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Call htsjdk's disableOnTheFlyModifications do disable header repairs #6013

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merged 2 commits into from May 1, 2019

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@marksantcroos
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commented May 1, 2019

Fixes #6012.

): VCFHeaderInfo = {
val codec = new htsjdk.variant.vcf.VCFCodec()
if (!repairHeader)

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tpoterba May 1, 2019

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I'd be happier just turning this off in all cases without any parameterization. This has caused nothing but trouble in the past!

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tpoterba May 1, 2019

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it certainly couldn't have been easy to find all the places we thread the parameters through, though! Nice work.

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@marksantcroos

marksantcroos May 1, 2019

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@tpoterba I'm happy to remove the conditional, if you are ok with that, that simplifies things obviously.

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tpoterba May 1, 2019

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yes, absolutely.

@tpoterba tpoterba self-assigned this May 1, 2019

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commented May 1, 2019

fixes #2822 🎉 🎉 🎉

@marksantcroos marksantcroos changed the title Expose htsjdk's disableOnTheFlyModifications as repair_header Call htsjdk's disableOnTheFlyModifications do disable header repairs May 1, 2019

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commented May 1, 2019

Awesome, thanks for the contribution!

@danking danking merged commit dac090e into hail-is:master May 1, 2019

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