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vdbCreate.swift
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vdbCreate.swift
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//
// VDBCreate.swift
// VDBCreate
//
// Copyright (c) 2022 Anthony West, Caltech
// Last modified 8/4/22
import Foundation
#if canImport(FoundationNetworking)
import FoundationNetworking
#endif
let version : String = "3.0"
let checkForVDBUpdate : Bool = true
let mpNumberDefault : Int = 12
let basePath : String = FileManager.default.currentDirectoryPath
let clArgc : Int = Int(CommandLine.argc)
var clArguments : [String] = CommandLine.arguments
var filteredArguments : [String] = []
var nuclMode : Bool = false
var includeAllN : Bool = false
var useStdInput : Bool = false
var overwrite : Bool = false
var pipeOutput : Bool = false
var mpNumber : Int = mpNumberDefault
if clArguments.count > 1 && clArguments[1] == "--version" {
print(version)
exit(0)
}
if clArguments.count > 2 {
for i in 1..<(clArguments.count-1) {
if clArguments[i] == "-m" || clArguments[i] == "-M" {
if let clInt = Int(clArguments[i+1]) {
mpNumber = clInt
clArguments.remove(at: i)
}
else {
print("Error - option m requires the number of threads to be specified")
exit(9)
}
clArguments.remove(at: i)
break
}
}
}
for i in 1..<clArgc {
if clArguments[i].first == "-" {
let options : Substring = clArguments[i].dropFirst()
if options.isEmpty {
print("Error - missing option")
exit(9)
}
for option in options {
switch option {
case "n":
nuclMode = true
case "N":
nuclMode = true
includeAllN = true
case "s","S":
useStdInput = true
case "o","O":
overwrite = true
case "p","P":
pipeOutput = true
default:
print("Error - invalid option")
exit(9)
}
}
}
else {
filteredArguments.append(clArguments[i])
}
}
if useStdInput {
filteredArguments.insert("vdb_tmp_file", at: 0)
}
if !pipeOutput {
print("SARS-CoV-2 Variant Database Creator Version \(version) Bjorkman Lab/Caltech")
}
if filteredArguments.isEmpty {
print("Error - missing alignment file name")
print("Usage: vdbCreate <alignment file name> <optional output file name>")
exit(9)
}
let msaFileName : String = filteredArguments[0]
var resultFileName : String = ""
if filteredArguments.count > 1 {
resultFileName = filteredArguments[1]
}
// MARK: - Autorelease Pool for Linux and Windows
#if os(Linux) || os(Windows)
// autorelease call used to minimize memory footprint
func autoreleasepool<Result>(invoking body: () throws -> Result) rethrows -> Result {
return try body()
}
#endif
// xterm ANSI codes for colored text
struct TColor {
static let reset = "\u{001B}[0;0m"
static let red = "\u{001B}[0;31m"
static let magenta = "\u{001B}[0;35m"
static let bold = "\u{001B}[1m" // "\u{001B}[22m"
}
final class VDBCreate {
static let serialQueue = DispatchQueue(label: "update check")
static var latestVersionStringBacking : String = ""
static var latestVersionString : String {
get {
serialQueue.sync {
return latestVersionStringBacking
}
}
set {
serialQueue.sync {
latestVersionStringBacking = newValue
}
}
}
// reads aligned DNA sequences, removes gaps, translates spike genes, and saves mutation lists
class func createDatabase(_ fileName: String, _ outputFileName: String = "", _ nucl: Bool = false, _ includeN: Bool = false) {
if checkForVDBUpdate {
checkForUpdates()
}
let lf : UInt8 = 10 // \n
let greaterChar : UInt8 = 62
let dashChar : UInt8 = 45
let slashChar : UInt8 = 47
let commaChar : UInt8 = 44
let spaceChar : UInt8 = 32
let aChar : UInt8 = 65
let verticalChar : UInt8 = 124
// let refNameString : String = ">hCoV-19/Wuhan/IPBCAMS-WH-01/2019|EPI_ISL_402123|2019-12-24|Asia"
let refNameString : String = ">hCoV-19/Wuhan/WIV04/2019|EPI_ISL_402124|2019-12-30|China"
let refChar2 : UInt8 = 104
let refNameArray : [UInt8] = [UInt8](refNameString.utf8)
let startSRef : Int = 21563 - 1
