
suite.Suite
outChannel chan *vcf.Variant
invalidChannel chan vcf.InvalidLine
}
func (suite *ChannelSuite) SetupTest() {
suite.outChannel = make(chan *vcf.Variant, 10)
suite.invalidChannel = make(chan vcf.InvalidLine, 10)
}
func (s *ChannelSuite) TestNoHeader() {
vcfLine := `1 847491 rs28407778 GTTTA G.... 745.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.842;ClippingRankSum=0.147;DB;DP=41;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.109;QD=18.19;ReadPosRankSum=0.334;VQSLOD=2.70;culprit=FS;set=variant GT:AD:DP:GQ:PL 0/1:16,25:41:99:774,0,434`
ioreader := strings.NewReader(vcfLine)
err := vcf.ToChannel(ioreader, s.outChannel, s.invalidChannel)
assert.Error(s.T(), err, "VCF line without header should return error")
}
func (s *ChannelSuite) TestInvalidLinesShouldReturnNothing() {
vcfLine := `#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 185423
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nunc tellus ligula, faucibus sed nibh sed, fringilla viverra enim.
A B C D E F`
ioreader := strings.NewReader(vcfLine)
err := vcf.ToChannel(ioreader, s.outChannel, s.invalidChannel)
assert.NoError(s.T(), err, "VCF with valid header should not return an error")
_, hasMore := <-s.outChannel
assert.False(s.T(), hasMore, "No variant should come out of the channel, it should be closed")
totalLines := 4
for i := 0; i < totalLines; i++ {
invalid := <-s.invalidChannel
assert.NotNil(s.T(), invalid)
assert.Error(s.T(), invalid.Err)
}
_, hasMore = <-s.invalidChannel
assert.False(s.T(), hasMore, fmt.Sprintf("More than %d variants came out of the invalid channel, it should be closed", totalLines))
}
func (s *ChannelSuite) TestToChannel() {
vcfLine := `#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 185423
1 847491 rs28407778 GTTTA G.... 745.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.842;ClippingRankSum=0.147;DB;DP=41;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.109;QD=18.19;ReadPosRankSum=0.334;VQSLOD=2.70;culprit=FS;set=variant GT:AD:DP:GQ:PL 0/1:16,25:41:99:774,0,434`
ioreader := strings.NewReader(vcfLine)
err := vcf.ToChannel(ioreader, s.outChannel, s.invalidChannel)
assert.NoError(s.T(), err, "Valid VCF line should not return error")
variant := <-s.outChannel
assert.NotNil(s.T(), variant, "One variant should come out of channel")
assert.Equal(s.T(), variant.Chrom, "1")
assert.Equal(s.T(), variant.Pos, 847490)
assert.Equal(s.T(), variant.Ref, "GTTTA")
assert.Equal(s.T(), variant.Alt, "G")
assert.Equal(s.T(), variant.ID, "rs28407778")
assert.Equal(s.T(), *variant.Qual, 745.77)
assert.Equal(s.T(), variant.Filter, "PASS")
assert.NotNil(s.T(), variant.Info)
assert.Exactly(s.T(), len(variant.Info), 18)
ac, ok := variant.Info["AC"]
assert.True(s.T(), ok, "AC key must be found")
assert.Equal(s.T(), ac, "1", "ac")
af, ok := variant.Info["AF"]
assert.True(s.T(), ok, "AF key must be found")
assert.Equal(s.T(), af, "0.500", "af")
db, ok := variant.Info["DB"]
assert.True(s.T(), ok, "DB key must be found")
booldb, isbool := db.(bool)
assert.True(s.T(), isbool, "DB value must be a boolean")
assert.True(s.T(), booldb)
assert.NotNil(s.T(), variant.Samples)
assert.Exactly(s.T(), len(variant.Samples), 1, "Valid VCF should contain one sample")
sampleMap := variant.Samples[0]
assert.NotNil(s.T(), sampleMap, "Genotype field mapping should not return nil")
assert.Exactly(s.T(), len(sampleMap), 5, "Sample map should have as many keys as there are formats")
gt, ok := sampleMap["GT"]
assert.True(s.T(), ok, "GT key must be found")
assert.Equal(s.T(), gt, "0/1", "gt")
