package vcfgo_test

import (

"io"

"strings"

"github.com/brentp/vcfgo"

. "gopkg.in/check.v1"

)

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;SVLEN=-297;CIPOS=-22,18;CIEND=-12,32 GT:GQ 0/1:12

3 9425916 . C <INS:ME:L1> 23 PASS SVTYPE=INS;END=9425916;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) {

}