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Add Hail-like AC, AN, and AF computation to variant stats V3 #731

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merged 33 commits into from
Aug 2, 2024

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awenocur
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@awenocur awenocur commented Jun 20, 2024

Take ref blocks into account when computing AF, and make two new fields: info_TILEDB_IAC and info_TILEDB_IAN available to data frames.

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@gspowley gspowley left a comment

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This will take multiple passes to review. Here's the first.

libtiledbvcf/src/dataset/tiledbvcfdataset.cc Outdated Show resolved Hide resolved
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@jdblischak jdblischak mentioned this pull request Jun 24, 2024
@awenocur awenocur force-pushed the adamwenocur/sc-44874/stats_reader branch 2 times, most recently from a7b2da6 to 2e447c3 Compare July 9, 2024 14:44
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i would expect some tests in here that are human readable. right now all I see if df.shape.

@awenocur awenocur force-pushed the adamwenocur/sc-44874/stats_reader branch from 2e447c3 to 94bcb60 Compare July 19, 2024 16:15
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@awenocur awenocur force-pushed the adamwenocur/sc-44874/stats_reader branch from f1c10e4 to c7be7cf Compare August 1, 2024 01:58
@awenocur awenocur force-pushed the adamwenocur/sc-44874/stats_reader branch from 3ef786b to 568f0d5 Compare August 1, 2024 14:43
@awenocur awenocur force-pushed the adamwenocur/sc-44874/stats_reader branch from 3311242 to b2fd97a Compare August 2, 2024 15:53
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Looks good!

Let's resolve the offline conversation before merging.

return normalized_ref + "," + normalized_alt;
}

std::string VariantStats::alt_string_v3(char* ref, char* alt) {
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Is there a difference in alt_string and alt_string_v3?

@awenocur awenocur merged commit ec45c63 into main Aug 2, 2024
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@awenocur awenocur deleted the adamwenocur/sc-44874/stats_reader branch August 2, 2024 19:30
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3 participants