From f40db2f0d57d4dbb664ba914882e4aa4928e28c8 Mon Sep 17 00:00:00 2001
From: james hadfield <hadfield.james@gmail.com>
Date: Mon, 21 Oct 2024 11:03:29 +1300
Subject: [PATCH] [cattle-flu] show timetree for genome build

Resolves #94
---
 Snakefile                                     | 24 ++++++++++++++++++-
 .../auspice_config_h5n1-cattle-outbreak.json  |  2 +-
 2 files changed, 24 insertions(+), 2 deletions(-)

diff --git a/Snakefile b/Snakefile
index bcc91af..63e4e60 100755
--- a/Snakefile
+++ b/Snakefile
@@ -518,6 +518,28 @@ def additional_export_config(wildcards):
 
     return args
 
+rule auspice_config:
+    """
+    Depending on the build we may make wildcard-dependent modifications to the auspice config JSON.
+    If we implement config overlays in augur this rule will become unnecessary.
+    """
+    input:
+        auspice_config = files.auspice_config,
+    output:
+        auspice_config = "results/{subtype}/{segment}/{time}/auspice-config.json",
+    run:
+        import json
+        with open(input.auspice_config) as fh:
+            config = json.load(fh)
+        if wildcards.subtype == "h5n1-cattle-outbreak":
+            if wildcards.segment == "genome":
+                config['display_defaults']['distance_measure'] = "num_date"
+            else:
+                config['display_defaults']['distance_measure'] = "div"
+        with open(output.auspice_config, 'w') as fh:
+            json.dump(config, fh, indent=2)
+
+
 rule export:
     """
     Export the files into results/ and then use a subsequent rule to move these to the
@@ -529,7 +551,7 @@ rule export:
         node_data = export_node_data_files,
         colors = files.colors,
         lat_longs = files.lat_longs,
-        auspice_config = files.auspice_config,
+        auspice_config = rules.auspice_config.output.auspice_config,
         description = files.description
     output:
         auspice_json = "results/{subtype}/{segment}/{time}/auspice-dataset.json"
diff --git a/config/h5n1-cattle-outbreak/auspice_config_h5n1-cattle-outbreak.json b/config/h5n1-cattle-outbreak/auspice_config_h5n1-cattle-outbreak.json
index 7a1d362..09ac49e 100755
--- a/config/h5n1-cattle-outbreak/auspice_config_h5n1-cattle-outbreak.json
+++ b/config/h5n1-cattle-outbreak/auspice_config_h5n1-cattle-outbreak.json
@@ -124,7 +124,7 @@
     "map_triplicate": false,
     "color_by": "host",
     "geo_resolution": "division",
-    "distance_measure": "div"
+    "distance_measure": "__VALUE_OVERWRITTEN_BY_SNAKEMAKE_PIPELINE__"
   },
   "filters": [
     "host",