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// Copyright ©2013 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 implements FAI fasta sequence file index handling.
package fai
import (
"encoding/csv"
"errors"
"io"
"strconv"
)
const (
nameField = iota
lengthField
startField
basesField
bytesField
)
var ErrNonUnique = errors.New("non-unique record name")
// Index is an FAI index.
type Index map[string]Record
// Record is a single FAI index record.
type Record struct {
// Name is the name of the sequence.
Name string
// Length is the length of the sequence.
Length int
// Start is the starting seek offset of
// the sequence.
Start int64
// BasesPerLine is the number of sequences
// bases per line.
BasesPerLine int
// BytesPerLine is the number of bytes
// used to represent each line.
BytesPerLine int
}
// Position returns the seek offset of the sequence position p for the
// given Record.
func (r Record) Position(p int) int64 {
if p < 0 || r.Length <= p {
panic("fai: index out of range")
}
return r.position(p)
}
func (r Record) position(p int) int64 {
return r.Start + int64(p/r.BasesPerLine*r.BytesPerLine+p%r.BasesPerLine)
}
// endOfLineOffset returns the number of bytes until the end of the line
// holding position p.
func (r Record) endOfLineOffset(p int) int {
if p/r.BasesPerLine == r.Length/r.BasesPerLine {
return r.Length - p
}
return r.BasesPerLine - p%r.BasesPerLine
}
func mustAtoi(fields []string, index, line int) int {
i, err := strconv.ParseInt(fields[index], 10, 0)
if err != nil {
panic(parseError(line, index, err))
}
return int(i)
}
func mustAtoi64(fields []string, index, line int) int64 {
i, err := strconv.ParseInt(fields[index], 10, 64)
if err != nil {
panic(parseError(line, index, err))
}
return i
}
// ReadFrom returns an Index from the stream provided by an io.Reader or an error. If the input
// contains non-unique records the error is a csv.ParseError identifying the second non-unique
// record.
func ReadFrom(r io.Reader) (idx Index, err error) {
tr := csv.NewReader(r)
tr.Comma = '\t'
tr.FieldsPerRecord = 5
defer func() {
r := recover()
if r != nil {
e, ok := r.(error)
if !ok {
panic(r)
}
if _, ok = r.(*csv.ParseError); !ok {
panic(r)
}
err = e
idx = nil
}
}()
for line := 1; ; line++ {
rec, err := tr.Read()
if err == io.EOF {
return idx, nil
}
if err != nil {
return nil, err
}
if idx == nil {
idx = make(Index)
} else if _, exists := idx[rec[nameField]]; exists {
return nil, parseError(line, 0, ErrNonUnique)
}
idx[rec[nameField]] = Record{
Name: rec[nameField],
Length: mustAtoi(rec, lengthField, line),
Start: mustAtoi64(rec, startField, line),
BasesPerLine: mustAtoi(rec, basesField, line),
BytesPerLine: mustAtoi(rec, bytesField, line),
}
}
}
func parseError(line, column int, err error) *csv.ParseError {
return &csv.ParseError{
StartLine: line,
Line: line,
Column: column,
Err: err,
}
}
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