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// Copyright ©2017 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 bam
import (
"bytes"
"fmt"
"io"
"sort"
"testing"
"github.com/biogo/hts/sam"
)
type byFunc struct {
less func(a, b *sam.Record) bool
recs []*sam.Record
}
func (r byFunc) Len() int { return len(r.recs) }
func (r byFunc) Less(i, j int) bool { return r.less(r.recs[i], r.recs[j]) }
func (r byFunc) Swap(i, j int) { r.recs[i], r.recs[j] = r.recs[j], r.recs[i] }
func sortBAM(r io.Reader, so sam.SortOrder, less func(a, b *sam.Record) bool, fn func(*sam.Record), shard int) error {
br, err := NewReader(r, 0)
if err != nil {
return fmt.Errorf("failed to open bam reader: %v", err)
}
defer br.Close()
h := br.Header().Clone()
h.SortOrder = so
recs := make([]*sam.Record, 0, shard)
var t []*Reader
it := sam.NewIterator(br)
for {
var n int
for it.Next() {
recs = append(recs, it.Record())
if len(recs) == cap(recs) {
r, err := writeSorted(h, recs, less)
if err != nil {
return err
}
defer r.Close()
t = append(t, r)
n, recs = len(recs), recs[:0]
}
}
if len(recs) != 0 {
r, err := writeSorted(h, recs, less)
if err != nil {
return err
}
defer r.Close()
t = append(t, r)
break
}
err = it.Error()
if n == 0 || err != nil {
break
}
}
if err != nil {
return fmt.Errorf("error during bam reading: %v", err)
}
m, err := NewMerger(less, t...)
if err != nil {
return fmt.Errorf("failed to create merger: %v", err)
}
sorted := sam.NewIterator(m)
for sorted.Next() {
fn(sorted.Record())
}
err = sorted.Error()
if err != nil {
return fmt.Errorf("error during bam reading: %v", err)
}
return nil
}
func writeSorted(h *sam.Header, recs []*sam.Record, less func(a, b *sam.Record) bool) (*Reader, error) {
if less != nil {
sort.Sort(byFunc{less, recs})
}
var buf bytes.Buffer
bw, err := NewWriter(&buf, h, 0)
if err != nil {
return nil, fmt.Errorf("failed to open bam writer: %v", err)
}
for _, r := range recs {
err = bw.Write(r)
if err != nil {
return nil, fmt.Errorf("failed to write record: %v", err)
}
}
err = bw.Close()
if err != nil {
return nil, fmt.Errorf("failed to close bam writer: %v", err)
}
r, err := NewReader(&buf, 0)
if err != nil {
return nil, fmt.Errorf("failed to open bam writer: %v", err)
}
return r, err
}
var mergerTests = []struct {
r func() io.Reader
so sam.SortOrder
less func(a, b *sam.Record) bool
expect func(a, b *sam.Record) bool
shard int
}{
{
r: func() io.Reader { return bytes.NewReader(bamHG00096_1000) },
so: sam.QueryName,
less: nil,
expect: (*sam.Record).LessByName,
shard: 199,
},
{
r: func() io.Reader { return bytes.NewReader(bamHG00096_1000) },
so: sam.QueryName,
less: nil,
expect: (*sam.Record).LessByName,
shard: 1e5,
},
{
r: func() io.Reader { return bytes.NewReader(bamHG00096_1000) },
so: sam.Unsorted,
less: nil,
expect: (*sam.Record).LessByCoordinate, // HG00096 is sorted by coordinate.
shard: 199,
},
}
func TestMerger(t *testing.T) {
for _, test := range mergerTests {
var recs []*sam.Record
fn := func(r *sam.Record) {
recs = append(recs, r)
}
var less func(a, b *sam.Record) bool
switch test.so {
case sam.UnknownOrder:
less = test.less
case sam.Unsorted:
case sam.QueryName:
less = (*sam.Record).LessByName
case sam.Coordinate:
less = (*sam.Record).LessByCoordinate
}
err := sortBAM(test.r(), test.so, less, fn, test.shard)
if err != nil {
t.Errorf("unexpected error: %v", err)
}
if less == nil {
continue
}
if !sort.IsSorted(byFunc{test.expect, recs}) {
t.Error("not in expected sort order")
}
}
}
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