Add DownsampleVcf tool #974
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #974 +/- ##
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+ Coverage 95.62% 95.64% +0.01%
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Files 126 127 +1
Lines 7364 7457 +93
Branches 506 521 +15
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+ Hits 7042 7132 +90
- Misses 322 325 +3
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| def hasNext: Boolean = iter.hasNext | ||
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| def isInOrder(current: Variant, next: Variant, currentIndex: Int, nextIndex: Int): Boolean = { |
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| def isInOrder(current: Variant, next: Variant, currentIndex: Int, nextIndex: Int): Boolean = { | |
| private def isInOrder(current: Variant, next: Variant, currentIndex: Int, nextIndex: Int): Boolean = { |
| /** Removes variants that are within a specified distance from a previous variant | ||
| * The end position of the current variant is compared with the start position of the following variant |
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| /** Removes variants that are within a specified distance from a previous variant | |
| * The end position of the current variant is compared with the start position of the following variant | |
| /** Removes variants that are within a specified distance from a previous variant. | |
| * The end position of the current variant is compared with the start position of the following variant. |
| } | ||
| } | ||
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| /** Downsamples variants using Allele Depths |
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| /** Downsamples variants using Allele Depths | |
| /** Downsamples variants by randomly sampling the total allele depths at the given proportion. |
| * calculated using total base count from the index and a target base count | ||
| * @return a new IndexedSeq of allele depths of the same length as `oldAds` | ||
| */ | ||
| def downsampleADs(oldAds: IndexedSeq[Int], proportion: Double, random: Random): IndexedSeq[Int] = { |
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nit: Function parameters should be the most general type possible. You could change this to IterableOnce[Int] and then below add .toIndexedSeq.
| } | ||
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| /** | ||
| * Does the downsampling on a Variant |
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| * Does the downsampling on a Variant | |
| * Re-genotypes a variant for each sample after downsampling the allele counts based on the given per-sample proportions. |
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| val random = new Random(42) | ||
| winnowed.foreach { v => | ||
| val ds = downsampleAndRegenotype(v, proportions = proportions, random = random, epsilon = epsilon) |
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no spaces between equals to be consistent with the rest of the codebase
| if (writeNoCall) { | ||
| outputVcf += ds | ||
| progress.record(ds) | ||
| } | ||
| else if (!ds.gts.forall(g => g.isNoCall)) { | ||
| outputVcf += ds | ||
| progress.record(ds) | ||
| } | ||
| } |
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| if (writeNoCall) { | |
| outputVcf += ds | |
| progress.record(ds) | |
| } | |
| else if (!ds.gts.forall(g => g.isNoCall)) { | |
| outputVcf += ds | |
| progress.record(ds) | |
| } | |
| } | |
| if (writeNoCall || !ds.gts.forall(g => g.isNoCall)) { | |
| outputVcf += ds | |
| progress.record(ds) | |
| } | |
| } |
| } | ||
| } | ||
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| progress.logLast() |
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probably nice to log how many reads were read, how many remained after winnowing, and how many were written. Consider three progress loggers?
| outputVcf.close() | ||
| } | ||
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| def buildOutputHeader(in: VcfHeader): VcfHeader = { |
| object Sample { | ||
| /** Load a set of samples from the 1KG metadata file. */ | ||
| def read(path: FilePath): Seq[Sample] = { | ||
| val lines = Io.readLines(path).dropWhile(_.startsWith("##")).map(line => line.dropWhile(_ == '#')) |
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This behavior is not described in the public API. Consider making this object and function private
| - [fgbio](#fgbio) | ||
| - [Goals](#goals) | ||
| - [Overview](#overview) | ||
| - [List of tools](#list-of-tools) | ||
| - [Building](#building) | ||
| - [Cloning the Repository](#cloning-the-repository) | ||
| - [Running the build](#running-the-build) | ||
| - [Command line](#command-line) | ||
| - [Include fgbio in your project](#include-fgbio-in-your-project) | ||
| - [Contributing](#contributing) | ||
| - [Authors](#authors) | ||
| - [License](#license) | ||
| - [Sponsorship](#sponsorship) | ||
| - [Become a sponsor](#become-a-sponsor) | ||
| - [Sponsors](#sponsors) |
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GitHub has TOC support so we could consider removing this maintenance burden.
https://github.blog/changelog/2021-04-13-table-of-contents-support-in-markdown-files/
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VS code also automatically updates the TOC. I don't care either way.
Add support for multi-allelic variants
Adds a tool to downsample VCFs based on allele depths. Currently only handles biallelic variants.