Fix missing data treatment in window average available loci setting #26

CMakeLists.txt

@@ -168,7 +168,7 @@ include( "${CMAKE_CURRENT_LIST_DIR}/tools/cmake/DownloadDependency.cmake" )
 # These are replaced by tools/cmake/update_dependencies.sh to the hashes that are currently checked out.
 # Thus, do not replace the hashes manually!
 SET( CLI11_COMMIT_HASH "5cb3efabce007c3a0230e4cc2e27da491c646b6c" ) #CLI11_COMMIT_HASH#
-SET( genesis_COMMIT_HASH "ca0afb161a540ce2eebda24e3f511cde86dbeaf0" ) #genesis_COMMIT_HASH#
+SET( genesis_COMMIT_HASH "7c49b5e897645d6ab4673e199987b02ea81c855e" ) #genesis_COMMIT_HASH#
 
 # Call the github download function, which takes four arguments:
 #  - LIBPATH    : Path to the libracy dir where dependencies are stored.

src/options/window_average.cpp

@@ -66,8 +66,8 @@ CLI::Option* WindowAverageOptions::add_window_average_opt_to_app(
         "Denominator to use when computing the average of a metric in a window: "
         "\n(1) `window-length`: Simply use the window length, which likely underestimates the metric, "
         "in particular in regions with low coverage and high missing data."
-        "\n(2) `available-loci`: Use the number of positions for which there was data at all, "
-        "independent of all filter settings."
+        "\n(2) `available-loci`: Use the number of positions for which there was data at all "
+        "(that is, absent or missing data is excluded), independent of all other filter settings."
         "\n(3) `valid-loci`: Use the number of positions that passed all quality and numerical "
         "filters (that is, excluding the SNP-related filters). This uses all positions of high "
         "quality, and is the recommended policy when the input contains data for all positions."