ad, ok := sampleMap["AD"]
assert.True(s.T(), ok, "AD key must be found")
assert.Equal(s.T(), ad, "16,25", "ad")
dp, ok := sampleMap["DP"]
assert.True(s.T(), ok, "AD key must be found")
assert.Equal(s.T(), dp, "41", "dp")
gq, ok := sampleMap["GQ"]
assert.True(s.T(), ok, "GQ key must be found")
assert.Equal(s.T(), gq, "99", "gq")
pl, ok := sampleMap["PL"]
assert.True(s.T(), ok, "PL key must be found")
assert.Equal(s.T(), pl, "774,0,434", "pl")
_, hasMore := <-s.outChannel
assert.False(s.T(), hasMore, "No second variant should come out of the channel, it should be closed")
_, hasMore = <-s.invalidChannel
assert.False(s.T(), hasMore, "No variant should come out of invalid channel, it should be closed")
}
func (s *ChannelSuite) TestLowercaseRefAlt() {
vcfLine := `#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 185423
1 847491 rs28407778 gt t 745.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.842;ClippingRankSum=0.147;DB;DP=41;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.109;QD=18.19;ReadPosRankSum=0.334;VQSLOD=2.70;culprit=FS;set=variant GT:AD:DP:GQ:PL 0/1:16,25:41:99:774,0,434`
ioreader := strings.NewReader(vcfLine)
err := vcf.ToChannel(ioreader, s.outChannel, s.invalidChannel)
assert.NoError(s.T(), err, "Valid VCF line should not return error")
variant := <-s.outChannel
assert.NotNil(s.T(), variant, "One variant should come out of channel")
assert.Equal(s.T(), variant.Ref, "GT")
assert.Equal(s.T(), variant.Alt, "T")
_, hasMore := <-s.outChannel
assert.False(s.T(), hasMore, "No second variant should come out of the channel, it should be closed")
_, hasMore = <-s.invalidChannel
assert.False(s.T(), hasMore, "No variant should come out of invalid channel, it should be closed")
}
func (s *ChannelSuite) TestMultipleAlternatives() {
vcfLine := `#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 185423
1 847491 rs28407778 G A,C 745.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.842;ClippingRankSum=0.147;DB;DP=41;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.109;QD=18.19;ReadPosRankSum=0.334;VQSLOD=2.70;culprit=FS;set=variant GT:AD:DP:GQ:PL 0/1:16,25:41:99:774,0,434`
ioreader := strings.NewReader(vcfLine)
err := vcf.ToChannel(ioreader, s.outChannel, s.invalidChannel)
assert.NoError(s.T(), err, "Valid VCF line should not return error")
variant := <-s.outChannel
assert.NotNil(s.T(), variant, "One variant should come out of channel")
assert.Equal(s.T(), variant.Alt, "A")
variant = <-s.outChannel
assert.NotNil(s.T(), variant, "Second variant should come out of channel")
assert.Equal(s.T(), variant.Alt, "C")
_, hasMore := <-s.outChannel
assert.False(s.T(), hasMore, "No third variant should come out of the channel, it should be closed")
_, hasMore = <-s.invalidChannel
assert.False(s.T(), hasMore, "No variant should come out of invalid channel, it should be closed")
}
func TestChannelSuite(t *testing.T) {
suite.Run(t, new(ChannelSuite))
}
type SampleSuite struct {
suite.Suite
}
func (s *SampleSuite) TestNoHeader() {
vcfLine := `1 847491 rs28407778 GTTTA G.... 745.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.842;ClippingRankSum=0.147;DB;DP=41;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.109;QD=18.19;ReadPosRankSum=0.334;VQSLOD=2.70;culprit=FS;set=variant GT:AD:DP:GQ:PL 0/1:16,25:41:99:774,0,434`
ioreader := strings.NewReader(vcfLine)
sampleIDs, err := vcf.SampleIDs(ioreader)
assert.Error(s.T(), err, "VCF without header should return error")
assert.Nil(s.T(), sampleIDs, "No slice of ids is expected on a vcf without header")
}
