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Hello, I was wondering whether any adjustments to the HapNe-IBD algorithm are needed to make it compatible with local ancestry filtered IBD segments? I'm imagining using the browning pipeline for ASIB…
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Would it be a good fit for corecheck to meaure and report on IBD times?
Should this run weekly?
To what height should the IBD be performed to?
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Previously indexes and headers were saved on the fly (while rn they are kept in a `HashMap` until calling `flush`), and `flush` was called periodically during IBD (now only after validating blocks onc…
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[2024-11-07 14:25:06] [DEBUG] DEBUG MODE ON
[2024-11-07 14:25:06] [DEBUG] INIT ibd2sql
[2024-11-07 14:25:06] [DEBUG] FORCE False
[2024-11-07 14:25:06] [DEBUG] SET False
[2024-11-07 14:25:06] [DEBU…
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Hi
I keep having issues with the resources. I was stuck at the region-to-gene step with 250k cells, then I subset the data to 160k cells and I were able to preceed up to eGRN analysis. Howevere th…
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D:\ibd2sql-main>python main.py sj4.ibd --sdi-table sj8.ibd --mysql5 --ddl
Traceback (most recent call last):
File "D:\ibd2sql-main\main.py", line 144, in
ddcw.init()
File "D:\ibd2sql-main…
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我修改了代码，解析速度大概1w/s，感觉有点慢。。
1.增加写文件sql或csv
--format=sql|csv
2.添加对指定字段进行简单过滤，例如where user_id in (20,21,22)
--where='3,20,21,22'
3.输出文件按行数分片,写1000w后自动生成新文件，以pageid结尾，可通过--page-start并行解析
--separate=…
yeshl updated
2 months ago
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The `SegSiteStructure` objects (defined [here](https://github.com/DanielSeidman/MutationScripts/blob/be44de33dcebcafa04677a3f711e6911a98137dc/MutationCaller3.py#L160)) look like they're intended to ho…
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Are the IBD probabilities functional at all? Has anyone tested them? If not, they should be hidden, or at least the expansion should be disabled.