"use strict";
var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
    return new (P || (P = Promise))(function (resolve, reject) {
        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
        step((generator = generator.apply(thisArg, _arguments || [])).next());
    });
};
var __importDefault = (this && this.__importDefault) || function (mod) {
    return (mod && mod.__esModule) ? mod : { "default": mod };
};
Object.defineProperty(exports, "__esModule", { value: true });
const fs_1 = __importDefault(require("fs"));
const _1 = require(".");
(() => __awaiter(void 0, void 0, void 0, function* () {
    const baseDir = '/home/thomas/Turbine-B/Data_2/RNAseqBWA/';
    const rnaDBPath = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10].map(n => '/home/thomas/NGS/ref/ncbi/RNA/human.' + n + '.rna.gbff');
    const dirs = fs_1.default.readdirSync(baseDir);
    /*const allResults = []
    for (const dir of dirs) {
        console.log(dir)
        const caseDir = baseDir + dir + '/'
        const proper = caseDir + 'bwa_mem_properly_on_human_NM.sorted.bam'
        const splitters = caseDir + 'bwa_mem_splitters_on_human_NM.sam'
        const discordants = caseDir + 'bwa_mem_discordants_on_human_NM.sam'

        const res = await analysisTranscript('NM_017617.5', proper, splitters, discordants, rnaDBPath)
        allResults.push({dir,res})
    }
    await fs.promises.writeFile('test/frommAcc.json', JSON.stringify(allResults, null, 4))*/
    const allCounts = [];
    for (const dir of dirs) {
        const r = yield (0, _1.openSam)(baseDir + dir + '/' + 'bwa_mem_properly_on_human_NM.sorted.bam', '', true);
        allCounts.push([dir, ...r].join('\t'));
    }
    console.log(allCounts);
    yield fs_1.default.promises.writeFile('test/allCounts.tsv', allCounts.join('\n'));
    /*const res = JSON.parse((await fs.promises.readFile('test/frommAcc.json')).toString())
    const lines = []

    console.log(res[0].dir);
    
    const txt = res.map((entry:any) => ([entry.dir,...entry.res.exons.reduce((p:any,c:any) => [...p, c.counts.all[0]],[])].join('\t'))).join('\n')
    
    await fs.promises.writeFile('test/CountsByExon.tsv', txt)*/
}))();