blob: 23086bfaf66c9edbdfa666aa0c442296c07fd5e3 (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
|
# MGAMMA Convert
MGamma can convert between different formats.
# Tags
* assigned: pjotrp, artyom
* type: feature
* priority: high
# Tasks
* [ ] Store genotypes as floats instead of doubles in lmdb
* [X] Required for the above: rework the type system in guile-gsl to allow float vectors/matrices
* [ ] Add annotations to genotype lmdb format - probably as the first named columns
* [ ] Provide a metadata header in JSON that tracks such info and a version
```
{type: "geno", version:0.01, float: true, anno:["name","chr","pos"]}
```
* [ ] Convert genotypes from strings using Rqtl2 CSV and metadata-JSON version of the control format, see
=> https://kbroman.org/qtl2/assets/vignettes/input_files.html
* [ ] Write kinship lmdb as floats (half size)
* [X] Add individual names as first column in kinship rows (implemented as plain unsigned ints for now)
* [ ] Somehow find the names for individuals? Is there a file format for that?
* [X] If symmetric only store half the data
* [ ] Add JSON meta header to track that information
* [ ] Support genodb database format:
=> ../../topics/database/genotype-database.gmi See the genotype-database topic
```
{type: "GRM", version:0.01, float: true, symmetric: true}
```
|
