func (s *S) TestReadFastq(c *check.C) {
r := fastq.NewReader(strings.NewReader(fq), linear.NewQSeq("", nil, alphabet.DNA, alphabet.Sanger))
m, _ := multi.NewMulti("", nil, seq.DefaultQConsensus)
a, err := NewReader(r, m).Read()
c.Check(err, check.Equals, nil)
c.Check(a.Rows(), check.Equals, 25)
}
func (s *S) TestReadFastq(c *check.C) {
var (
obtainNfq []string
obtainQL [][]alphabet.QLetter
)
sc := seqio.NewScanner(
fastq.NewReader(
bytes.NewBufferString(fq0),
linear.NewQSeq("", nil, alphabet.DNA, alphabet.Sanger),
),
)
for sc.Next() {
t := sc.Seq().(*linear.QSeq)
header := t.Name()
if desc := t.Description(); len(desc) > 0 {
header += " " + desc
}
obtainNfq = append(obtainNfq, header)
obtainQL = append(obtainQL, (t.Slice().(alphabet.QLetters)))
}
c.Check(sc.Error(), check.Equals, nil)
c.Check(obtainNfq, check.DeepEquals, expectNfq)
c.Check(obtainQL, check.DeepEquals, expectQL)
}