let endSRef : Int = 25384 - 3
/*
let cdsDictionary : [String:(Int,Int)] = ["Spike":(21563,25384),
"N":(28274,29533), // Nucleocapsid
"E":(26245,26472), // Envelope protein
"M":(26523,27191), // Membrane protein
"NS3":(25393,26220), // ORF3a protein
"NS6":(27202,27387), // ORF6 protein
"NS7a":(27394,27759), // ORF7a protein
"NS7b":(27756,27887), // ORF7b
"NS8":(27894,28259), // ORF8 protein
"NSP1":(266,805),
"NSP2":(806,2719),
"NSP3":(2720,8554),
"NSP4":(8555,10054),
"NSP5":(10055,10972), // 3C-like proteinase 3CLpro
"NSP6":(10973,11842),
"NSP7":(11843,12091),
"NSP8":(12092,12685), // Primase ORF8
"NSP9":(12686,13024),
"NSP10":(13025,13441),
"NSP11":(13442,13480),
"NSP12":(13442,16236), // RdRp frameshift at 13468
"NSP13":(16237,18039), // helicase
"NSP14":(18040,19620), // 3′-to-5′ exonuclease
"NSP15":(19621,20658), // endoRNAse
"NSP16":(20659,21552)] // 2′O'ribose methyltransferase
*/
let filePath : String = "\(basePath)/\(fileName)"
var deleteTmpFile : Bool = false
if !FileManager.default.fileExists(atPath: filePath) {
if useStdInput {
do {
try "tmp file".write(to: URL(fileURLWithPath: filePath), atomically: true, encoding: .ascii)
}
catch {
print("Error writing temporary file at \(filePath)")
exit(9)
}
deleteTmpFile = true
}
else {
print("Error input vdb file \(filePath) not found")
exit(9)
}
}
defer {
if deleteTmpFile {
try? FileManager.default.removeItem(atPath: filePath)
}
}
guard let fileStream : InputStream = InputStream(fileAtPath: filePath) else { print("Error reading alignment file \(filePath)"); return }
let standardInput : FileHandle = FileHandle.standardInput
let blockBufferSize : Int = 1_000_000_000
let streamBufferSize : Int = 950_000_000
let bufferSize : Int = 50000
let lastMaxSize : Int = bufferSize
let lineN : UnsafeMutablePointer<UInt8> = UnsafeMutablePointer<UInt8>.allocate(capacity: blockBufferSize + lastMaxSize)
let outBufferSize : Int = 200_000_000
let mpNumberMin : Int = mpNumber > 2 ? mpNumber-2 : mpNumber
let outBufferSizeMP : Int = outBufferSize/mpNumberMin
let outBufferWriteSize : Int = (!pipeOutput) ? 50_000_000 : 10_000
var outBufferAll : [UInt8] = Array(repeating: 0, count: outBufferSize)
var outBufferPositionAll : Int = 0
var outBufferMP : [[UInt8]] = Array(repeating:Array(repeating: 0, count: outBufferSizeMP), count: mpNumber)
var outBufferPositionMP : [Int] = Array(repeating: 0, count: mpNumber)
var tmpBufferMP : [[UInt8]] = Array(repeating:Array(repeating: 0, count: bufferSize), count: mpNumber)
var tmpBufferPositionMP : [Int] = Array(repeating: 0, count: mpNumber)
var cdsBufferMP : [[UInt8]] = Array(repeating:Array(repeating: 0, count: bufferSize), count: mpNumber)
var cdsBufferPositionMP : [Int] = Array(repeating: 0, count: mpNumber)
var refBuffer : [UInt8] = Array(repeating: 0, count: bufferSize)
var refBufferPosition : Int = 0
var refNoGap : [Bool] = Array(repeating: false, count: bufferSize)
var refProtein : [UInt8] = []
fileStream.open()
// prepare output file
var vdbFileName : String
if !outputFileName.isEmpty {
vdbFileName = outputFileName
}
else {
vdbFileName = "vdb_msa.txt"
let fileName = fileName.replacingOccurrences(of: "Codon", with: "")
if fileName.count == 14 {
if fileName.prefix(4) == "msa_" && fileName.suffix(6) == ".fasta" {
let dateString = fileName.prefix(8).suffix(4)
if let _ = Int(dateString) {
let date = Date()
if let year = Calendar.current.dateComponents([.year], from: date).year {
vdbFileName = "vdb_\(dateString)\(year-2000).txt"
}
}
}
}
if nucl {
vdbFileName = vdbFileName.replacingOccurrences(of: ".txt", with: "_nucl.txt")
}
}
let outFileName : String = "\(basePath)/\(vdbFileName)"
if FileManager.default.fileExists(atPath: outFileName) && !overwrite && !pipeOutput {
print("Error - output file \(outFileName) already exists. Use option -o to overwrite.")
