package main

import (
	"bufio"
	"errors"
	"fmt"
	"io/ioutil"
	"os"
	"strings"
	"time"
)

const (
	inputFileName = "input_tiny.vcf"
)

var (
	errNoMatch = errors.New("no match")

	// Used by readSequenceIndexed
	chromosomePositionIndex map[string]string
)

func readSequenceLineByLine(inputChromosome, inputPosition string) (reference *string, err error) {
	file, err := os.Open(inputFileName)
	if err != nil {
		return nil, err
	}
	defer file.Close()
	scanner := bufio.NewScanner(file)
	for scanner.Scan() {
		ln := scanner.Text()
		if strings.HasPrefix(ln, "#") {
			continue
		}
		rows := strings.Split(ln, "\t")
		if len(rows) < 3 {
			continue
		}
		var (
			chromosome = rows[0]
			position   = rows[1]
			ref        = rows[3]
		)
		if inputChromosome == chromosome && inputPosition == position {
			reference = &ref
			return
		}
	}
	return nil, errNoMatch
}

func readSequenceFullRead(inputChromosome, inputPosition string) (reference *string, err error) {
	rawData, err := ioutil.ReadFile(inputFileName)
	if err != nil {
		return nil, err
	}
	lines := strings.Split(string(rawData), "\n")
	for _, ln := range lines {
		if strings.HasPrefix(ln, "#") {
			continue
		}
		rows := strings.Split(ln, "\t")
		if len(rows) < 3 {
			continue
		}
		var (
			chromosome = rows[0]
			position   = rows[1]
			ref        = rows[3]
		)
		if inputChromosome == chromosome && inputPosition == position {
			reference = &ref
			return
		}
	}
	return nil, errNoMatch
}

func readSequenceIndexed(inputChromosome, inputPosition string) (reference *string, err error) {
	if chromosomePositionIndex == nil {
		chromosomePositionIndex = make(map[string]string, 0)
		var rawData []byte
		rawData, err = ioutil.ReadFile(inputFileName)
		if err != nil {
			return nil, err
		}
		lines := strings.Split(string(rawData), "\n")
		for _, ln := range lines {
			if strings.HasPrefix(ln, "#") {
				continue
			}
			rows := strings.Split(ln, "\t")
			if len(rows) < 3 {
				continue
			}
			var (
				chromosome = rows[0]
				position   = rows[1]
				ref        = rows[3]
			)
			key := chromosome + position
			chromosomePositionIndex[key] = ref
		}
	}
	inputKey := inputChromosome + inputPosition
	val, found := chromosomePositionIndex[inputKey]
	if found {
		return &val, nil
	}
	return nil, errNoMatch
}

func main() {
	ref, err := readSequenceFullRead("chr1", "16837")
	if err != nil {
		panic(err)
	}
	fmt.Println("ref=", *ref)

	ref2, err := readSequenceLineByLine("chr1", "16837")
	if err != nil {
		panic(err)
	}
	fmt.Println("ref2=", *ref2)
}