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// Copyright ©2015 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 csi
import (
"encoding/binary"
"errors"
"fmt"
"io"
"sort"
"github.com/biogo/hts/bgzf"
"github.com/biogo/hts/bgzf/index"
)
// ReadFrom reads the CSI index from the given io.Reader. Note that
// the csi specification states that the index is stored as BGZF, but
// ReadFrom does not perform decompression.
func ReadFrom(r io.Reader) (*Index, error) {
var (
idx Index
magic [3]byte
err error
)
err = binary.Read(r, binary.LittleEndian, &magic)
if err != nil {
return nil, err
}
if magic != csiMagic {
return nil, errors.New("csi: magic number mismatch")
}
version := []byte{0}
_, err = io.ReadFull(r, version)
if err != nil {
return nil, err
}
idx.Version = version[0]
if idx.Version != 0x1 && idx.Version != 0x2 {
return nil, fmt.Errorf("csi: unknown version: %d", version[0])
}
err = binary.Read(r, binary.LittleEndian, &idx.minShift)
if err != nil {
return nil, err
}
if int32(idx.minShift) < 0 {
return nil, errors.New("csi: invalid minimum shift value")
}
err = binary.Read(r, binary.LittleEndian, &idx.depth)
if err != nil {
return nil, err
}
if int32(idx.depth) < 0 {
return nil, errors.New("csi: invalid index depth value")
}
var n int32
err = binary.Read(r, binary.LittleEndian, &n)
if err != nil {
return nil, err
}
if n > 0 {
idx.Auxilliary = make([]byte, n)
_, err = io.ReadFull(r, idx.Auxilliary)
if err != nil {
return nil, err
}
}
binLimit := uint32(((1 << ((idx.depth + 1) * nextBinShift)) - 1) / 7)
idx.refs, err = readIndices(r, idx.Version, binLimit)
if err != nil {
return nil, err
}
var nUnmapped uint64
err = binary.Read(r, binary.LittleEndian, &nUnmapped)
if err == nil {
idx.unmapped = &nUnmapped
} else if err != io.EOF {
return nil, err
}
idx.isSorted = true
return &idx, nil
}
func readIndices(r io.Reader, version byte, binLimit uint32) ([]refIndex, error) {
var n int32
err := binary.Read(r, binary.LittleEndian, &n)
if err != nil {
return nil, err
}
if n == 0 {
return nil, nil
}
idx := make([]refIndex, n)
for i := range idx {
idx[i].bins, idx[i].stats, err = readBins(r, version, binLimit)
if err != nil {
return nil, err
}
}
return idx, nil
}
func readBins(r io.Reader, version byte, binLimit uint32) ([]bin, *index.ReferenceStats, error) {
var nBins int32
err := binary.Read(r, binary.LittleEndian, &nBins)
if err != nil {
return nil, nil, err
}
if nBins == 0 {
return nil, nil, nil
}
if uint32(nBins) > binLimit {
return nil, nil, fmt.Errorf("csi: invalid bin count: %d > %d", nBins, binLimit)
}
var stats *index.ReferenceStats
bins := make([]bin, nBins)
statsDummyBin := binLimit + 1
for i := 0; i < len(bins); i++ {
err = binary.Read(r, binary.LittleEndian, &bins[i].bin)
if err != nil {
return nil, nil, fmt.Errorf("csi: failed to read bin number: %v", err)
}
var vOff uint64
err = binary.Read(r, binary.LittleEndian, &vOff)
if err != nil {
return nil, nil, fmt.Errorf("csi: failed to read left virtual offset: %v", err)
}
bins[i].left = makeOffset(vOff)
if version == 0x2 {
err = binary.Read(r, binary.LittleEndian, &bins[i].records)
if err != nil {
return nil, nil, fmt.Errorf("csi: failed to read record count: %v", err)
}
}
var nChunks int32
err = binary.Read(r, binary.LittleEndian, &nChunks)
if err != nil {
return nil, nil, fmt.Errorf("csi: failed to read bin count: %v", err)
}
if bins[i].bin == statsDummyBin {
if nChunks != 2 {
return nil, nil, errors.New("csi: malformed dummy bin header")
}
stats, err = readStats(r)
if err != nil {
return nil, nil, err
}
bins = bins[:len(bins)-1]
i--
continue
}
bins[i].chunks, err = readChunks(r, nChunks)
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) ([]bgzf.Chunk, error) {
if n == 0 {
return nil, nil
}
var (
vOff uint64
err error
)
chunks := make([]bgzf.Chunk, n)
for i := range chunks {
err = binary.Read(r, binary.LittleEndian, &vOff)
if err != nil {
return nil, fmt.Errorf("csi: failed to read chunk begin virtual offset: %v", err)
}
chunks[i].Begin = makeOffset(vOff)
err = binary.Read(r, binary.LittleEndian, &vOff)
if err != nil {
return nil, fmt.Errorf("csi: failed to read chunk end virtual offset: %v", err)
}
chunks[i].End = makeOffset(vOff)
}
if !sort.IsSorted(byBeginOffset(chunks)) {
sort.Sort(byBeginOffset(chunks))
}
return chunks, nil
}
func readStats(r io.Reader) (*index.ReferenceStats, error) {
var (
vOff uint64
stats index.ReferenceStats
err error
)
err = binary.Read(r, binary.LittleEndian, &vOff)
if err != nil {
return nil, fmt.Errorf("bam: failed to read index stats chunk begin virtual offset: %v", err)
}
stats.Chunk.Begin = makeOffset(vOff)
err = binary.Read(r, binary.LittleEndian, &vOff)
if err != nil {
return nil, fmt.Errorf("bam: failed to read index stats chunk end virtual offset: %v", err)
}
stats.Chunk.End = makeOffset(vOff)
err = binary.Read(r, binary.LittleEndian, &stats.Mapped)
if err != nil {
return nil, fmt.Errorf("bam: failed to read index stats mapped count: %v", err)
}
err = binary.Read(r, binary.LittleEndian, &stats.Unmapped)
if err != nil {
return nil, fmt.Errorf("bam: failed to read index stats unmapped count: %v", err)
}
return &stats, nil
}
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