return
}
if !pipeOutput {
FileManager.default.createFile(atPath: outFileName, contents: nil, attributes: nil)
}
guard let outFileHandle : FileHandle = (!pipeOutput) ? FileHandle(forWritingAtPath: outFileName) : FileHandle.standardOutput else {
print("Error - could not write to file \(outFileName)")
return
}
// find reference sequence and setup refNoGap to indicate non-gap positions
var lineCount : Int = 0
var greaterPosition : Int = -1
var lfAfterGreaterPosition : Int = 0
var lastLf : Int = 0
var checkCount : Int = 0
var atRef : Bool = false
var lastBufferSize : Int = 0
var firstLoadBytesRead : Int = 0
while (useStdInput || fileStream.hasBytesAvailable) && !atRef {
var bytesRead : Int = 0
var endOfStream : Bool = false
if !useStdInput {
bytesRead = fileStream.read(&lineN[lastBufferSize], maxLength: blockBufferSize)
}
else {
let _ = autoreleasepool { () -> Void in
var skipDone : Bool = false
while true {
let data : Data = standardInput.availableData
if data.count == 0 {
endOfStream = true
break
}
var skippedCount : Int = 0
if skipDone {
data.copyBytes(to: &lineN[lastBufferSize+bytesRead], count: data.count)
}
else {
var startPos : Int = Int.max
for i in 0..<(data.count-1) {
if data[i] == greaterChar && data[i+1] == refChar2 {
startPos = i
break
}
}
if startPos != Int.max {
data.copyBytes(to: &lineN[lastBufferSize+bytesRead], from: startPos..<data.count)
skipDone = true
skippedCount = startPos
}
else {
print("Error - starting position of alignment not found")
return
}
}
bytesRead += data.count - skippedCount
if bytesRead > streamBufferSize {
break
}
}
}
if firstLoadBytesRead == 0 {
firstLoadBytesRead = bytesRead
}
if bytesRead == 0 && endOfStream {
break
}
}
let bytesAvailable : Bool = useStdInput ? (bytesRead > 0 && !endOfStream) : fileStream.hasBytesAvailable
let bytesReadAdj : Int = bytesRead + lastBufferSize
refLoop: for pos in 0..<bytesReadAdj {
switch lineN[pos] {
case lf:
if lfAfterGreaterPosition == 0 {
lfAfterGreaterPosition = pos
checkCount += 1
if checkCount % 100000 == 0 && !pipeOutput {
print("isolate count \(checkCount)")
}
if refNameArray.count == pos-greaterPosition {
atRef = true
var counter : Int = 0
for i in greaterPosition..<pos {
if refNameArray[counter] != lineN[i] {
atRef = false
break
}
counter += 1
}
if atRef && !pipeOutput {
print("reference found")
}
}
}
else {
if atRef {
memmove(&refBuffer[refBufferPosition], &lineN[lastLf+1], pos-lastLf-1)
refBufferPosition += pos-lastLf-1
}
}
lastLf = pos
lineCount += 1
if lineN[pos+1] == greaterChar && bytesReadAdj-pos < lastMaxSize && bytesAvailable && !atRef {
// stop read and start next block
lastBufferSize = bytesReadAdj-pos-1
var counter : Int = 0
for i in pos+1..<bytesReadAdj {
lineN[counter] = lineN[i]
counter += 1
}
break refLoop
}
case greaterChar:
if atRef {
var refBaseCount : Int = 0
for i in 0..<refBufferPosition {
if refBuffer[i] != dashChar {
refBaseCount += 1
refNoGap[i] = true
}
}
break refLoop
}
greaterPosition = pos
lfAfterGreaterPosition = 0
default:
break
}
}
}
