Refactoring windows and padding for assembly and genotyping #6358
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Closes #5676. |
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Assigning to @takutosato because it's pertinent to Mutect2 and because I have dumped enough on the engine team lately. |
davidbenjamin
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jamesemery
takutosato
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Feb 4, 2020
src/main/java/org/broadinstitute/hellbender/engine/spark/AssemblyRegionArgumentCollection.java
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| * | ||
| * A genotyping region is an interval surrounding an active region in which we perform pair-HMM and Smith-Waterman alignment. Even though | ||
| * we ultimately only genotype and call variants within the active region, we call entire haplotypes as an intermediate step, hence the | ||
| * needed for an expanded genotyping region. The parameters {@code snpPaddingForGenotyping} and {@code indelPaddingForGenotyping} determine |
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I think mentioning the defaults here (snp genotyping padding = 25, indel genotyping padding = 75, assembly region padding = 100) would be helpful for the reader (i.e. me)
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I'm nervous about hard-coding numbers -- what if they change? -- but I replaced the {@code }s with {@link }s so the reader can quickly navigate to the defaults in the IDE.
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@takutosato Back to you. How does the |
takutosato
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Feb 5, 2020
| * Importantly active regions are excusively a matter of delegating responsibility for calling and have nothing to do with the size | ||
| * of the span over which we perform local assembly and pair-HMM. | ||
| * in the same active region. The size of active regions are determined by the variants present, {@link AssemblyRegionArgumentCollection.activeProbThreshold}, | ||
| * and {@link AssemblyRegionArgumentCollection.maxProbPropagationDistance}, and are bounded by the parameters {@link AssemblyRegionArgumentCollection.minAssemblyRegionSize} |
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Thanks these links work great
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@jamesemery Here it is. It will make sense to review this one commit at a time. I have done my best to produce a clean commit history.