add yte config

README.md

@@ -860,6 +860,8 @@ The earth sciences folder contain subfolders for different data formats encounte
   - ncbi_user_settings.mkfg: Minimal NCBI user settings
   - paraphase_config.yaml: Minimal paraphase config for PRODH
   - config_baysor.toml: Sample config file to run the baysor module.
+  - config_template.yte.yaml: YTE compatible exemplary config file
+  - yte_map_file.yaml: map file to test YTE
 - csv
   - 'test.csv': exemplary comma-separated file obtained from [here](https://bioinf.shenwei.me/csvtk/usage/#split)
 - models

data/generic/config/config_template.yte.yaml

@@ -0,0 +1,34 @@
+species:
+  heterozygosity: 0.001
+  germline-mutation-rate: 1e-3
+  ploidy:
+    male:
+      all: 2
+      X: 1
+      Y: 1
+    female:
+      all: 2
+      X: 2
+      Y: 0
+  genome-size: 3.5e9
+
+samples:
+  tumor:
+    sex: ?sex
+    somatic-effective-mutation-rate: 1e-6
+    inheritance:
+      clonal:
+        from: normal
+        somatic: true
+    contamination:
+      by: normal
+      fraction: 0.1
+  normal:
+    sex: ?sex
+    somatic-effective-mutation-rate: 1e-10
+
+events:
+  somatic_tumor_high: "normal:0.0 & tumor:[0.1,1.0]"
+  somatic_tumor_low: "normal:0.0 & tumor:]0.0,0.1["
+  somatic_normal: "normal:]0.0,0.5["
+  germline: "normal:0.5 | normal:1.0"

data/generic/config/yte_map_file.yaml

@@ -0,0 +1 @@
+sex: female