if !atRef {
print("Error - reference not found\n alignment must include \(refNameString)")
return
}
var uppercase : Bool = true
for tc in 0..<refBufferPosition {
if refBuffer[tc] != dashChar {
uppercase = refBuffer[tc] < 90
break
}
}
// translation constants
let lowercase : UInt8
if uppercase {
lowercase = 0
}
else {
lowercase = 32
}
let a : UInt8 = 65 + lowercase
let t : UInt8 = 84 + lowercase
let g : UInt8 = 71 + lowercase
let c : UInt8 = 67 + lowercase
let nuclN : UInt8 = 78 + lowercase
let aaA : UInt8 = 65
// let aaB : UInt8 = 66
let aaC : UInt8 = 67
let aaD : UInt8 = 68
let aaE : UInt8 = 69
let aaF : UInt8 = 70
let aaG : UInt8 = 71
let aaH : UInt8 = 72
let aaI : UInt8 = 73
// let aaJ : UInt8 = 74
let aaK : UInt8 = 75
let aaL : UInt8 = 76
let aaM : UInt8 = 77
let aaN : UInt8 = 78
// let aaO : UInt8 = 79
let aaP : UInt8 = 80
let aaQ : UInt8 = 81
let aaR : UInt8 = 82
let aaS : UInt8 = 83
let aaT : UInt8 = 84
// let aaU : UInt8 = 85
let aaV : UInt8 = 86
let aaW : UInt8 = 87
let aaX : UInt8 = 88
let aaY : UInt8 = 89
// let aaZ : UInt8 = 90
let aaSTOP : UInt8 = 42
// write current outBuffer to file
func writeBufferToFile() {
if outBufferPositionAll == 0 {
return
}
do {
try outFileHandle.write(contentsOf: outBufferAll[0..<outBufferPositionAll])
outBufferPositionAll = 0
}
catch {
print("Error writing vdb mutation file")
exit(9)
}
}
// removes insertions from tmpBuffer while copying into cdsBuffer, then translates
func condenseAndTranslate(cdsBuffer: inout [UInt8], cdsBufferPosition: inout Int, outBuffer: inout [UInt8], outBufferPosition: inout Int, tmpBuffer: inout [UInt8], tmpBufferPosition: inout Int) {
// condense based on reference sequence - this ignores insertions
var insertions : [(Int,[UInt8])] = []
var currentInsertion : (Int,[UInt8]) = (0,[])
for pos in 0..<tmpBufferPosition {
if refNoGap[pos] {
cdsBuffer[cdsBufferPosition] = tmpBuffer[pos]
cdsBufferPosition += 1
}
else if tmpBuffer[pos] != dashChar {
if cdsBufferPosition != currentInsertion.0 {
if currentInsertion.0 != 0 {
// var allN : Bool = true
// for val in currentInsertion.1 {
// if val != nuclN {
// allN = false
// break
// }
// }
// if !allN {
insertions.append(currentInsertion)
// }
}
currentInsertion.0 = cdsBufferPosition
currentInsertion.1 = [tmpBuffer[pos]]
}
else {
currentInsertion.1.append(tmpBuffer[pos])
}
}
}
if currentInsertion.0 != 0 {
// var allN : Bool = true
// for val in currentInsertion.1 {
// if val != nuclN {
// allN = false
// break
// }
// }
// if !allN {
insertions.append(currentInsertion)
// }
}
// if !insertions.isEmpty {
// let insertionsMap = insertions.map { ($0.0,String($0.1.map { Character(UnicodeScalar($0)) })) }
// print("insertions = \(insertionsMap)")
// }
if !nucl {
var translatedInsertions : [(Int,[UInt8])] = []
for i in 0..<insertions.count {
if insertions[i].0 > startSRef && insertions[i].0 < endSRef {
let trans : [UInt8] = translateInsertion(&insertions[i].1)
if !trans.isEmpty {
let pos : Int = (insertions[i].0 - startSRef) / 3
var insName : [UInt8] = [105,110,115] // ins
