Add settings for distance and threshold to the configuration

Snakefile

@@ -74,10 +74,13 @@ rule gvcf2coverage:
         lambda wildcards: config["samples"][wildcards.sample]["gvcf"]
     output:
         temp("{sample}/varda/{sample}_coverage_ucsc.varda")
+    params:
+        threshold = config["settings"]["threshold"],
+        distance = config["settings"]["distance"]
     container:
         containers["gvcf2coverage"]
     shell:
-        "gvcf2coverage -t 10 -d 0 < {input} > {output}"
+        "gvcf2coverage -t {params.threshold} -d {params.distance} < {input} > {output}"
 
 rule cov_cthreepo:
     input:

test/config/config-GIAB-chrM.json

@@ -5,5 +5,9 @@
       "gvcf": "test/data/16699289_chrM.g.vcf",
       "vcf": "test/data/16699289_chrM.vcf"
     }
+  },
+  "settings": {
+    "threshold": 10,
+    "distance": 0
   }
 }

test/config/config-multiallelic.json

@@ -5,5 +5,9 @@
       "gvcf": "test/data/16699289_chrM.g.vcf",
       "vcf": "test/data/fake_chrM_multiallelic.vcf"
     }
+  },
+  "settings": {
+    "threshold": 10,
+    "distance": 0
   }
 }

test/config/config-noalt-uncalled.json

@@ -5,5 +5,9 @@
       "gvcf": "test/data/16699289_chrM.g.vcf",
       "vcf": "test/data/16699289_chrM_noalt_uncalled.vcf"
     }
+  },
+  "settings": {
+    "threshold": 10,
+    "distance": 0
   }
 }