func (s *TBXSuite) TestRead(c *C) {
t, err := cgotbx.New("data/vt.norm.vcf.gz")
c.Assert(err, IsNil)
rdr, err := t.Get("chr1", 50000, 90000)
c.Assert(err, IsNil)
str, err := ioutil.ReadAll(rdr)
c.Assert(err, IsNil)
c.Assert(len(str) != 0, Equals, true)
}
func main2() {
/*
f, err := os.Create("q.pprof")
if err != nil {
panic(err)
}
pprof.StartCPUProfile(f)
defer pprof.StopCPUProfile()
*/
t, err := cgotbx.New(os.Args[1])
if err != nil {
log.Fatal(err)
}
var rdr io.Reader
for i := 0; i < 1000; i++ {
tot := 0
f, err := xopen.Ropen(os.Args[1])
check(err)
vcf, err := vcfgo.NewReader(f, true)
check(err)
t0 := 0
for {
v := vcf.Read()
if v == nil {
break
}
ts := time.Now()
for k := 0; k < 100; k++ {
rdr, err = t.Get(v.Chrom(), int(v.Start()), int(v.Start())+1)
check(err)
brdr := bufio.NewReader(rdr)
//fmt.Fprintln(os.Stderr, v.Chrom(), v.Start(), v.Start()+1)
j := 0
for l, err := brdr.ReadString('\n'); err == nil; l, err = brdr.ReadString('\n') {
//fmt.Fprintln(os.Stderr, "...", l[:20])
_ = l
tot += 1
j += 1
}
if j == 0 {
log.Fatal("should have found something")
}
}
t0 += int(time.Since(ts).Nanoseconds())
}
log.Println(tot, float64(t0)*1e-9)
}
}
func (s *TBXSuite) TestLongLine(c *C) {
t, err := cgotbx.New("data/vt.norm.vcf.gz")
c.Assert(err, IsNil)
rdr, err := t.Get("chr1", 915415, 915428)
c.Assert(err, IsNil)
b := bufio.NewReader(rdr)
line, e := b.ReadString('\n')
log.Println(line)
c.Assert(e, IsNil)
line, e = b.ReadString('\n')
log.Println(line[:20])
c.Assert(e, IsNil)
line, e = b.ReadString('\n')
c.Assert(e, Equals, io.EOF)
}
