global.go

package main

import (
	"os"
	"path/filepath"
	"regexp"
	"time"

	"github.com/go-redis/redis"
	"github.com/pelletier/go-toml"
	"github.com/tealeg/xlsx/v3"
	"github.com/xuri/excelize/v2"

	"github.com/liserjrqlxue/anno2xlsx/v2/anno"
)

// os
var (
	ex, _        = os.Executable()
	exPath       = filepath.Dir(ex)
	dbPath       = filepath.Join(exPath, "db")
	etcPath      = filepath.Join(exPath, "etc")
	templatePath = filepath.Join(exPath, "template")
)

// family list
var sampleList []string

// to-do add exon count info of transcript
var exonCount = make(map[string]string)

// 特殊位点库
var specVarDb = make(map[string]bool)

// 遗传相符
var inheritDb = make(map[string]map[string]int)

var qualityColumn []string

// WESIM
var (
	resultColumn, qcColumn, cnvColumn       []string
	resultFile, qcFile, exonFile, largeFile *os.File
)

var qualitys []map[string]string
var qualityKeyMap = make(map[string]string)

// tier2
var isEnProduct = make(map[string]bool)
var isEN bool

var transEN = map[string]string{
	"是":    "Yes",
	"否":    "No",
	"备注说明": "Note",
}

// regexp
var (
	isGz      = regexp.MustCompile(`\.gz$`)
	isComment = regexp.MustCompile(`^##`)
	isMT      = regexp.MustCompile(`MT|chrM`)
	isHom     = regexp.MustCompile(`^Hom`)
)

var redisDb *redis.Client

var snvs []string

var acmgSFGene = make(map[string]bool)

// WGS
var (
	wgsXlsx *xlsx.File
	MTTitle []string
	tier1Db = make(map[string]bool)
)

var (
	logFile   *os.File
	tier2     *xlsxTemplate
	err       error
	ts        = []time.Time{time.Now()}
	step      = 0
	sampleMap = make(map[string]bool)
	stats     = make(map[string]int)

	tier1Xlsx           *xlsx.File
	filterVariantsTitle []string
	exonCnvTitle        []string
	largeCnvTitle       []string
	tier3Titles         []string

	tier3Xlsx  *excelize.File
	tier3SW    *excelize.StreamWriter
	tier3RowID = 1
)

// TomlTree Global toml config
var TomlTree *toml.Tree

// database
var (
	aesCode = "c3d112d6a47a0a04aad2b9d2d2cad266"
	gene2id map[string]string
	chpo    anno.AnnoDb
	revel   revelDb

	// 突变频谱
	spectrumDb anno.EncodeDb
	// 基因-疾病
	diseaseDb anno.EncodeDb
	geneList  = make(map[string]bool)
	// ACMG SF
	acmgSecondaryFindingDb anno.EncodeDb
	sfCode                 = "b7ea138a9842cbb832271bdcf4478310"
	// 耳聋数据库
	hearingLossDb anno.EncodeDb
	hlCode        = "6d276bc509883dbafe05be835ad243d7"
	// 新生儿数据库
	newBornDb anno.EncodeDb
	nbCode    = "afe0ba6b37644a81cedc2364ee414c7f"
	// 孕前数据库
	prePregnancyDb anno.EncodeDb
	ppCode         = "118b09d39a5d3ecd56f9bd4f351dd6d6"
	// PHGDTag
	phgdTagKey string
	phgdTagSep string
	phgdTagDb  [][]string
)

// ACMG
var (
	acmgDb string
)

// find duplicate
var countVar = make(map[string]int)
var duplicateVar = make(map[string][]map[string]string)
var deleteVar = make(map[string]bool)
var transcriptLevel = make(map[string]int)
var tier1Count int

// log
var cycle1Count int
var cycle2Count int

// flag to var
var outputTier3 = false
var homFixRatioThreshold = 0.85

// json
//var tier1Json *os.File
var tier1Data []map[string]string

// 假阳性
var fpDb = make(map[string]map[string]string)