var p : Int = pos // outBufferPosition - startBufPos
var tmpBuf : [UInt8] = []
repeat {
let pd : Int = p / 10
let pr : Int = p % 10
tmpBuf.append(UInt8(pr) + 48)
p = pd
} while p != 0
insName.append(contentsOf: tmpBuf.reversed())
insName.append(contentsOf: trans)
insName.append(spaceChar)
translatedInsertions.append((pos,insName))
}
}
}
// if !translatedInsertions.isEmpty {
// let insertionsMap = translatedInsertions.map { ($0.0,String($0.1.map { Character(UnicodeScalar($0)) })) }
// print("translatedInsertions = \(insertionsMap)")
// }
translate(cdsBuffer: &cdsBuffer, outBuffer: &outBuffer, outBufferPosition: &outBufferPosition, insertions: &translatedInsertions)
}
else {
var formattedInsertions : [(Int,[UInt8])] = []
for i in 0..<insertions.count {
if insertions[i].0 > 0 && insertions[i].0 < refProtein.count {
if !insertions[i].1.isEmpty {
let pos : Int = insertions[i].0
var insName : [UInt8] = [105,110,115] // ins
var p : Int = pos // outBufferPosition - startBufPos
var tmpBuf : [UInt8] = []
repeat {
let pd : Int = p / 10
let pr : Int = p % 10
tmpBuf.append(UInt8(pr) + 48)
p = pd
} while p != 0
insName.append(contentsOf: tmpBuf.reversed())
insName.append(contentsOf: insertions[i].1)
insName.append(spaceChar)
formattedInsertions.append((pos,insName))
}
}
}
nuclMutations(cdsBuffer: &cdsBuffer, outBuffer: &outBuffer, outBufferPosition: &outBufferPosition, insertions: &formattedInsertions)
}
tmpBufferPosition = 0
cdsBufferPosition = 0
}
if !nucl {
// make reference protein
tmpBufferMP[0] = refBuffer
tmpBufferPositionMP[0] = refBufferPosition
condenseAndTranslate(cdsBuffer: &cdsBufferMP[0], cdsBufferPosition: &cdsBufferPositionMP[0], outBuffer: &outBufferMP[0], outBufferPosition: &outBufferPositionMP[0], tmpBuffer: &tmpBufferMP[0], tmpBufferPosition: &tmpBufferPositionMP[0])
outBufferPositionMP[0] = 0
}
else {
for pos in 0..<refBufferPosition {
if refNoGap[pos] {
refProtein.append(refBuffer[pos])
}
}
}
// main scan
lineCount = 0
greaterPosition = -1
lfAfterGreaterPosition = 0
lastLf = 0
fileStream.close()
guard let fileStream2 : InputStream = InputStream(fileAtPath: filePath) else { print("Error reading file \(filePath)"); return }
fileStream2.open()
checkCount = 0
var checkCountTotal : Int = 0
var lastCheckPrinted : Int = 0
lastBufferSize = 0
var shouldRead : Bool = true
while useStdInput || fileStream2.hasBytesAvailable {
if !pipeOutput {
updateStatusReadout()
}
if !shouldRead {
break
}
shouldRead = false
var bytesRead : Int = 0
var endOfStream : Bool = false
if !useStdInput {
bytesRead = fileStream2.read(&lineN[lastBufferSize], maxLength: blockBufferSize)
}
else {
if firstLoadBytesRead == 0 {
let _ = autoreleasepool { () -> Void in
while true {
let data : Data = standardInput.availableData
if data.count == 0 {
endOfStream = true
break
}
data.copyBytes(to: &lineN[lastBufferSize+bytesRead], count: data.count)
bytesRead += data.count
if bytesRead > streamBufferSize {
// test below added to prevent crash on Linux - optimization bug?
