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Yf contaminate and estimate bid #384
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nh13
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Dec 19, 2020
| /* | ||
| * The MIT License | ||
| * | ||
| * Copyright (c) 2016 Fulcrum Genomics LLC |
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Suggested change
| * Copyright (c) 2016 Fulcrum Genomics LLC | |
| * Copyright (c) 2020 Fulcrum Genomics LLC |
| * and run VBID with different number of target snps to evaluate | ||
| * dependance of VBID on contamination & depth & number of target snps | ||
| */ | ||
| @clp(description = "Example FASTQ to BAM pipeline.", group = classOf[Pipelines]) |
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Longer description? Also, not a FASTQ to BAM pipeline
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What are the output files it creates?
| val tmpBam = out.resolve(prefix + ".tmp.bam") | ||
| val metricsPrefix: Some[DirPath] = Some(out.resolve(prefix)) | ||
| Files.createDirectories(out) | ||
| val bamYield = new mutable.HashMap[PathToBam, Int] |
| bams.map(bam => { | ||
| val metricPath: Path = out.resolve(prefix + bam.getFileName + ".qualityYieldMetrics") | ||
| val hsMetrics = new CollectHsMetrics(in = bam, ref = ref, targets = targets, prefix = Some(out.resolve(prefix))) | ||
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| val pairsOfBam = for (x <- bams; y <- bams) yield (x, y) | ||
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| pairsOfBam.foreach { case (x, y) => { | ||
| contaminations.foreach(c => { |
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| contaminations.foreach(c => { | |
| contaminations.foreach { c => |
| val bamYield = new mutable.HashMap[PathToBam, Int] | ||
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| bams.map(bam => { | ||
| val metricPath: Path = out.resolve(prefix + bam.getFileName + ".qualityYieldMetrics") |
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Can the suffix be the same one that CollectMultipleMetrics would produce? Then MultiQC can be used too!
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Why is this qualityYieldMetrics when the output is presumably from HsMetrics?
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| val xyContaminatedBam = out.resolve(prefix + "__" + x.getFileName + "__" + y.getFileName + | ||
| "__" + c + ".bam") |
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why double underscores? also, use string interpolation.
Suggested change
| val xyContaminatedBam = out.resolve(prefix + "__" + x.getFileName + "__" + y.getFileName + | |
| "__" + c + ".bam") | |
| val xyContaminatedBam = out.resolve(f"${prefix}__${x.getFileName}__${y.getFileName}__${c}.bam") |
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| root ==> downsample ==> mergedownsampled | ||
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| depths filter (d => d <= resultantDepth) foreach { d => { |
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| depths filter (d => d <= resultantDepth) foreach { d => { | |
| depths.filter(_ <= resultantDepth).foreach { d => |
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| depths filter (d => d <= resultantDepth) foreach { d => { | ||
| val outDownsampled = out.resolve(prefix + "__" + x.getFileName + "__" + y.getFileName + | ||
| "__" + c + "__target__" + d + ".bam") |
| /* | ||
| * The MIT License | ||
| * | ||
| * Copyright (c) 2015 Fulcrum Genomics LLC |
… appropriately downsample it using the targets.
… parts: -- simulate and generate bams -- downsample bam and contaminate bams -- downsample markers and estimate contamination
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just a quick draft to get comments on my first attempt at using dagr.
@tfenne