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package vcfgo_test
import (
"io"
"strings"
"testing"
"github.com/brentp/vcfgo"
. "gopkg.in/check.v1"
)
func Test(t *testing.T) { TestingT(t) }
var cnvStr = `##fileformat=VCFv4.1
##fileDate=20100501
##reference=1000GenomesPilot-NCBI36
##assembly=ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/sv/breakpoint_assemblies.fasta
##INFO=<ID=BKPTID,Number=.,Type=String,Description="ID of the assembled alternate allele in the assembly file">
##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##ALT=<ID=DEL,Description="Deletion">
##ALT=<ID=DEL:ME:ALU,Description="Deletion of ALU element">
##ALT=<ID=DEL:ME:L1,Description="Deletion of L1 element">
##ALT=<ID=DUP,Description="Duplication">
##ALT=<ID=DUP:TANDEM,Description="Tandem Duplication">
##ALT=<ID=INS,Description="Insertion of novel sequence">
##ALT=<ID=INS:ME:ALU,Description="Insertion of ALU element">
##ALT=<ID=INS:ME:L1,Description="Insertion of L1 element">
##ALT=<ID=INV,Description="Inversion">
##ALT=<ID=CNV,Description="Copy number variable region">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype quality">
##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number genotype for imprecise events">
##FORMAT=<ID=CNQ,Number=1,Type=Float,Description="Copy number genotype quality for imprecise events">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001
2 321682 . T <DEL> 6 PASS SVTYPE=DEL;END=321887;SVLEN=-205;CIPOS=-56,20;CIEND=-10,62 GT:GQ 0/1:12
2 14477084 . C <DEL:ME:ALU> 12 PASS SVTYPE=DEL;END=14477381;CIPOS=-22,18;CIEND=-12,32 GT:GQ 0/1:12
3 9425916 . C <INS:ME:L1> 23 PASS SVTYPE=INS;SVLEN=6027;CIPOS=-16,22 GT:GQ 1/1:15
3 12665100 . A <DUP> 14 PASS SVTYPE=DUP;END=12686200;SVLEN=21100;CIPOS=-500,500;CIEND=-500,500 GT:GQ:CN:CNQ ./.:0:3:16.2
4 18665128 . T <DUP:TANDEM> 11 PASS SVTYPE=DUP;END=18665204;SVLEN=76;CIPOS=-10,10;CIEND=-10,10 GT:GQ:CN:CNQ ./.:0:5:8.3
4 18665128 . T <INV> 11 PASS SVTYPE=INS;END=18665204;SVLEN=76;CIPOS=-10,10;CIEND=-10,10 GT:GQ:CN:CNQ ./.:0:5:8.3
4 18665128 . T <CNV> 11 PASS SVTYPE=DUP;END=18665204;SVLEN=76;CIPOS=-10,10;CIEND=-10,10 GT:GQ:CN:CNQ ./.:0:5:8.3
4 43266825 rs369548269 T <DEL> . . ON=0;OLD_MULTIALLELIC=4:43266825:T/TAC/<DEL> GT 0/1
5 755892 175981_1 N ]1:759001]N 112.69 PASS AC=4;AF=0.01361;ALG=PROD;AN=294;CIEND=-10,29;CIEND95=0,34;CIPOS=-30,29;CIPOS95=28,32;EVENT=175981;EXVAR=0.00508;HW=0.00;HetPct=2.7;HomRefPct=97.3;HomVarPct=0.0;IMPRECISE;MATEID=1 GT 0/1`
//1 2827694 rs2376870 CGTGGATGCGGGGAC C . PASS SVTYPE=DEL;END=2827762;HOMLEN=1;HOMSEQ=G;SVLEN=-68 GT:GQ 1/1:13.9
type CNVSuite struct {
reader io.Reader
vcfStr string
}
var _ = Suite(&CNVSuite{vcfStr: cnvStr})
func (s *CNVSuite) SetUpTest(c *C) {
s.reader = strings.NewReader(s.vcfStr)
}
