From 5b8bcb863e9fea080a6dc6e56a3e660bb2269079 Mon Sep 17 00:00:00 2001 From: Lucas Czech Date: Tue, 16 Jul 2024 17:39:28 +0200 Subject: [PATCH] Fix missing data treatment in window average available loci setting #26 --- CMakeLists.txt | 2 +- libs/genesis | 2 +- src/options/window_average.cpp | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index d05f601..91774d3 100644 --- a/CMakeLists.txt +++ b/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. diff --git a/libs/genesis b/libs/genesis index ca0afb1..7c49b5e 160000 --- a/libs/genesis +++ b/libs/genesis @@ -1 +1 @@ -Subproject commit ca0afb161a540ce2eebda24e3f511cde86dbeaf0 +Subproject commit 7c49b5e897645d6ab4673e199987b02ea81c855e diff --git a/src/options/window_average.cpp b/src/options/window_average.cpp index f4423a8..0ef87d0 100644 --- a/src/options/window_average.cpp +++ b/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."