// Copyright © 2016-2019 Wei Shen <shenwei356@gmail.com>
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
// in the Software without restriction, including without limitation the rights
// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
// copies of the Software, and to permit persons to whom the Software is
// furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included in
// all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
// THE SOFTWARE.

package cmd

import (
	"fmt"
	"io"
	"math/rand"
	"runtime"

	"github.com/shenwei356/bio/seq"
	"github.com/shenwei356/bio/seqio/fastx"
	"github.com/shenwei356/xopen"
	"github.com/spf13/cobra"
)

// sampleCmd represents the sample command
var sampleCmd = &cobra.Command{
	GroupID: "set",

	Use:   "sample",
	Short: "sample sequences by number or proportion",
	Long: `sample sequences by number or proportion.

Attention:
1. Do not use '-n' on large FASTQ files, it loads all seqs into memory!
   use 'seqkit sample -p 0.1 seqs.fq.gz | seqkit head -n N' instead!

`,
	Run: func(cmd *cobra.Command, args []string) {
		if len(args) > 1 {
			checkError(fmt.Errorf("no more than one file needed (%d)", len(args)))
		}

		config := getConfigs(cmd)
		alphabet := config.Alphabet
		idRegexp := config.IDRegexp
		// lineWidth := config.LineWidth
		outFile := config.OutFile
		quiet := config.Quiet
		seq.AlphabetGuessSeqLengthThreshold = config.AlphabetGuessSeqLength
		seq.ValidateSeq = false
		runtime.GOMAXPROCS(config.Threads)

		files := getFileListFromArgsAndFile(cmd, args, true, "infile-list", !config.SkipFileCheck)

		seed := getFlagInt64(cmd, "rand-seed")
		twoPass := getFlagBool(cmd, "two-pass")
		number := getFlagInt64(cmd, "number")
		proportion := getFlagFloat64(cmd, "proportion")

		file := files[0]

		if twoPass && isStdin(file) {
			checkError(fmt.Errorf("two-pass mode (-2) will failed when reading from stdin. please disable flag: -2"))
		}

		if number == 0 && proportion == 0 {
			checkError(fmt.Errorf("one of flags -n (--number) and -p (--proportion) needed"))
		}

		if number < 0 {
			checkError(fmt.Errorf("value of -n (--number) and should be greater than 0"))
		}
		if proportion < 0 || proportion > 1 {
			checkError(fmt.Errorf("value of -p (--proportion) (%f) should be in range of (0, 1]", proportion))
		}

		outfh, err := xopen.Wopen(outFile)
		checkError(err)
		defer outfh.Close()

		rand.Seed(seed)
		// randg := randomFloat64Generator(seed)

		n := int64(0)
		var record *fastx.Record
		if number > 0 { // by number
			if !quiet {
				log.Info("sample by number")
			}

			if twoPass {
				// first pass, get seq number
				if !quiet {
					log.Info("first pass: counting seq number")
				}
				seqNum, err := fastx.GetSeqNumber(file)
				checkError(err)

				if !quiet {
					log.Infof("seq number: %d", seqNum)
				}

				proportion = float64(number) / float64(seqNum) * 1.1

				// second pass
				if !quiet {
					log.Info("second pass: reading and sampling")
				}
				fastxReader, err := fastx.NewReader(alphabet, file, idRegexp)
				checkError(err)
			LOOP:
				for {
					record, err = fastxReader.Read()
					if err != nil {
						if err == io.EOF {
							break
						}
						checkError(err)
						break
					}
					if fastxReader.IsFastq {
						config.LineWidth = 0
						fastx.ForcelyOutputFastq = true
					}

					// if <-randg <= proportion {
					if rand.Float64() <= proportion {
						n++
						record.FormatToWriter(outfh, config.LineWidth)
						if n == number {
							break LOOP
						}
					}
				}
				fastxReader.Close()
			} else {
				if !quiet {
					log.Info("loading all sequences into memory...")
				}
				records, err := fastx.GetSeqs(file, alphabet, config.Threads, 10, idRegexp)
				checkError(err)

				if len(records) > 0 && len(records[0].Seq.Qual) > 0 {
					config.LineWidth = 0
				}

				proportion = float64(number) / float64(len(records)) * 1.1

				for _, record := range records {
					// if <-randg <= proportion {
					if rand.Float64() <= proportion {
						n++
						record.FormatToWriter(outfh, config.LineWidth)
						if n == number {
							break
						}
					}
				}
			}
		} else {
			if !quiet {
				log.Info("sample by proportion")
			}

			fastxReader, err := fastx.NewReader(alphabet, file, idRegexp)
			checkError(err)
			for {
				record, err = fastxReader.Read()
				if err != nil {
					if err == io.EOF {
						break
					}
					checkError(err)
					break
				}
				if fastxReader.IsFastq {
					config.LineWidth = 0
					fastx.ForcelyOutputFastq = true
				}

				// if <-randg <= proportion {
				if rand.Float64() <= proportion {
					n++
					record.FormatToWriter(outfh, config.LineWidth)
				}
			}
			fastxReader.Close()
		}

		if !quiet {
			log.Infof("%d sequences outputted", n)
		}
	},
}

func init() {
	RootCmd.AddCommand(sampleCmd)

	sampleCmd.Flags().Int64P("rand-seed", "s", 11, "random seed. For paired-end data, use the same seed across fastq files to sample the same read pairs")
	sampleCmd.Flags().Int64P("number", "n", 0, "sample by number (result may not exactly match), DO NOT use on large FASTQ files.")
	sampleCmd.Flags().Float64P("proportion", "p", 0, "sample by proportion")
	sampleCmd.Flags().BoolP("two-pass", "2", false, "2-pass mode read files twice to lower memory usage. Not allowed when reading from stdin")
}