func (s *CNVSuite) TestDupIns(c *C) {
r, err := vcfgo.NewReader(s.reader, false)
c.Assert(err, IsNil)
var v *vcfgo.Variant
v = r.Read() //.(*vcfgo.Variant)
c.Assert(int(v.End()), Equals, 321887)
left, right, ok := v.CIPos()
c.Assert(ok, Equals, true)
c.Assert(int(left), Equals, 321682-56-1)
c.Assert(int(right), Equals, 321682+20)
eleft, eright, ok := v.CIEnd()
c.Assert(ok, Equals, true)
c.Assert(int(eleft), Equals, 321887-10-1)
c.Assert(int(eright), Equals, 321887+62)
v = r.Read() //.(*vcfgo.Variant)
c.Assert(int(v.End()), Equals, 14477381)
v = r.Read() //.(*vcfgo.Variant)
c.Assert(int(v.Start()), Equals, 9425915)
c.Assert(int(v.End()), Equals, 9431943)
v = r.Read() //.(*vcfgo.Variant)
c.Assert(int(v.End()), Equals, 12686200)
v = r.Read() //.(*vcfgo.Variant)
c.Assert(int(v.End()), Equals, 18665204)
v = r.Read() //.(*vcfgo.Variant) // INS
c.Assert(int(v.End()), Equals, 18665204)
v = r.Read() //.(*vcfgo.Variant) // CNV
c.Assert(int(v.End()), Equals, 18665204)
v = r.Read() //.(*vcfgo.Variant) // CNV
c.Assert(int(v.End()), Equals, 43266825)
left, right, ok = v.CIPos()
c.Assert(left, Equals, v.Start())
c.Assert(right, Equals, v.Start()+uint32(1))
c.Assert(ok, Equals, false)
eleft, eright, ok = v.CIEnd()
c.Assert(eleft, Equals, v.End()-1)
c.Assert(eright, Equals, v.End())
c.Assert(ok, Equals, false)
v = r.Read() //.(*vcfgo.Variant) // BND
c.Assert(int(v.Start()), Equals, 755891)
c.Assert(int(v.End()), Equals, 755891+1)
}
var svlenNumberAStr = `##fileformat=VCFv4.1
##fileDate=20100501
##reference=1000GenomesPilot-NCBI36
##assembly=ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/sv/breakpoint_assemblies.fasta
##INFO=<ID=SVLEN,Number=A,Type=Integer,Description="Length of structural variant">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##ALT=<ID=DEL,Description="Deletion">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001
1 1000 . T <DEL> 60 PASS SVTYPE=DEL;SVLEN=100 GT 0/1
1 2000 . A <DEL>,<DEL> 60 PASS SVTYPE=DEL;SVLEN=150,200 GT 1/2
`
type SVLENNumberASuite struct {
reader io.Reader
vcfStr string
}
var _ = Suite(&SVLENNumberASuite{vcfStr: svlenNumberAStr})
func (s *SVLENNumberASuite) SetUpTest(c *C) {
s.reader = strings.NewReader(s.vcfStr)
}
func (s *SVLENNumberASuite) TestSVLENNumberA(c *C) {
r, err := vcfgo.NewReader(s.reader, false)
c.Assert(err, IsNil)
var v *vcfgo.Variant
// Test single alternative allele with SVLEN Number=A
v = r.Read()
c.Assert(v, NotNil)
c.Assert(int(v.Start()), Equals, 999) // 0-based
c.Assert(int(v.End()), Equals, 1100) // 1000 + 100
// Test multiple alternative alleles with SVLEN Number=A
v = r.Read()
c.Assert(v, NotNil)
c.Assert(int(v.Start()), Equals, 1999) // 0-based
c.Assert(int(v.End()), Equals, 2150) // 2000 + 150 (first alt allele)
}
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