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package parsers_test
import (
"testing"
"github.com/brentp/irelate/parsers"
. "gopkg.in/check.v1"
)
func Test(t *testing.T) { TestingT(t) }
type BamSuite struct{}
var _ = Suite(&BamSuite{})
type ip struct {
chrom string
start uint32
end uint32
}
func (p ip) Chrom() string {
return p.chrom
}
func (p ip) Start() uint32 {
return p.start
}
func (p ip) End() uint32 {
return p.end
}
func (s *BamSuite) TestBamQuery(c *C) {
b, err := parsers.NewBamQueryable("../data/ex.bam")
c.Assert(err, IsNil)
reg := ip{"chr1", 3048448, 3049340}
q, err := b.Query(reg)
c.Assert(err, IsNil)
j := 0
for rec, e := q.Next(); e == nil; rec, e = q.Next() {
c.Assert(rec.Chrom(), Equals, "chr1")
j++
}
c.Assert(j, Equals, 2)
}
|
