Fix conflicting usage of parameter 'decon'.

bencardoen · Nov 4, 2024 · 94beaa4 · 94beaa4
1 parent c6d08a7
commit 94beaa4
Show file tree

Hide file tree

Showing 2 changed files with 2 additions and 1 deletion.
diff --git a/docs/src/postprocessing.md b/docs/src/postprocessing.md
@@ -84,6 +84,7 @@ A convenience script is provided to further aggregate the output of this stage.
 ```python
 python3 scripts/coverage.py  --inputdirectory DIR --outputdirectory <where to save your ouput>
 ```
+You may need to switch `python3` with `python`, depending on your installation.
 
 This will print summary output and save a file `coverage_aggregated.csv`. The columns Coverage % mito by contacts, mean per cell and ncontacts mean are the columns you'll be most interested in.
 

diff --git a/src/SubPrecisionContactDetection.jl b/src/SubPrecisionContactDetection.jl
@@ -1703,7 +1703,7 @@ function get_defaults()
     default_args["save-numerical-data"]=false
     default_args["inregex"]="*[1,2].tif"
     default_args["outpath"] = ""
-    default_args["mode"] = "non-decon"
+    default_args["mode"] = "decon"
     default_args["deconvolved"] = true
     default_args["sigmas"] = "1-1-1"
     default_args["lpsigmas"] = "1-1-1"