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optimizeRun.mjs
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optimizeRun.mjs
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import {sample, pooledSample} from './component.mjs';
//function to create sample object from testcase file(LIMS request)
function createSampleObject(sampleMap) {
var sampleObject = new sample(sampleMap['pool'], sampleMap['sampleId'],sampleMap['recipe'],sampleMap['requestId'],sampleMap['requestName'],
sampleMap['altConcentration'],sampleMap['concentrationUnits'],sampleMap['volume'],sampleMap['barcodeSeq'],sampleMap['runType'],
sampleMap['readNum'],sampleMap['remainingReads']);
return sampleObject;
}
//function to create sampleList by merging pooledsamples from sample object list
function createSampleList(sampleObjectList){
var sampleList = [];
const samplePoolList = new Map();
for (let i = 0; i < sampleObjectList.length; i++){
if(sampleObjectList[i].poolID === undefined){
sampleList.push(sampleObjectList[i]);
}else{
if(samplePoolList.has(sampleObjectList[i].poolID)){
var temp = samplePoolList.get(sampleObjectList[i].poolID)
temp.push(sampleObjectList[i]);
samplePoolList.set(sampleObjectList[i].poolID,temp)
}else{
samplePoolList.set(sampleObjectList[i].poolID, [sampleObjectList[i]]);
}
}
}
for (const value of samplePoolList.values()){
var pooledSampleObject = new pooledSample(value);
sampleList.push(pooledSampleObject);
}
return(sampleList);
}
// function for barcode checking between two samples
function barcodeCollision(seq1, seq2, length, numOfMismatch){
var seq1_frag = seq1.substr(0,length);
var seq2_frag = seq2.substr(0,length);
var mismatch1 = 0;
var mismatch2 = 0;
if (seq1.includes('-')){
for (let i = 0; i < seq1_frag.indexOf('-'); i++){
if (seq1_frag[i] != seq2_frag[i]){
mismatch1 = mismatch1 + 1;
}
}
for (let i = seq1_frag.indexOf('-'); i < seq1_frag.length; i++){
if (seq1_frag[i] != seq2_frag[i]){
mismatch2 = mismatch2 + 1;
}
}
} else{
for (let i = 0; i < length; i++){
if (seq1_frag[i] != seq2_frag[i]){
mismatch1 = mismatch1 + 1;
}
}
}
if (mismatch1 <= numOfMismatch * 2 && mismatch2 <= numOfMismatch * 2){
return true;
} else{
return false;
}
}
//function for list barcode checking
function listBarcodeCollision(seqList1, seqList2, numOfMismatch){
//merge single barcode/list barcode into one array
var emptyList = [];
emptyList.push(seqList1, seqList2);
var newSeqList = emptyList.flat();
//get minimum barcode length
var minLength = 30;
for (let i = 0; i < newSeqList.length; i++){
if(newSeqList[i].length < minLength){
minLength = newSeqList[i].length;
}
}
//check barcode collision one by one
for(let i = 0; i < newSeqList.length - 1; i++){
for(let j = i + 1; j < newSeqList.length; j++){
if (barcodeCollision(newSeqList[i], newSeqList[j], minLength, numOfMismatch)){
return true;
}
}
}
return false;
}
//function to calculates total reads from a list of samples
function getTotalReads(listOfSamples) {
var totalReadsNum = 0;
for(let i = 0; i < listOfSamples.length; i++){
totalReadsNum = totalReadsNum + listOfSamples[i].readsRequest;
}
return totalReadsNum;
}
//function for checking barcode of pools that contain pool normal(not tested yet)
//return false if collison caused by pool normal
function checkPoolNormal(pool1, pool2, numOfMismatch){
var minLength = 30;
for (let i = 0; i < pool1.barcodeSeq.length; i++){
if(pool1.barcodeSeq[i].length < minLength){
minLength = pool1.barcodeSeq[i].length ;
}
}
for (let i = 0; i < pool2.barcodeSeq.length; i++){
if(pool2.barcodeSeq[i].length < minLength){
minLength = pool2.barcodeSeq[i].length ;
}
}
for (let i = 0; i < pool1.barcodeSeq.length; i++){
for (let j = 0; j < pool2.barcodeSeq.length; j++){
if (barcodeCollision(pool1.barcodeSeq[i], pool2.barcodeSeq[j],minLength,numOfMismatch) && !(i == 0 && j == 0)){
return true;
}
}
}
return false;
}
//function for checking whether barcode collison happens between two samples
function sampleBarcodeCollision(sample1, sample2, numOfMismatch){
if (sample1.poolID !== undefined && sample2.poolID !== undefined
&& sample1.containNormal == true && sample2.containNormal == true){
return checkPoolNormal(sample1, sample2, numOfMismatch);
}else{
return listBarcodeCollision(sample1.barcodeSeq, sample2.barcodeSeq, numOfMismatch);
}
}
// function for seperating samples into different groups based on barcode
function getCollisionGroup(sampleList){
var freeList = sampleList.concat();
var groupList = [];
var collisionList = [];
//function to sort collisionList by collision times
function makeSortedCollisionList(collisionList1){
var collisionMap = new Map();
for(let i = 0; i < collisionList1.length; i++){
let count = 0;
for(let j = 0; j < collisionList1.length; j++){
if((i != j) && (sampleBarcodeCollision(collisionList1[i], collisionList1[j],0))){
count = count + 1;
}
}
collisionMap.set(collisionList1[i], count);
}
const collisionMapSorted = new Map([...collisionMap.entries()].sort((a, b) => b[1] - a[1]));
var collisionListSorted1 = [];
for (const key of collisionMapSorted.keys()){
collisionListSorted1.push(key);
}
return collisionListSorted1;
}
// seperate the samples into freeList and collisionList based on barcode
for(let i = 0; i < sampleList.length; i++){
for(let j = 0; j < sampleList.length; j++){
let collision = false;
if((i != j) && (sampleBarcodeCollision(sampleList[i], sampleList[j],0))){
//remove the sample with collision barcode from freeList
for(let m = 0; m < freeList.length; m++){
if (freeList[m] === sampleList[i]) {
freeList.splice(m, 1);
}
}
//then push the sample with collision barcode into collisionList
collisionList.push(sampleList[i]);
break;
}
}
}
//create groupList based on sortedcollisonlist(based on collision times)
var collisionListSorted = makeSortedCollisionList(collisionList);
for (let i = 0; i < collisionListSorted.length; i++){
if (groupList.length != 0){
for (let x = 0; x < groupList.length; x++){
var add = true;
for(let y = 0; y < groupList[x].length; y++){
if(sampleBarcodeCollision(collisionListSorted[i], groupList[x][y],0)){
add = false;
break;
}
}
if(add == true){
groupList[x].push(collisionListSorted[i]);
break;
}
}
if(add == false){
groupList.push([collisionListSorted[i]]);
}
}else{
groupList.push([collisionListSorted[i]]);
}
}
return groupList;
}
// assigned the samples to the lanes according to project, recipe, and reads number
// var totalReads = getTotalReads(sampleList);
// var laneCapacity = totalReads/laneNumber;
// create recipe desired group,
// sorted the free list by projects and recipe and seperate into groups
// search the existing samples in the lane and fill in by project or recipe
// function for deciding optimized run by given sample list(grouped samples)
function optimizeRun(sampleList){
}
export {createSampleObject, createSampleList, getCollisionGroup, sampleBarcodeCollision, getTotalReads};