Merge branch 'master' into panel/mhwg

.github/workflows/cibuild.yml

@@ -9,7 +9,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [3.7, 3.8, 3.9]
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
 
     steps:
     - uses: actions/checkout@v1

CHANGELOG.md

@@ -2,10 +2,11 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
-## Unreleased
+## [0.11] 2023-10-25
 
 ### Added 
 - A new table flagging markers with repetitive content (see #147).
+- A new column in the `microhapdb.frequencies` table containing the number of observed haplotypes used to compute frequency estimates for each population group (see #151).
 
 ### Changed
 - Merged RSIDs resolved during database build now propagated to the final marker definition (see #149).

dbbuild/README.md

@@ -112,20 +112,21 @@ It includes the following fields.
 - `Population`: the unique identifer of the population
 - `Allele`: the allele of each variant in the microhap, separated by pipe symbols
 - `Frequency`: the frequency of the allele in the specified population (a real number between 0.0 and 1.0)
+- `Count`: the total number of alleles (denominator) used to compute the given population frequency estimate
 
 For example, the first few lines of the `frequency.tsv` for van der Gaag (2018) look like this.
 
 ```csv
-Marker,Population,Allele,Frequency
-mh06PK-24844,MHDBP-383d86606a,T|C|G|C|C|C|A|A|G|A,0.000
-mh06PK-24844,MHDBP-936bc36f79,T|C|G|C|C|C|A|A|G|A,0.000
-mh06PK-24844,MHDBP-3dab7bdd14,T|C|G|C|C|C|A|A|G|A,0.123
-mh06PK-24844,MHDBP-383d86606a,T|C|G|C|C|T|A|A|G|G,0.566
-mh06PK-24844,MHDBP-936bc36f79,T|C|G|C|C|T|A|A|G|G,0.586
-mh06PK-24844,MHDBP-3dab7bdd14,T|C|G|C|C|T|A|A|G|G,0.425
-mh06PK-24844,MHDBP-383d86606a,C|C|G|C|C|C|A|A|G|A,0.071
-mh06PK-24844,MHDBP-936bc36f79,C|C|G|C|C|C|A|A|G|A,0.000
-mh06PK-24844,MHDBP-3dab7bdd14,C|C|G|C|C|C|A|A|G|A,0.329
+Marker,Population,Allele,Frequency,Count
+mh06PK-24844,MHDBP-383d86606a,T|C|G|C|C|C|A|A|G|A,0.000,99
+mh06PK-24844,MHDBP-936bc36f79,T|C|G|C|C|C|A|A|G|A,0.000,87
+mh06PK-24844,MHDBP-3dab7bdd14,T|C|G|C|C|C|A|A|G|A,0.123,73
+mh06PK-24844,MHDBP-383d86606a,T|C|G|C|C|T|A|A|G|G,0.566,99
+mh06PK-24844,MHDBP-936bc36f79,T|C|G|C|C|T|A|A|G|G,0.586,87
+mh06PK-24844,MHDBP-3dab7bdd14,T|C|G|C|C|T|A|A|G|G,0.425,73
+mh06PK-24844,MHDBP-383d86606a,C|C|G|C|C|C|A|A|G|A,0.071,99
+mh06PK-24844,MHDBP-936bc36f79,C|C|G|C|C|C|A|A|G|A,0.000,87
+mh06PK-24844,MHDBP-3dab7bdd14,C|C|G|C|C|C|A|A|G|A,0.329,73
 ```
 
 ### `population.csv`
@@ -200,6 +201,7 @@ They can be installed using pip and/or conda.
 - UCSC liftover chain files
     - hg19ToHg38
     - hg38ToHg19
+- UCSC RepeatMasker track
 
 The following command will download data files required for the database build.
 

dbbuild/build.py

@@ -73,6 +73,7 @@ def cleanup_frequencies(freq):
     freq.loc[(freq.Marker.str.startswith("mh05KK-120")) & (freq.Source == "Kidd2018") & (freq.NumVars == 3), "Marker"] = "mh05KK-120.v1"
     freq.loc[(freq.Marker.str.startswith("mh05KK-120")) & (freq.Source == "Kidd2018") & (freq.NumVars == 4), "Marker"] = "mh05KK-120.v2"
     freq = freq.drop(columns="NumVars")
+    freq["Count"] = freq["Count"].astype("Int16")
     return freq