func (s *SampleSuite) TestValidHeaderNoSample() {
vcfLine := `#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
1 847491 rs28407778 GTTTA G.... 745.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.842;ClippingRankSum=0.147;DB;DP=41;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.109;QD=18.19;ReadPosRankSum=0.334;VQSLOD=2.70;culprit=FS;set=variant GT:AD:DP:GQ:PL 0/1:16,25:41:99:774,0,434`
ioreader := strings.NewReader(vcfLine)
sampleIDs, err := vcf.SampleIDs(ioreader)
assert.NoError(s.T(), err, "VCF with valid header should not return error")
assert.Nil(s.T(), sampleIDs, "No slice of ids should be returned on a vcf with a valid header that doesn't contain any sample")
}
func (s *SampleSuite) TestOneSample() {
vcfLine := `#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 185423
1 847491 rs28407778 GTTTA G.... 745.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.842;ClippingRankSum=0.147;DB;DP=41;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.109;QD=18.19;ReadPosRankSum=0.334;VQSLOD=2.70;culprit=FS;set=variant GT:AD:DP:GQ:PL 0/1:16,25:41:99:774,0,434`
ioreader := strings.NewReader(vcfLine)
sampleIDs, err := vcf.SampleIDs(ioreader)
assert.NoError(s.T(), err, "VCF with valid header should not return error")
assert.NotNil(s.T(), sampleIDs, "A slice of ids should be returned on a vcf with a valid header")
assert.Exactly(s.T(), len(sampleIDs), 1, "Slice of ids should have only one element")
assert.Equal(s.T(), sampleIDs[0], "185423")
}
func (s *SampleSuite) TestThreeSamples() {
vcfLine := `#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 185423 776182 091635
1 847491 rs28407778 GTTTA G.... 745.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.842;ClippingRankSum=0.147;DB;DP=41;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.109;QD=18.19;ReadPosRankSum=0.334;VQSLOD=2.70;culprit=FS;set=variant GT:AD:DP:GQ:PL 0/1:16,25:41:99:774,0,434`
ioreader := strings.NewReader(vcfLine)
sampleIDs, err := vcf.SampleIDs(ioreader)
assert.NoError(s.T(), err, "VCF with valid header should not return error")
assert.NotNil(s.T(), sampleIDs, "A slice of ids should be returned on a vcf with a valid header")
assert.Exactly(s.T(), len(sampleIDs), 3, "Slice of ids should have three elements")
assert.Equal(s.T(), sampleIDs[0], "185423")
assert.Equal(s.T(), sampleIDs[1], "776182")
assert.Equal(s.T(), sampleIDs[2], "091635")
}
func TestSampleSuite(t *testing.T) {
suite.Run(t, new(SampleSuite))
}
type InfoSuite struct {
suite.Suite
outChannel chan *vcf.Variant
invalidChannel chan vcf.InvalidLine
}
func (suite *InfoSuite) SetupTest() {
suite.outChannel = make(chan *vcf.Variant, 10)
suite.invalidChannel = make(chan vcf.InvalidLine, 10)
}
func (s *InfoSuite) TestInfo() {
vcfLine := `#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 185423
1 847491 rs28407778 GTTTA G.... 745.77 PASS AC=1;AF=0.500;AN=2;BaseQRankSum=0.842;ClippingRankSum=0.147;DB;DP=41;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.109;QD=18.19;ReadPosRankSum=0.334;VQSLOD=2.70;culprit=FS;set=variant GT:AD:DP:GQ:PL 0/1:16,25:41:99:774,0,434`
ioreader := strings.NewReader(vcfLine)
err := vcf.ToChannel(ioreader, s.outChannel, s.invalidChannel)
assert.NoError(s.T(), err, "Valid VCF line should not return error")
variant := <-s.outChannel
assert.NotNil(s.T(), variant, "One variant should come out of channel")
assert.NotNil(s.T(), variant.AlleleCount)
assert.Equal(s.T(), *variant.AlleleCount, 1)
assert.NotNil(s.T(), variant.AlleleFrequency)
assert.Equal(s.T(), *variant.AlleleFrequency, 0.5)
