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Use specific handling of no-call in variant detail #990

merged 5 commits into from Feb 20, 2018


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cmdcolin commented Feb 15, 2018

This code handles variant no-call (represented as a .) to address #980

The previous code made this turn into "ref" because gtIndex being '.' going into parseInt('.') being NaN was handled the same way as the reference genotype of gtIndex being 0

This handles the '.' separately and just displays the dot in the genotype table


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rbuels commented Feb 19, 2018

@cmdcolin does any of our test data have no-call sections that exercise this code path? What's a good place where I can see this in action?


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cmdcolin commented Feb 19, 2018

I modified the volvox.test.vcf.gz to have some of the samples include no-call ./. instead of 0/0 (after 10000 bp all of the variants have this)

In the view details popup you can see in the genotype table says "no-call / no-call" for these now (on dev branch it displays these as reference)

screenshot-localhost-2018 02 19-17-33-00

Could add an automated test if interested

@rbuels rbuels added this to the 1.12.5 milestone Feb 20, 2018

@rbuels rbuels merged commit f5d05d6 into dev Feb 20, 2018

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@cmdcolin cmdcolin deleted the variant_no_call branch Feb 26, 2018

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