if bytesRead == Int.max {
print("bytesRead = \(bytesRead)")
}
break
}
}
}
if bytesRead == 0 && lastBufferSize == 0 && endOfStream {
break
}
}
else {
bytesRead = firstLoadBytesRead
firstLoadBytesRead = 0
}
}
let bytesAvailable : Bool = useStdInput ? (bytesRead > 0 && !endOfStream) : fileStream2.hasBytesAvailable
let bytesReadAdj : Int = bytesRead + lastBufferSize
lastBufferSize = 0
// setup multithreaded processing
var mp_number : Int = mpNumber
if bytesReadAdj < 500_000 {
mp_number = 1
}
var sema : [DispatchSemaphore] = []
for _ in 0..<mp_number-1 {
sema.append(DispatchSemaphore(value: 0))
}
let greaterChar : UInt8 = 62
var cuts : [Int] = [0]
let cutSize : Int = bytesReadAdj/mp_number
for i in 1..<mp_number {
var cutPos : Int = i*cutSize
while lineN[cutPos] != greaterChar {
cutPos += 1
}
cuts.append(cutPos)
}
cuts.append(bytesReadAdj)
var ranges : [(Int,Int)] = []
var lfAdd : Int = 0
if !bytesAvailable {
if lineN[bytesReadAdj-1] == lf {
lineN[bytesReadAdj] = greaterChar
}
else {
lineN[bytesReadAdj] = lf
lineN[bytesReadAdj+1] = greaterChar
lfAdd = 1
}
}
for i in 0..<mp_number {
if bytesAvailable || i != mp_number-1 {
ranges.append((cuts[i],cuts[i+1]+1))
}
else {
ranges.append((cuts[i],cuts[i+1]+1+lfAdd))
}
}
DispatchQueue.concurrentPerform(iterations: mp_number) { index in
let checkTotalMP = pos2LoopMP(mp_index: index, mp_range: ranges[index])
if index != 0 && index != mp_number-1 {
sema[index-1].wait()
}
_ = outBufferMP[index].withUnsafeBufferPointer { outBufferMPPointer in
memmove(&outBufferAll[outBufferPositionAll], outBufferMPPointer.baseAddress!, outBufferPositionMP[index])
}
// simple memmove statement crashes
// memmove(&outBufferAll[outBufferPositionAll], &outBufferMP[index][0], outBufferPositionMP[index])
// explicit copy is slower than memmove
// for i in 0..<outBufferPositionMP[index] {
// outBufferAll[outBufferPositionAll+i] = outBufferMP[index][i]
// }
outBufferPositionAll += outBufferPositionMP[index]
outBufferPositionMP[index] = 0
checkCountTotal += checkTotalMP
if index != mp_number - 1 {
sema[index].signal()
}
}
if checkCountTotal - lastCheckPrinted > 100_000 && !pipeOutput {
print("isolate count \(checkCountTotal)")
lastCheckPrinted = checkCountTotal
}
if outBufferPositionAll > outBufferWriteSize {
writeBufferToFile()
}
if !bytesAvailable {
break
}
func pos2LoopMP(mp_index: Int, mp_range: (Int,Int)) -> Int {
var greaterPosition : Int = -1
var lfAfterGreaterPosition : Int = 0
var firstSlashPosition : Int = 0
var lastLf : Int = 0
var checkCount : Int = 0
var checkCountTotal : Int = 0
var lineCount : Int = 0
var lastWaitDone : Bool = false
pos2Loop: for pos in mp_range.0..<mp_range.1 {
switch lineN[pos] {
case lf:
if lfAfterGreaterPosition == 0 {
lfAfterGreaterPosition = pos
if firstSlashPosition == 0 {
memmove(&outBufferMP[mp_index][outBufferPositionMP[mp_index]], &lineN[greaterPosition], pos-greaterPosition)
outBufferPositionMP[mp_index] += pos-greaterPosition
}
else {
outBufferMP[mp_index][outBufferPositionMP[mp_index]] = greaterChar
outBufferPositionMP[mp_index] += 1
memmove(&outBufferMP[mp_index][outBufferPositionMP[mp_index]], &lineN[firstSlashPosition+1], pos-firstSlashPosition-1)
