Drop pre-compute of bases and phase #47

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jamescasbon opened this Issue Jun 11, 2012 · 2 comments

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jamescasbon commented Jun 11, 2012

Please see branch 'performance'.

I have made a number of tweaks which result in 37% faster parsing of the 1kg VCF (see vcf/test/prof.py).

The breaking change is that most of the time is spent precomputing these. @arq5x this was your change, are you bothered if it goes?

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jamescasbon Jun 12, 2012

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jamescasbon commented Jun 12, 2012

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arq5x Jun 12, 2012

Hi James,
I think this makes sense in the interest of a more broadly useful API. I will need to keep the pre-computation in my fork because of my use case (I need these values for every variant, so pre-computing actually saves me time).
Aaron

arq5x commented Jun 12, 2012

Hi James,
I think this makes sense in the interest of a more broadly useful API. I will need to keep the pre-computation in my fork because of my use case (I need these values for every variant, so pre-computing actually saves me time).
Aaron

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