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no indel tables in BQSR tables by default #1821

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merged 1 commit into from May 16, 2016
Merged

no indel tables in BQSR tables by default #1821

merged 1 commit into from May 16, 2016

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akiezun
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@akiezun akiezun commented May 14, 2016

I want to skip indels by default in BQSR. We know if does not affect results but it's faster and we want speed out of the box.

@lbergelson can you review?

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coveralls commented May 14, 2016 •
edited

Coverage Status

Coverage remained the same at 82.274% when pulling 027506d on ak_BQSR_noIndelsByDefault into 4780534 on master.

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@akiezun Are there any tests that run now without indelBQSR on?
When you say doesn't affect results you mean byte identical or analysis shows it's unimportant? I'm assuming some minor differences but not meaningful.

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akiezun commented May 16, 2016

yes. BothStepsOfBQSRIntegrationTest - the results are qual-for-qual identical (see #1056)

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lbergelson commented May 16, 2016 •
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👍

@lbergelson lbergelson merged commit 421eb29 into master May 16, 2016
@lbergelson lbergelson deleted the ak_BQSR_noIndelsByDefault branch May 16, 2016 14:20
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