Fix RAW_MQ header inconsistencies after reblocking #6276
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I can confirm that this fixes the production WGS reblocking issue. |
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Lots of files are changed because I changed the key name for RAW_MQ to include |
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@tlangs once we cut a release with this PR we can update and merge your reblocking workflow in dsde-pipelines. |
lbergelson
approved these changes
Nov 22, 2019
| @@ -158,6 +158,7 @@ public void onTraversalStart() { | |||
| final Set<VCFHeaderLine> headerLines = new HashSet<>(inputHeaders); | |||
| // Remove GCVFBlocks, legacy headers, and annotations that aren't informative for single samples | |||
| headerLines.removeIf(vcfHeaderLine -> vcfHeaderLine.getKey().startsWith(GVCFWriter.GVCF_BLOCK) || | |||
| (vcfHeaderLine.getKey().equals("INFO")) && ((VCFInfoHeaderLine)vcfHeaderLine).getID().equals(GATKVCFConstants.RAW_RMS_MAPPING_QUALITY_DEPRECATED) || //remove old (maybe wrong type) and add new with deprecated note | |||
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I hate these classes so much.
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I had a copy-paste guffaw when I deprecated the RAW_MQ header that changed the type to be incorrect. After reblocking, the new header is correct, but conflicting and GenomicsDB is understandably not pleased. Now there is a single, correct RAW_MQ header after reblocking.