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Hello,
I simulated 2k samples and 50k SNPs, for which `RaPID` returned around 6000 IBD segments.
On this data, `snpknock2` seems basically stuck at `Generating related knockoffs` (waited ~30 min …
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I got this error message
```
Python(86357,0x1171a15c0) malloc: Incorrect checksum for freed object 0x7fa5a028a800: probably modified after being freed.
Corrupt value: 0x41117b6000000000
Python(863…
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See #1708 for more background on the ``ibd_segments`` method (currently ``find_ibd``)
The idea here is that the IbdSegments gives us access to useful simple summaries of the IBD segments, which may…
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As we're going through the IBD API and making room for it to do more general things (e.g. #1663), I think it makes sense to be more concrete about what the current ``find_ibd`` method does: it returns…
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See #1639 . In the future, we may wish to expand `find_ibd` so that summary statistics are calculated and updated internally as the segments are discovered. This would prevent the need for large numbe…
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With the updates to find_ibd in #1637 it's now possible to reason about the IBD segments without having to explicitly convert them all to Python objects, removing a significant memory block. However,…
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### The problem
Updating from 2022.3.7 to 2022.4.0, the database migration never finished. CPU and IO utilization was 0. I checked the running MariaDB processes and saw this:
```
MariaDB [home_as…
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I simulated some genotypes and want to generate their knockoffs. I tried following the [tutorial](https://msesia.github.io/knockoffgwas/tutorial.html) and have a few questions, if I may?
1. Is the …
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The current ``samples`` argument to find_ibd requires us to provide an explicit list of pairs of nodes we want to record ibd segments for. This is a bad idea for a number of reasons I think:
1. It'…
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The C test test_ibd_finder_samples_are_descendants is interesting, as it checks for IBD relationships in the following case:
```
const char *multi_root_tree_ex_nodes = "1 0 -1 -1\n" /* 4 5 …