Create tools for SV VCF cleaning #8996
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This looks great overall. I have some suggestions on style and some places where you can reuse other classes. I did not mark all places where you can add final to variable declarations, just a few cases. You may not need to create a separate "Engine" class for the internals here unless you think some of the components would be reusable in another step or if it makes testing easier.
src/main/java/org/broadinstitute/hellbender/tools/walkers/sv/SVCleanPt1a.java
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src/main/java/org/broadinstitute/hellbender/tools/walkers/sv/SVCleanPt1a.java
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src/main/java/org/broadinstitute/hellbender/tools/walkers/sv/SVCleanPt1a.java
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src/main/java/org/broadinstitute/hellbender/tools/walkers/sv/SVCleanPt1a.java
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src/main/java/org/broadinstitute/hellbender/tools/walkers/sv/SVCleanPt1a.java
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src/main/java/org/broadinstitute/hellbender/tools/walkers/sv/SVCleanPt1a.java
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| @Argument( | ||
| fullName = OUTPUT_REVISED_EVENTS_LIST_LONG_NAME, | ||
| doc="Output list of revised genotyped events" | ||
| ) | ||
| private GATKPath outputRevisedEventsList; |
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Will it be possible to build this info directly into the VCF rather than have this extra file?
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Updated accordingly - added this as a new flag in the INFO field.
src/main/java/org/broadinstitute/hellbender/tools/spark/sv/utils/GATKSVVCFConstants.java
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| private void processSVType(VariantContext variant, VariantContextBuilder builder) { | ||
| final String svType = variant.getAttributeAsString(GATKSVVCFConstants.SVTYPE, null); | ||
| if (svType != null && variant.getAlleles().stream().noneMatch(allele -> allele.getDisplayString().contains(GATKSVVCFConstants.ME))) { |
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Better to parse the alleles with GATKSVVariantContextUtils.getSymbolicAlleleSymbols() and check for ME. Sometimes the alt is just <INS:ME>.
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Updated accordingly - thanks for the pointer.
| failSet = readLastColumn(failList); | ||
| passSet = readLastColumn(passList); |
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You could use TableReader here. It would require you to add header lines to the lists in the WDL, which would be okay too. See TableUtils.reader() and look at some implementations to see examples.
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Updated accordingly - thanks for the tip. For visibility, I have made corresponding changes to GATK-SV in broadinstitute/gatk-sv#733.
…VCleanPt1a.java Co-authored-by: Mark Walker <[email protected]>
…VCleanPt1a.java Co-authored-by: Mark Walker <[email protected]>
…VCleanPt1a.java Co-authored-by: Mark Walker <[email protected]>
…VCleanPt1a.java Co-authored-by: Mark Walker <[email protected]>
…VCleanPt1a.java Co-authored-by: Mark Walker <[email protected]>
This PR is intended to introduce several new tools related to the CleanVcf workflow in GATK-SV, which the use of these tools being documented in broadinstitute/gatk-sv#733. These tools are intended to introduce several enhancements over the existing implementation, including but not limited to: