Pileup-based read error corrector #6470
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@davidbenjamin Can I assume that you didn't change |
takutosato
requested changes
Feb 28, 2020
...va/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/PileupReadErrorCorrector.java
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...va/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/PileupReadErrorCorrector.java
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| for (int n = firstEdit; n <= lastEdit; n++) { | ||
| bases[edits.get(n).getLeft()] = edits.get(n).getRight(); | ||
| quals[edits.get(n).getLeft()] = GOOD_QUAL; |
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This chunk doesn't get triggered by the UnitTest—why?
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It does now. Totally rewrote the test.
...roadinstitute/hellbender/tools/walkers/haplotypecaller/PileupReadErrorCorrectorUnitTest.java
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...roadinstitute/hellbender/tools/walkers/haplotypecaller/PileupReadErrorCorrectorUnitTest.java
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Yes you can. |
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back to @takutosato |
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Closes #4868.
@takutosato This reduces false positives and improves speed at no cost to sensitivity. I'm not quite ready to turn it on by default but I want it in the code to begin experiments, such as combining with linked de Bruijn graphs and FFPE error correction.