assert.NotNil(s.T(), variant.TotalAlleles)
assert.Equal(s.T(), *variant.TotalAlleles, 2)
assert.NotNil(s.T(), variant.InDBSNP)
assert.True(s.T(), *variant.InDBSNP)
assert.NotNil(s.T(), variant.Depth)
assert.Equal(s.T(), *variant.Depth, 41)
assert.NotNil(s.T(), variant.MappingQuality)
assert.Equal(s.T(), *variant.MappingQuality, 60.0)
assert.NotNil(s.T(), variant.MAPQ0Reads)
assert.Equal(s.T(), *variant.MAPQ0Reads, 0)
assert.Nil(s.T(), variant.AncestralAllele)
assert.Nil(s.T(), variant.BaseQuality)
assert.Nil(s.T(), variant.Cigar)
assert.Nil(s.T(), variant.End)
assert.Nil(s.T(), variant.InHapmap2)
assert.Nil(s.T(), variant.InHapmap3)
assert.Nil(s.T(), variant.NumberOfSamples)
assert.Nil(s.T(), variant.StrandBias)
assert.Nil(s.T(), variant.IsSomatic)
assert.Nil(s.T(), variant.IsValidated)
assert.Nil(s.T(), variant.In1000G)
_, hasMore := <-s.outChannel
assert.False(s.T(), hasMore, "No second variant should come out of the channel, it should be closed")
_, hasMore = <-s.invalidChannel
assert.False(s.T(), hasMore, "No variant should come out of invalid channel, it should be closed")
}
func (s *InfoSuite) TestMultiple() {
vcfLine := `#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 185423
5 159478089 rs80263784 GTT G,GT 198.19 . AC=1,2;AF=0.500,0.600;AN=2;BaseQRankSum=1.827;ClippingRankSum=1.323;DB;DP=20;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=60.00;MQ0=0;MQRankSum=0.441;QD=5.74;ReadPosRankSum=0.063;set=variant5 GT:AD:DP:GQ:PL 1/2:2,9,9:20:99:425,145,183,175,0,166
5 159478089 rs80263784 GTT G,GT 198.19 . AC=1,2;AF=0.500,0.600;AN=3,4;BaseQRankSum=1.827;ClippingRankSum=1.323;DB;DP=20;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=60.00;MQ0=0;MQRankSum=0.441;QD=5.74;ReadPosRankSum=0.063;set=variant5 GT:AD:DP:GQ:PL 1/2:2,9,9:20:99:425,145,183,175,0,166`
ioreader := strings.NewReader(vcfLine)
err := vcf.ToChannel(ioreader, s.outChannel, s.invalidChannel)
assert.NoError(s.T(), err, "Valid VCF line should not return error")
// first variant
variant := <-s.outChannel
assert.NotNil(s.T(), variant, "One variant should come out of channel")
assert.NotNil(s.T(), variant.AlleleCount)
assert.Equal(s.T(), *variant.AlleleCount, 1)
assert.NotNil(s.T(), variant.AlleleFrequency)
assert.Equal(s.T(), *variant.AlleleFrequency, 0.5)
assert.NotNil(s.T(), variant.TotalAlleles)
assert.Equal(s.T(), *variant.TotalAlleles, 2)
// second variant
variant, hasMore := <-s.outChannel
assert.True(s.T(), hasMore, "Second variant should be in the channel")
assert.NotNil(s.T(), variant, "Second variant should come out of channel")
assert.NotNil(s.T(), variant.AlleleCount)
assert.Equal(s.T(), *variant.AlleleCount, 2)
assert.NotNil(s.T(), variant.AlleleFrequency)
assert.Equal(s.T(), *variant.AlleleFrequency, 0.6)
assert.NotNil(s.T(), variant.TotalAlleles)
assert.Equal(s.T(), *variant.TotalAlleles, 2)
// third variant
variant, hasMore = <-s.outChannel
assert.True(s.T(), hasMore, "Third variant should be in the channel")
assert.NotNil(s.T(), variant, "Third variant should come out of channel")
assert.NotNil(s.T(), variant.TotalAlleles)
assert.Equal(s.T(), *variant.TotalAlleles, 3)
// fourth variant
variant, hasMore = <-s.outChannel
assert.True(s.T(), hasMore, "Fourth variant should be in the channel")
assert.NotNil(s.T(), variant, "Fourth variant should come out of channel")
assert.NotNil(s.T(), variant.TotalAlleles)
assert.Equal(s.T(), *variant.TotalAlleles, 4)
_, hasMore = <-s.outChannel
assert.False(s.T(), hasMore, "No fifth variant should come out of the channel, it should be closed")
