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Patch O(n^2) algorithm in VCFHeader.addMetadataLineLookupEntry() #3448

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droazen opened this issue Aug 15, 2017 · 4 comments
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Patch O(n^2) algorithm in VCFHeader.addMetadataLineLookupEntry() #3448

droazen opened this issue Aug 15, 2017 · 4 comments
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HTSJDK PRIORITY_HIGH profiling
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Engine-4.0

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@droazen
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droazen commented Aug 15, 2017

VCFHeader.addMetadataLineLookupEntry() is showing up in profiles of, eg., the 20k gnomAD run as around ~15% of total runtime of 16-hour jobs. This is due to a O(n^2) algorithm that @cmnbroad identified. We should prioritize a fix for this in htsjdk.
@droazen droazen added this to the Engine-4.0 milestone Aug 15, 2017
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droazen commented Aug 15, 2017

@cmnbroad Could you please make this your highest priority when you get back? Thanks!

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@drozen htsjdk PR is here. I'm running gatk tests locally as a sanity check.

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Tests passed, PR is reviewed and merged into htsjdk.

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Closing via samtools/htsjdk#968 and #3504.

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