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// Copyright ©2020 The bíogo Authors. All rights reserved.
// Use of this source code is governed by a BSD-style
// license that can be found in the LICENSE file.
package fai
import (
"encoding/json"
"io"
"io/ioutil"
"os"
"path/filepath"
"testing"
)
func TestFile(t *testing.T) {
files, err := filepath.Glob("testdata/*.fa")
if err != nil {
t.Fatalf("unexpected error: %v", err)
}
for _, p := range files {
f, err := os.Open(p + ".fai")
if err != nil {
t.Errorf("unexpected error: %v", err)
continue
}
idx, err := ReadFrom(f)
f.Close()
if err != nil {
t.Errorf("unexpected error: %v", err)
continue
}
b, err := ioutil.ReadFile(p + ".json")
if err != nil {
t.Errorf("unexpected error: %v", err)
continue
}
var tests []struct {
Seq string
Start, End int
Want string
}
err = json.Unmarshal(b, &tests)
if err != nil {
t.Errorf("unexpected error: %v", err)
continue
}
f, err = os.Open(p)
if err != nil {
t.Errorf("unexpected error: %v", err)
continue
}
m := NewFile(f, idx)
for _, test := range tests {
var s *Seq
if test.Start == -1 {
s, err = m.Seq(test.Seq)
} else {
s, err = m.SeqRange(test.Seq, test.Start, test.End)
}
if err != nil {
t.Errorf("unexpected error: %v", err)
continue
}
for _, bufSize := range []int{10, 100, 1000} {
buf := make([]byte, bufSize)
var got []byte
for {
n, err := s.Read(buf)
got = append(got, buf[:n]...)
if err != nil {
if err == io.EOF {
break
}
t.Errorf("unexpected error: %v", err)
}
}
if test.Start != -1 && len(got) != test.End-test.Start {
t.Errorf("unexpected sequence length: got:%d want:%d", len(got), test.End-test.Start)
}
if string(got) != test.Want {
t.Errorf("unexpected sequence: got:%q want:%q", got, test.Want)
}
s.Reset()
}
}
f.Close()
}
}
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