_, hasMore = <-s.invalidChannel
assert.False(s.T(), hasMore, "No variant should come out of invalid channel, it should be closed")
}
func TestInfoSuite(t *testing.T) {
suite.Run(t, new(InfoSuite))
}
type FixSuffixSuite struct {
suite.Suite
outChannel chan *vcf.Variant
invalidChannel chan vcf.InvalidLine
}
func (suite *FixSuffixSuite) SetupTest() {
suite.outChannel = make(chan *vcf.Variant, 10)
suite.invalidChannel = make(chan vcf.InvalidLine, 10)
}
func (s *FixSuffixSuite) TestSimpleVariant() {
vcfLine := `#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 185423
1 138829 . GC TC,G 198.19 . AC=1,2;AF=0.500,0.600;AN=2;BaseQRankSum=1.827;ClippingRankSum=1.323;DB;DP=20;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=60.00;MQ0=0;MQRankSum=0.441;QD=5.74;ReadPosRankSum=0.063;set=variant5 GT:AD:DP:GQ:PL 1/2:2,9,9:20:99:425,145,183,175,0,166`
ioreader := strings.NewReader(vcfLine)
err := vcf.ToChannel(ioreader, s.outChannel, s.invalidChannel)
assert.NoError(s.T(), err, "Valid VCF line should not return error")
// first variant
variant := <-s.outChannel
assert.NotNil(s.T(), variant, "One variant should come out of channel")
assert.Equal(s.T(), variant.Ref, "G")
assert.Equal(s.T(), variant.Alt, "T")
// second variant
variant, hasMore := <-s.outChannel
assert.True(s.T(), hasMore, "Second variant should be in the channel")
assert.NotNil(s.T(), variant, "Second variant should come out of channel")
assert.Equal(s.T(), variant.Ref, "GC")
assert.Equal(s.T(), variant.Alt, "G")
_, hasMore = <-s.outChannel
assert.False(s.T(), hasMore, "No third variant should come out of the channel, it should be closed")
_, hasMore = <-s.invalidChannel
assert.False(s.T(), hasMore, "No variant should come out of invalid channel, it should be closed")
}
func (s *FixSuffixSuite) TestBigSuffix() {
vcfLine := `#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT 185423
1 879415 . CGGCCACGTCCCCCTATGGAGGG C,TGGCCACGTCCCCCTATGGAGGG,CGGCCACGTCCCCCTATGGAGGGGGCCACGTCCCCCTATGGAGGG 198.19 . AC=1,2;AF=0.500,0.600;AN=2;BaseQRankSum=1.827;ClippingRankSum=1.323;DB;DP=20;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=60.00;MQ0=0;MQRankSum=0.441;QD=5.74;ReadPosRankSum=0.063;set=variant5 GT:AD:DP:GQ:PL 1/2:2,9,9:20:99:425,145,183,175,0,166`
ioreader := strings.NewReader(vcfLine)
err := vcf.ToChannel(ioreader, s.outChannel, s.invalidChannel)
assert.NoError(s.T(), err, "Valid VCF line should not return error")
// first variant
variant := <-s.outChannel
assert.NotNil(s.T(), variant, "One variant should come out of channel")
assert.Equal(s.T(), variant.Ref, "CGGCCACGTCCCCCTATGGAGGG")
assert.Equal(s.T(), variant.Alt, "C")
// second variant
variant, hasMore := <-s.outChannel
assert.True(s.T(), hasMore, "Second variant should be in the channel")
assert.NotNil(s.T(), variant, "Second variant should come out of channel")
assert.Equal(s.T(), variant.Ref, "C")
assert.Equal(s.T(), variant.Alt, "T")
// third variant
variant, hasMore = <-s.outChannel
assert.True(s.T(), hasMore, "Third variant should be in the channel")
assert.NotNil(s.T(), variant, "Third variant should come out of channel")
assert.Equal(s.T(), variant.Ref, "C")
assert.Equal(s.T(), variant.Alt, "CGGCCACGTCCCCCTATGGAGGG")
_, hasMore = <-s.outChannel
assert.False(s.T(), hasMore, "No fourth variant should come out of the channel, it should be closed")
_, hasMore = <-s.invalidChannel
assert.False(s.T(), hasMore, "No variant should come out of invalid channel, it should be closed")
}
func TestFixSuffixSuite(t *testing.T) {
suite.Run(t, new(FixSuffixSuite))
}