func TestIntervalLine(t *testing.T) {
s := []byte("chr1\t1235\t4567\tasdf")
i, _ := parsers.IntervalFromBedLine(s)
if i.Start() != uint32(1235) {
t.Error("expected start of 1235")
}
}
func (t *Tabix) Get(q interfaces.IPosition) []interfaces.IPosition {
//cs := C.CString(fmt.Sprintf("%s:%d-%d", q.Chrom(), q.Start()+1, q.End()))
ch := C.CString(q.Chrom())
cs := C.tbx_name2id(t.tbx, ch)
itr := C.tabix_itr_queryi(t.tbx, cs, C.int(q.Start()), C.int(q.End()))
kstr := C.kstring_t{}
overlaps := make([]interfaces.IPosition, 0, 4)
l := C.int(10)
for l > 0 {
l := C.atbx_itr_next(t.htf, t.tbx, itr, &kstr)
if l < 0 {
break
}
//res := C.GoString(kstr.s)
if t.typ == VCF {
b := C.bcf_init()
ret := C.vcf_parse(&kstr, t.hdr, b)
if ret < 0 {
log.Printf("error parsing %s\n", C.GoStringN(kstr.s, C.int(kstr.l)))
}
overlaps = append(overlaps, NewVariant(b, t.hdr, 1))
} else if t.typ == BED {
iv, err := parsers.IntervalFromBedLine(C.GoBytes(unsafe.Pointer(kstr.s), C.int(kstr.l)))
if err != nil {
log.Printf("error parsing %s:%s\n", C.GoStringN(kstr.s, C.int(kstr.l)), err)
}
if iv != nil {
overlaps = append(overlaps, iv)
}
}
}
C.hts_itr_destroy(itr)
C.free(unsafe.Pointer(ch))
C.free(unsafe.Pointer(kstr.s))
return overlaps
}
func (s *APISuite) SetUpTest(c *C) {
h.Infos["DP"] = &vcfgo.Info{Id: "DP", Description: "depth", Number: "1", Type: "Integer"}
h.Infos["SVLEN"] = &vcfgo.Info{Id: "SVLEN", Description: "SVLEN", Number: "1", Type: "Integer"}
h.Infos["CIPOS"] = &vcfgo.Info{Id: "CIPOS", Description: "CIPOS", Number: "2", Type: "Integer"}
h.Infos["CIEND"] = &vcfgo.Info{Id: "CIEND", Description: "CIEND", Number: "2", Type: "Integer"}
h.Infos["AF"] = &vcfgo.Info{Id: "AF", Description: "AF", Number: "1", Type: "Float"}
h.Infos["AC_AFR"] = &vcfgo.Info{Id: "AF_AFR", Description: "AF_AFR", Number: "1", Type: "Float"}
vv := *v1
vv.Info_ = vcfgo.NewInfoByte([]byte("DP=35"), h)
s.v1 = &parsers.Variant{IVariant: &vv}
s.v1.SetSource(0)
v2 := *v1
v2.Info_ = vcfgo.NewInfoByte([]byte("DP=44"), h)
s.v2 = &parsers.Variant{IVariant: &v2}
s.v2.Info().Set("AC_AFR", 33)
s.v2.SetSource(1)
sv1.Info_ = vcfgo.NewInfoByte([]byte("DP=35;SVLEN=15;CIPOS=-5,5;CIEND=-8,8"), h)
s.sv1 = &parsers.Variant{IVariant: sv1}
s.sv1.SetSource(0)
v3 := *v1
v3.Info_ = vcfgo.NewInfoByte([]byte("DP=88"), h)
s.v3 = &parsers.Variant{IVariant: &v3}
s.v3.SetSource(1)
v, e := v1.Info_.Get("DP")
c.Assert(e, IsNil)
c.Assert(v, Equals, 35)
v, e = v2.Info_.Get("DP")
c.Assert(e, IsNil)
c.Assert(v, Equals, 44)
v, e = v3.Info_.Get("DP")
c.Assert(e, IsNil)
c.Assert(v, Equals, 88)
s.v1.AddRelated(s.v2)
s.v1.AddRelated(s.v3)
s.sv1.AddRelated(s.v2)
s.sv1.AddRelated(s.v3)
c.Assert(2, Equals, len(s.v1.Related()))
sbed, err := parsers.IntervalFromBedLine([]byte("chr1\t224\t244\t111\t222"))
c.Assert(err, IsNil)
s.bed = sbed.(*parsers.Interval)
s.bed.SetSource(2)
s.v1.AddRelated(s.bed)
s.sv1.AddRelated(s.bed)
s.src = Source{
File: "example/fitcons.bed",
Op: "mean",
Name: "fitcons_mean",
Column: 4,
Field: "",
Index: 1,
}
s.src0 = Source{
File: "example/exac.vcf",
Op: "first",
Column: -1,
Field: "AC_AFR",
Name: "AC_AFR",
Index: 0,
}
empty := make([]PostAnnotation, 0)
code := `
function sum(t)
local sum = 0
for i=1,#t do
sum = sum + t[i]
end
return sum
end
function mean(t)
return sum(t) / #t
end
`
s.annotator = NewAnnotator([]*Source{&s.src0, &s.src}, code, false, true, empty)
}
func makeBed(chrom string, start int, end int, val float32) *parsers.Interval {
i, _ := parsers.IntervalFromBedLine([]byte(fmt.Sprintf("%s\t%d\t%d\t%.3f", chrom, start, end, val)))
return i.(*parsers.Interval)
}