outBufferPositionMP[mp_index] += pos-firstSlashPosition-1
}
if outBufferMP[mp_index][outBufferPositionMP[mp_index]-1] < aChar {
outBufferMP[mp_index][outBufferPositionMP[mp_index]] = verticalChar
outBufferPositionMP[mp_index] += 1
}
outBufferMP[mp_index][outBufferPositionMP[mp_index]] = commaChar
outBufferPositionMP[mp_index] += 1
checkCount += 1
checkCountTotal += 1
if checkCountTotal % 100000 == 0 && !pipeOutput {
print("isolate count \(checkCountTotal)")
}
}
else {
memmove(&tmpBufferMP[mp_index][tmpBufferPositionMP[mp_index]], &lineN[lastLf+1], pos-lastLf-1)
tmpBufferPositionMP[mp_index] += pos-lastLf-1
}
lastLf = pos
lineCount += 1
case greaterChar:
if checkCount > 0 {
checkCount = 0
condenseAndTranslate(cdsBuffer: &cdsBufferMP[mp_index], cdsBufferPosition: &cdsBufferPositionMP[mp_index], outBuffer: &outBufferMP[mp_index], outBufferPosition: &outBufferPositionMP[mp_index], tmpBuffer: &tmpBufferMP[mp_index], tmpBufferPosition: &tmpBufferPositionMP[mp_index])
}
greaterPosition = pos
lfAfterGreaterPosition = 0
firstSlashPosition = 0
if mp_index == mp_number-1 && bytesReadAdj-pos < lastMaxSize {
// stop read and start next block
if !lastWaitDone {
if mp_number > 1 {
sema[mp_number-1-1].wait()
}
lastWaitDone = true
}
if bytesAvailable {
shouldRead = true
lastBufferSize = bytesReadAdj-pos
var counter : Int = 0
for i in pos..<bytesReadAdj {
lineN[counter] = lineN[i]
counter += 1
}
break pos2Loop
}
}
case slashChar:
if firstSlashPosition == 0 {
firstSlashPosition = pos
}
default:
break
}
}
return checkCountTotal
}
}
fileStream2.close()
writeBufferToFile()
if !pipeOutput {
do {
try outFileHandle.synchronize()
try outFileHandle.close()
}
catch {
print("Error 2 writing vdb mutation file")
return
}
print("VDB file \(vdbFileName) written")
}
lineN.deallocate()
// attempt to codon align gaps
func codonAlign(cdsBuffer: inout [UInt8]) {
posLoop: for pos in stride(from: startSRef, to: endSRef, by: 3) {
var gapCount : Int = 0
for pp in pos..<pos+3 {
if cdsBuffer[pp] == dashChar {
gapCount += 1
}
}
if gapCount == 0 || gapCount == 3 {
continue
}
// prepare next gapped codon
var nextPos : Int = 0
var nextGap : Int = 0
for npos in stride(from:pos+3, to: endSRef, by:3) {
// var nextGap : Int = 0
nextGap = 0
for pp in npos..<npos+3 {
if cdsBuffer[pp] == dashChar {
nextGap += 1
}
}
if nextGap == 3 {
continue
}
if nextGap == 0 {
continue posLoop // cannot codon align
}
// push gap forward
nextPos = npos
if nextGap == 1 { // final: -NN
if cdsBuffer[npos+1] == dashChar {
cdsBuffer[npos+1] = cdsBuffer[npos]
cdsBuffer[npos] = dashChar
}
else if cdsBuffer[npos+2] == dashChar {
cdsBuffer[npos+2] = cdsBuffer[npos+1]
cdsBuffer[npos+1] = cdsBuffer[npos]
cdsBuffer[npos] = dashChar
}
}
else {
// nextGap == 2 final: --N
if cdsBuffer[npos+1] != dashChar {
cdsBuffer[npos+2] = cdsBuffer[npos+1]
cdsBuffer[npos+1] = dashChar
}
else if cdsBuffer[npos] != dashChar {
cdsBuffer[npos+2] = cdsBuffer[npos]
cdsBuffer[npos] = dashChar
}
}
break
}
if nextGap == 3 {
continue posLoop // cannot codon align
}
if gapCount == 1 {
// push gap back
if cdsBuffer[pos] == dashChar {
cdsBuffer[pos] = cdsBuffer[pos+1]
cdsBuffer[pos+1] = cdsBuffer[pos+2]
}
