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hisat2 hpv18 index and hpv16 alignment tests
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,79 @@ | ||
| import * as atomic from "../operations/atomicOperations"; | ||
| import {RunBowtie2Alignment} from "../operations/RunBowtie2Alignment"; | ||
| import * as L6R1HPV16Align from "./L6R1HPV16Align"; | ||
|
|
||
| export async function testL6R1HPV16Hisat2Alignment() : Promise<void> | ||
| { | ||
| return new Promise<void>((resolve,reject) => { | ||
| atomic.updates.removeAllListeners().on("runHisat2Alignment",function(op : RunBowtie2Alignment){ | ||
| if(op.flags.failure) | ||
| { | ||
| console.log(`Failed to align`); | ||
| return reject(); | ||
| } | ||
| else if(op.flags.success) | ||
| { | ||
| console.log(JSON.stringify(op.alignData,undefined,4)); | ||
| if(op.alignData.summary.reads == 2689) | ||
| console.log(`${op.alignData.alias} has correct number of reads`); | ||
| else | ||
| return reject(); | ||
|
|
||
| if(op.alignData.summary.mates == 4714) | ||
| console.log(`${op.alignData.alias} has correct number of mates`); | ||
| else | ||
| return reject(); | ||
|
|
||
| if(op.alignData.summary.overallAlignmentRate == 12.61) | ||
| console.log(`${op.alignData.alias} has correct overall alignment rate`); | ||
| else | ||
| return reject(); | ||
|
|
||
| if(op.alignData.varScanSNPSummary.minVarFreq == 0.2) | ||
| console.log(`${op.alignData.alias} has correct minimum variable frequency`); | ||
| else | ||
| return reject(); | ||
|
|
||
| if(op.alignData.varScanSNPSummary.minCoverage == 8) | ||
| console.log(`${op.alignData.alias} has correct minimum coverage`); | ||
| else | ||
| return reject(); | ||
|
|
||
| if(op.alignData.varScanSNPSummary.minAvgQual == 15) | ||
| console.log(`${op.alignData.alias} has correct minimum average quality`); | ||
| else | ||
| return reject(); | ||
|
|
||
| if(op.alignData.varScanSNPSummary.pValueThresh == 0.01) | ||
| console.log(`${op.alignData.alias} has correct p-value threshold`); | ||
| else | ||
| return reject(); | ||
|
|
||
| if(op.alignData.varScanSNPSummary.SNPsReported == 11) | ||
| console.log(`${op.alignData.alias} has correct predicted SNPs`); | ||
| else | ||
| return reject(); | ||
|
|
||
| if(op.alignData.varScanSNPSummary.indelsReported == 0) | ||
| console.log(`${op.alignData.alias} has correct indels reported`); | ||
| else | ||
| return reject(); | ||
|
|
||
| if(op.alignData.idxStatsReport[0].mappedReads == 678) | ||
| console.log(`${op.alignData.alias} has correct number of mapped reads`); | ||
| else | ||
| return reject(); | ||
|
|
||
| if(op.alignData.idxStatsReport[0].unMappedReads == 12) | ||
| console.log(`${op.alignData.alias} has correct number of unmapped reads`); | ||
| else | ||
| return reject(); | ||
|
|
||
| L6R1HPV16Align.set(op.alignData); | ||
|
|
||
| return resolve(); | ||
|
|
||
| } | ||
| }); | ||
| }); | ||
| } |
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