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// Copyright ©2014 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 internal
import (
"encoding/binary"
"fmt"
"io"
"sort"
"github.com/biogo/hts/bgzf"
)
// ReadIndex reads the Index from the given io.Reader.
func ReadIndex(r io.Reader, n int32, typ string) (Index, error) {
var (
idx Index
err error
)
idx.Refs, err = readIndices(r, n, typ)
if err != nil {
return idx, err
}
var nUnmapped uint64
err = binary.Read(r, binary.LittleEndian, &nUnmapped)
if err == nil {
idx.Unmapped = &nUnmapped
} else if err != io.EOF {
return idx, err
}
idx.IsSorted = true
// Set the index of the last record to max int to
// prevent addition of records out of order. This
// means that the only way to append to an index is
// to re-index and add to that created index.
// TODO(kortschak) See if index appending is feasible
// and needed.
idx.LastRecord = int(^uint(0) >> 1)
return idx, nil
}
func readIndices(r io.Reader, n int32, typ string) ([]RefIndex, error) {
var err error
idx := make([]RefIndex, n)
for i := range idx {
idx[i].Bins, idx[i].Stats, err = readBins(r, typ)
if err != nil {
return nil, err
}
idx[i].Intervals, err = readIntervals(r, typ)
if err != nil {
return nil, err
}
}
return idx, nil
}
func readBins(r io.Reader, typ string) ([]Bin, *ReferenceStats, error) {
var n int32
err := binary.Read(r, binary.LittleEndian, &n)
if err != nil {
return nil, nil, err
}
if n == 0 {
return nil, nil, nil
}
var stats *ReferenceStats
bins := make([]Bin, n)
for i := 0; i < len(bins); i++ {
err = binary.Read(r, binary.LittleEndian, &bins[i].Bin)
if err != nil {
return nil, nil, fmt.Errorf("%s: failed to read bin number: %v", typ, err)
}
err = binary.Read(r, binary.LittleEndian, &n)
if err != nil {
return nil, nil, fmt.Errorf("%s: failed to read bin count: %v", typ, err)
}
if bins[i].Bin == StatsDummyBin {
if n != 2 {
return nil, nil, fmt.Errorf("%s: malformed dummy bin header", typ)
}
stats, err = readStats(r, typ)
if err != nil {
return nil, nil, err
}
bins = bins[:len(bins)-1]
i--
continue
}
bins[i].Chunks, err = readChunks(r, n, typ)
if err != nil {
return nil, nil, err
}
}
if !sort.IsSorted(byBinNumber(bins)) {
sort.Sort(byBinNumber(bins))
}
return bins, stats, nil
}
func readChunks(r io.Reader, n int32, typ string) ([]bgzf.Chunk, error) {
if n == 0 {
return nil, nil
}
chunks := make([]bgzf.Chunk, n)
var buf [16]byte
for i := range chunks {
// Get the begin and end offset in a single read.
_, err := io.ReadFull(r, buf[:])
if err != nil {
return nil, fmt.Errorf("%s: failed to read chunk virtual offset: %v", typ, err)
}
chunks[i].Begin = makeOffset(binary.LittleEndian.Uint64(buf[:8]))
chunks[i].End = makeOffset(binary.LittleEndian.Uint64(buf[8:]))
}
if !sort.IsSorted(byBeginOffset(chunks)) {
sort.Sort(byBeginOffset(chunks))
}
return chunks, nil
}
func readStats(r io.Reader, typ string) (*ReferenceStats, error) {
var (
vOff uint64
stats ReferenceStats
err error
)
err = binary.Read(r, binary.LittleEndian, &vOff)
if err != nil {
return nil, fmt.Errorf("%s: failed to read index stats chunk begin virtual offset: %v", typ, err)
}
stats.Chunk.Begin = makeOffset(vOff)
err = binary.Read(r, binary.LittleEndian, &vOff)
if err != nil {
return nil, fmt.Errorf("%s: failed to read index stats chunk end virtual offset: %v", typ, err)
}
stats.Chunk.End = makeOffset(vOff)
err = binary.Read(r, binary.LittleEndian, &stats.Mapped)
if err != nil {
return nil, fmt.Errorf("%s: failed to read index stats mapped count: %v", typ, err)
}
err = binary.Read(r, binary.LittleEndian, &stats.Unmapped)
if err != nil {
return nil, fmt.Errorf("%s: failed to read index stats unmapped count: %v", typ, err)
}
return &stats, nil
}
func readIntervals(r io.Reader, typ string) ([]bgzf.Offset, error) {
var n int32
err := binary.Read(r, binary.LittleEndian, &n)
if err != nil {
return nil, err
}
if n == 0 {
return nil, nil
}
offsets := make([]bgzf.Offset, n)
// chunkSize determines the number of offsets consumed by each binary.Read.
const chunkSize = 512
var vOffs [chunkSize]uint64
for i := 0; i < int(n); i += chunkSize {
l := min(int(n)-i, len(vOffs))
err = binary.Read(r, binary.LittleEndian, vOffs[:l])
if err != nil {
return nil, fmt.Errorf("%s: failed to read tile interval virtual offset: %v", typ, err)
}
for k := 0; k < l; k++ {
offsets[i+k] = makeOffset(vOffs[k])
}
}
if !sort.IsSorted(byVirtOffset(offsets)) {
sort.Sort(byVirtOffset(offsets))
}
return offsets, nil
}
func min(a, b int) int {
if a < b {
return a
}
return b
}
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