From a33b062cb2631064c9d5323ddc208933caf28624 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Tue, 7 May 2024 11:24:27 +0200
Subject: Precompute

---
 issues/gemma/lmm-precomputed-scores.gmi | 37 +++++-----------------
 issues/strainid-wrong-for-bxd.gmi       | 56 +++++++++++++++++++++++++++++++++
 2 files changed, 64 insertions(+), 29 deletions(-)
 create mode 100644 issues/strainid-wrong-for-bxd.gmi

(limited to 'issues')

diff --git a/issues/gemma/lmm-precomputed-scores.gmi b/issues/gemma/lmm-precomputed-scores.gmi
index 744d51a..8db9722 100644
--- a/issues/gemma/lmm-precomputed-scores.gmi
+++ b/issues/gemma/lmm-precomputed-scores.gmi
@@ -7,36 +7,15 @@ Here we will track introducing a new precomputation of scores for GN. Interestin
 * assigned: pjotrp
 * priority: high
 * type: bug, enhancement
-* status: unclear
+* status: ongoing
 * keywords: database, gemma, reaper
 
-# Old storage
-
-The old reaper scores are in
-
-```
-MariaDB [db_webqtl]> select ProbeSetId,ProbeSetFreezeId,Locus,LRS,additive from ProbeSetXRef limit 10;
-+------------+------------------+----------------+------------------+--------------------+
-| ProbeSetId | ProbeSetFreezeId | Locus          | LRS              | additive           |
-+------------+------------------+----------------+------------------+--------------------+
-|          1 |                1 | rs13480619     |  12.590069931048 |        -0.28515625 |
-|          2 |                1 | rs29535974     | 10.5970737900941 | -0.116783333333333 |
-|          3 |                1 | rs49742109     |  6.0970532702754 |  0.112957489878542 |
-|          4 |                1 | rsm10000002321 | 11.7748675511731 | -0.157113725490196 |
-|          5 |                1 | rsm10000019445 | 10.9232633740162 |  0.114764705882353 |
-|          6 |                1 | rsm10000017255 | 8.45741703245224 | -0.200034412955466 |
-|          7 |                1 | rs4178505      | 7.46477918183565 |  0.104331983805668 |
-|          8 |                1 | rsm10000144086 | 12.1201771258006 | -0.134278431372548 |
-|          9 |                1 | rsm10000014965 | 11.8837168740735 |  0.341458333333334 |
-|         10 |                1 | rsm10000020208 | 10.2809848009836 | -0.173866666666667 |
-+------------+------------------+----------------+------------------+--------------------+
-10 rows in set (0.000 sec)
-```
-
-This means for every dataset one single maximum score gets stored (?)
-
-Moved to
+# Tasks
 
-=> ../../topics/systems/mariadb/precompute-mapping-input-data.gmi
+* [ ] Add the log values, effect size and number of individuals to the xapian search.
+
+# Note
 
-* closed
+First implementation in
+
+=> ../../topics/systems/mariadb/precompute-mapping-input-data.gmi
diff --git a/issues/strainid-wrong-for-bxd.gmi b/issues/strainid-wrong-for-bxd.gmi
new file mode 100644
index 0000000..21bd2d8
--- /dev/null
+++ b/issues/strainid-wrong-for-bxd.gmi
@@ -0,0 +1,56 @@
+# StrainId wrong
+
+# Tags
+* assigned: arthurc
+* type: bug
+* status: unknown
+
+# Info
+
+When I do:
+
+```
+MariaDB [db_webqtl]> SELECT StrainId,Strain.Name FROM Strain, StrainXRef WHERE StrainXRef.StrainId = Strain.Id AND StrainXRef.InbredSetId = 1;
+```
+
+I get a list of BXDs (good), but also
+
+```
+|      333 | BXH2              |
+|      334 | BXH3              |
+|      336 | BXH5              |
+|      342 | BXH11             |
+|      343 | BXH12             |
+|    43879 | BXH12a            |
+|    43880 | BXH13             |
+|    43881 | HXB1              |
+|    43882 | HXB2              |
+|    43883 | HXB3              |
+|    43884 | HXB4              |
+```
+
+This is probably wrong?
+
+
+```
+MariaDB [db_webqtl]> select * from InbredSet where InbredSetId=1 limit 3;
++----+-------------+---------------+------+-----------+------------+--------+-----------------+-------------+---------------------------------
+-----------------+-------------+-------------+---------------+
+| Id | InbredSetId | InbredSetName | Name | SpeciesId | FullName   | public | MappingMethodId | GeneticType | Family
+                 | FamilyOrder | MenuOrderId | InbredSetCode |
++----+-------------+---------------+------+-----------+------------+--------+-----------------+-------------+---------------------------------
+-----------------+-------------+-------------+---------------+
+|  1 |           1 | BXD           | BXD  |         1 | BXD Family |      2 | 1               | riset       | Reference Populations (replicate
+ average, SE, N) |           1 |           0 | BXD           |
++----+-------------+---------------+------+-----------+------------+--------+-----------------+-------------+---------------------------------
+-----------------+-------------+-------------+---------------+
+
+MariaDB [db_webqtl]> select * from StrainXRef where InbredSetId=1 and StrainID=43889 limit 3;
++-------------+----------+---------+------------------+----------------+
+| InbredSetId | StrainId | OrderId | Used_for_mapping | PedigreeStatus |
++-------------+----------+---------+------------------+----------------+
+|           1 |    43889 |    1247 | N                | NULL           |
++-------------+----------+---------+------------------+----------------+
+```
+
+Not a BXD. Not even a mouse.
-- 
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