aligner/index.ts

import { spawn } from 'child_process';
import { cpus } from 'os';
import fs from 'fs'
import path from 'path';
import * as fastq from "fastq";
import type { queueAsPromised } from "fastq";

const async_exec = (prog: string, args: string[], onData: Function) => {
    return new Promise((resolve, reject) => {
        const child = spawn(prog, args, {shell: true})

        child.stdout.on('data', data => onData(data.toString().trim()))
        child.stderr.on('data', data => onData(data.toString().trim()))

        child.on('error', err => reject(err))
        child.on('exit', code => resolve(code))
    })
}
const invReplace = (regex: RegExp, string: string, by = '_') => string.split('').map(letter => letter.match(regex) ? letter : by).join('')

const writeSequence = async (sequenceName:string, sequence:string, filePath: string, lineN = 80) => {
  return new Promise<boolean>(async(resolve, reject) => {
    try {
      const r = new RegExp(".{1," + lineN + "}","g");
      const regex_sam_restriction: RegExp = /[>0-9A-Za-z!#$%&+\./:;?@^_|~-]|[\n\t]/g;
      const nSeqName = invReplace(regex_sam_restriction, sequenceName)
      await fs.promises.writeFile(filePath, '>' + nSeqName + '\n' + sequence.match(r)?.join('\n').toUpperCase())
      resolve(true)
    } catch (error) {
      console.log(error)
      reject(false)
    }
  })
}

const makeReference = async (sequenceName:string, sequence:string, filePath: string, lineN = 80) => {
  if (await writeSequence(sequenceName, sequence, filePath, lineN)) await async_exec('bwa', ['index', filePath], () => console.log)
}

const asyncBwaMem = (
    refPath   : string,
    reads     : string | Array<string> | Array<Array<string>>,
    // R1        : string | Array<string>,
    // R2        : string | Array<string>,
    runName   : string,
    libName   : string,
    outputDir : string,
    onData    : Function,
    options?  : any,
) => {
    return new Promise<string[]>(async (resolve, reject) => {
      try {
        const defaultOptions = {
          output_discordant: true,
          output_splitted: true,
          output_unmapped: true
        }
    
        if (typeof options === 'undefined') {
          options = defaultOptions
        } else {
          options = {...defaultOptions, ...options}
        }
    
        const refName = path.parse(refPath).name
      
        const bwa        = 'bwa'
        const samblaster = 'samblaster'
        const samtools   = 'samtools'
        const sambamba   = 'sambamba'
    
        let readsIn: string
        let isPairedEnd = false
    
        if (Array.isArray(reads) ) {
          isPairedEnd = true
          console.log('Assuming paired end reads');
          
          const [R1, R2] = reads
          const R1_arr = Array.isArray(R1) ? R1.join(' ') : R1
          const R2_arr = Array.isArray(R2) ? R2.join(' ') : R2
        
          const R1_kitty = R1_arr.slice(-2) === 'gz' ? 'zcat' : 'cat'
          const R2_kitty = R2_arr.slice(-2) === 'gz' ? 'zcat' : 'cat'
        
          const R1_in = `'< ${R1_kitty} ${R1_arr}'`
          const R2_in = `'< ${R2_kitty} ${R2_arr}'`
          readsIn = R1_in + ' ' + R2_in
        } else {
          readsIn = reads
        }
    
        let bam       = path.join(outputDir, `bwa_mem_properly_on_${refName}.bam`)
        let bamSorted = path.join(outputDir, `bwa_mem_properly_on_${refName}.sorted.bam`)
        let retObj: any = { bamSorted } 
        if(options?.remove_mapped) {
          bam = '/dev/null'
          delete retObj.bamSorted
        }
    
        const threads = String(cpus().length)


    
        let samblasterCmd: Array<string> = []
        // https://github.com/GregoryFaust/samblaster
        samblasterCmd = ['|', samblaster, 
          '--addMateTags',
          '-a', // Accept duplicate marks already in input file
          '-e', // Exclude reads marked as duplicates from discordant, splitter, and/or unmapped
        ]

        if (options?.output_discordant || options?.output_splitted) {
          console.log('Using samblaster');
          if(options?.output_discordant) {
            if(!isPairedEnd) {
              console.log('Discordant reads can be found only in paired reads, skipping')
            } else {
              const discordantFile = path.join(outputDir, `bwa_mem_discordants_on_${refName}.sam`)
              console.log('Discordant reads file path: ', discordantFile);
              samblasterCmd = [...samblasterCmd, '-d', discordantFile]
              retObj = {...retObj, discordantFile}
            }
          }
    
          if (!isPairedEnd) {
            samblasterCmd = [...samblasterCmd, '--ignoreUnmated']
          }
    
          if(options?.output_splitted) {
            const splitterFile   = path.join(outputDir, `bwa_mem_splitters_on_${refName}.sam`)
            console.log('Splitted reads file path: ', splitterFile);
            samblasterCmd = [...samblasterCmd, '-s', splitterFile]
            retObj = {...retObj, splitterFile}
          }
        }

        if(options?.output_unmapped) {
          const unmappedFile   = path.join(outputDir, `bwa_mem_unmapped_on_${refName}.fq`)
          console.log('Unmapped reads file path: ', unmappedFile);
          samblasterCmd = [...samblasterCmd, '-u', unmappedFile]
          retObj = {...retObj, unmappedFile}
        }

        if(!fs.existsSync(refPath+'.amb')) {
          await async_exec(bwa, ['index', refPath], (message: string) => onData('[BWA-INDEX] ' + message))
        }

        console.log(options, samblasterCmd);
        

        const code = await async_exec(
        bwa, ['mem',
          '-t', threads,
          '-R', `"@RG\\tPL:Illumina\\tID:${+(new Date)}\\tSM:${runName}\\tLB:${libName}"`,
          refPath, 
          readsIn,
        ...samblasterCmd,
        '|',
        samtools,
          'view',
          '-Sb',
          '-',
        '>',
        bam
        ], (message: string) => onData('[BWA-MEM] ' + message))
        onData('[BWA-MEM][EXIT CODE] ' + code)
        
        if(retObj.bamSorted) {
          const code_sort = await async_exec(
            sambamba, ['sort',
              '-t', threads,
              bam
          ], (message: string) => onData('[SAMBAMBA-SORT] ' + message))
          onData('[SAMBAMBA-SORT][EXIT CODE] ' + code_sort)
          fs.unlinkSync(bam)
        }
        
        resolve(retObj)
      } catch (err) {
        reject(err)
      }
    })
}

type Task = {
  refPath   : string,
  reads     : string | Array<string> | Array<Array<string>> ;
  runName   : string;
  libName   : string;
  outputDir : string;
  onData    : Function
}

const asyncBwaMemWorker = async (args:any) => {
  const {refPath, reads, runName, libName, outputDir, onData}  = args
  await asyncBwaMem(refPath, reads, runName, libName, outputDir, onData)
}

const scheduleAsyncBwaMem = async (
  allReads: Array<Array<string>> | Array<Array<Array<string>>>,
  refPath   : string,
  runName   : string,
  libName   : string,
  allOutputDir : string,
  onData    : Function
) => {
  const q: queueAsPromised<Task> = fastq.promise(asyncBwaMemWorker, 1)
  await Promise.all(allReads.map((reads,i) => q.push({refPath, reads, runName, libName, outputDir:allOutputDir[i], onData})))
}

export { asyncBwaMem, writeSequence, makeReference, scheduleAsyncBwaMem }