Permutect dataset engine outputs contig and read group indices, not names #8860
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meganshand
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Jun 4, 2024
| @@ -106,7 +128,7 @@ public void addData(final ReferenceContext ref, final VariantContext vc, Optiona | |||
| final M2ArgumentCollection.Mutect3DatasetMode mutect3DatasetMode) { | |||
| final String refBases = ReferenceBases.annotate(ref, vc); | |||
| final String refAllele = vc.getReference().getBaseString(); | |||
| final String contig = vc.getContig(); | |||
| final int contigIndex = sequenceDictionary.getSequenceIndex(vc.getContig()); | |||
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What happens if the sequence dictionary is null? Is that checked for somewhere? Or does GATK not allow input BAMs with no sequence dictionary?
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The sequence dictionary ultimately comes from Mutect2::getBestAvailableSequenceDictionary(), so it's not going to be null even if the BAM doesn't have one. Would you like me to put in some Utils.nonNull checks somewhere? (for future-proofing and/or peace of mind)
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Nope, it sounds like getBestAvailableSequenceDictionary() is already handling that check, so that should be fine.
davidbenjamin
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This is important for Infogain and other potential hybrid data because it will allow Permutect to separately normalize within each read group and otherwise keep track of different read groups downstream.
It also makes the data structures in Permutect much more convenient because numeric data is easier to write to a memory map.