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|
package vcfgo
import (
"os"
"testing"
. "gopkg.in/check.v1"
)
func Test(t *testing.T) { TestingT(t) }
type VCFSuite struct{}
var _ = Suite(&VCFSuite{})
var infotests = []struct {
input string
exp *Info
}{
{`##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">`,
&Info{Id: "NS", Number: "1", Type: "Integer", Description: "Number of Samples With Data"}},
{`##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">`,
&Info{Id: "DP", Number: "1", Type: "Integer", Description: "Total Depth"}},
{`##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">`,
&Info{Id: "AF", Number: "A", Type: "Float", Description: "Allele Frequency"}},
{`##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">`,
&Info{Id: "AA", Number: "1", Type: "String", Description: "Ancestral Allele"}},
{`##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">`,
&Info{Id: "DB", Number: "0", Type: "Flag", Description: "dbSNP membership, build 129"}},
{`##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">`,
&Info{Id: "H2", Number: "0", Type: "Flag", Description: "HapMap2 membership"}},
}
var formattests = []struct {
input string
exp *SampleFormat
}{
{`##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">`,
&SampleFormat{Id: "GT", Number: "1", Type: "String", Description: "Genotype"}},
{`##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">`,
&SampleFormat{Id: "GQ", Number: "1", Type: "Integer", Description: "Genotype Quality"}},
{`##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">`,
&SampleFormat{Id: "HQ", Number: "2", Type: "Integer", Description: "Haplotype Quality"}},
{`##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">`,
&SampleFormat{Id: "DP", Number: "1", Type: "Integer", Description: "Read Depth"}},
}
var filtertests = []struct {
filter string
exp []string
}{
{`##FILTER=<ID=q10,Description="Quality below 10">`,
[]string{"q10", "Quality below 10"}},
{`##FILTER=<ID=s50,Description="Less than 50% of samples have data">`,
[]string{"s50", "Less than 50% of samples have data"}},
}
var samplelinetests = []struct {
line string
exp []string
}{
{`#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003`, []string{"NA00001", "NA00002", "NA00003"}},
{`#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT`, []string{}},
}
func (s *VCFSuite) TestHeaderInfoParse(c *C) {
for _, v := range infotests {
obs, err := parseHeaderInfo(v.input)
c.Assert(err, IsNil)
c.Assert(obs, DeepEquals, v.exp)
c.Assert(obs.String(), Equals, v.input)
}
}
func (s *VCFSuite) TestHeaderFormatParse(c *C) {
for _, v := range formattests {
obs, err := parseHeaderFormat(v.input)
c.Assert(err, IsNil)
c.Assert(obs, DeepEquals, v.exp)
c.Assert(obs.String(), Equals, v.input)
}
}
func (s *VCFSuite) TestHeaderFilterParse(c *C) {
for _, v := range filtertests {
obs, err := parseHeaderFilter(v.filter)
c.Assert(err, IsNil)
c.Assert(obs, DeepEquals, v.exp)
}
}
func (s *VCFSuite) TestHeaderVersionParse(c *C) {
obs, err := parseHeaderFileVersion(`##fileformat=VCFv4.2`)
c.Assert(err, IsNil)
c.Assert(obs, Equals, "4.2")
}
func (s *VCFSuite) TestHeaderBadVersionParse(c *C) {
_, err := parseHeaderFileVersion(`##fileformat=VFv4.2`)
c.Assert(err, ErrorMatches, "file format error.*")
}
func (s *VCFSuite) TestHeaderContigParse(c *C) {
m, err := parseHeaderContig(`##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>`)
c.Assert(err, IsNil)
c.Assert(m, DeepEquals, map[string]string{"assembly": "B36", "md5": "f126cdf8a6e0c7f379d618ff66beb2da", "species": "\"Homo sapiens\"", "taxonomy": "x", "ID": "20", "length": "62435964"})
}
func (s *VCFSuite) TestHeaderExtra(c *C) {
obs, err := parseHeaderExtraKV("##key=value")
c.Assert(err, IsNil)
c.Assert(obs[0], Equals, "key")
c.Assert(obs[1], Equals, "value")
}
func (s *VCFSuite) TestHeaderSampleLine(c *C) {
for _, v := range samplelinetests {
r, err := parseSampleLine(v.line)
c.Assert(err, IsNil)
c.Assert(r, DeepEquals, v.exp)
}
}
func (s *VCFSuite) TestIssue5(c *C) {
rdr, err := os.Open("test-multi-allelic.vcf")
c.Assert(err, IsNil)
vcf, err := NewReader(rdr, false)
c.Assert(err, IsNil)
variant := vcf.Read()
samples := variant.Samples
c.Assert(samples[0].GT, DeepEquals, []int{2, 2})
c.Assert(samples[1].GT, DeepEquals, []int{2, 2})
c.Assert(samples[2].GT, DeepEquals, []int{2, 2})
}
|