else if cdsBuffer[pos+1] == dashChar {
cdsBuffer[pos+1] = cdsBuffer[pos+2]
}
var nextBase : Int = pos+3
while cdsBuffer[nextBase] == dashChar {
nextBase += 1
}
cdsBuffer[pos+2] = cdsBuffer[nextBase]
cdsBuffer[nextBase] = dashChar
}
if gapCount == 2 {
// push gap forward
if cdsBuffer[pos+1] != dashChar {
cdsBuffer[pos] = cdsBuffer[pos+1]
cdsBuffer[pos+1] = dashChar
}
else if cdsBuffer[pos+2] != dashChar {
cdsBuffer[pos] = cdsBuffer[pos+2]
cdsBuffer[pos+2] = dashChar
}
// N-- -NN -> --- NNN
var nextBase : Int = nextPos+1
if cdsBuffer[nextBase] == dashChar {
nextBase += 1
}
if cdsBuffer[nextBase] == dashChar {
// Difficult codon alignment
if !pipeOutput {
print("Warning - codon alignment not optimal")
}
nextBase -= 2
if cdsBuffer[nextBase] == dashChar && !pipeOutput {
print("Warning - codon alignment not possible")
}
}
let ngap : Int = nextBase - 1
if ngap < 0 {
if !pipeOutput {
print("Warning ngap = \(ngap) pos = \(pos)")
}
continue
}
cdsBuffer[ngap] = cdsBuffer[pos]
cdsBuffer[pos] = dashChar
}
}
// swap 68 and 70 if necessary
let s68 : Int = startSRef + 67*3
if cdsBuffer[s68] == dashChar && cdsBuffer[s68+1] == dashChar && cdsBuffer[s68+2] == dashChar {
if cdsBuffer[s68+3] == dashChar && cdsBuffer[s68+4] == dashChar && cdsBuffer[s68+5] == dashChar {
cdsBuffer[s68] = cdsBuffer[s68+6]
cdsBuffer[s68+1] = cdsBuffer[s68+7]
cdsBuffer[s68+2] = cdsBuffer[s68+8]
cdsBuffer[s68+6] = dashChar
cdsBuffer[s68+7] = dashChar
cdsBuffer[s68+8] = dashChar
}
}
// swap 240,241 and 243,244 if necessary
let s240 : Int = startSRef + 239*3
if cdsBuffer[s240] == dashChar && cdsBuffer[s240+1] == dashChar && cdsBuffer[s240+2] == dashChar {
if cdsBuffer[s240+3] == dashChar && cdsBuffer[s240+4] == dashChar && cdsBuffer[s240+5] == dashChar {
if cdsBuffer[s240+6] == dashChar && cdsBuffer[s240+7] == dashChar && cdsBuffer[s240+8] == dashChar {
cdsBuffer[s240] = cdsBuffer[s240+9]
cdsBuffer[s240+1] = cdsBuffer[s240+10]
cdsBuffer[s240+2] = cdsBuffer[s240+11]
cdsBuffer[s240+9] = dashChar
cdsBuffer[s240+10] = dashChar
cdsBuffer[s240+11] = dashChar
cdsBuffer[s240+3] = cdsBuffer[s240+12]
cdsBuffer[s240+4] = cdsBuffer[s240+13]
cdsBuffer[s240+5] = cdsBuffer[s240+14]
cdsBuffer[s240+12] = dashChar
cdsBuffer[s240+13] = dashChar
cdsBuffer[s240+14] = dashChar
}
}
}
}
// translates sequence in cdsBuffer, compares this to the reference, and writes mutations to outBuffer
func translate(cdsBuffer: inout [UInt8], outBuffer: inout [UInt8], outBufferPosition: inout Int, insertions: inout [(Int,[UInt8])]) {
let makeRef : Bool = refProtein.isEmpty
var aaPos : Int = 0
var currentInsertion : Int = 0
var currentInsertionPos : Int = Int.max
if !insertions.isEmpty {
currentInsertionPos = insertions[currentInsertion].0
}
// var outBufferAA : [UInt8] = Array(repeating: 0, count: bufferSize)
// var outBufferAAPosition : Int = 0
codonAlign(cdsBuffer: &cdsBuffer)
for pos in stride(from: startSRef, to: endSRef, by: 3) {
var aa : UInt8 = 0
switch cdsBuffer[pos] {
case a:
switch cdsBuffer[pos+1] {
case a:
switch cdsBuffer[pos+2] {
case a,g:
aa = aaK
case t,c:
aa = aaN
default:
aa = aaX
}
case c:
aa = aaT
case t:
switch cdsBuffer[pos+2] {
case a,c,t:
aa = aaI
case g:
aa = aaM
default:
aa = aaX
}