Reorder sample deletion count filter

lczech · May 7, 2024 · a8283ab · a8283ab
1 parent d4488fd
commit a8283ab
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Showing 2 changed files with 26 additions and 26 deletions.
diff --git a/lib/genesis/population/filter/sample_counts_filter_numerical.cpp b/lib/genesis/population/filter/sample_counts_filter_numerical.cpp
@@ -134,6 +134,21 @@ bool apply_sample_counts_filter_numerical(
         transform_zero_out_by_max_count( sample, params.max_count );
     }
 
+    // Check deletions.
+    if(
+        params.deletions_count_limit > 0
+        && sample.d_count > 0
+        && sample.d_count >= params.deletions_count_limit
+    ) {
+        // if( params.clear_filtered ) {
+        //     sample.clear();
+        // }
+
+        sample.status.set( SampleCountsFilterTag::kAboveDeletionsCountLimit );
+        ++stats[SampleCountsFilterTag::kAboveDeletionsCountLimit];
+        return false;
+    }
+
     // Empty?
     auto const sum = nucleotide_sum( sample );
     if( sum == 0 ) {
@@ -166,21 +181,6 @@ bool apply_sample_counts_filter_numerical(
         return false;
     }
 
-    // Check deletions.
-    if(
-        params.deletions_count_limit > 0
-        && sample.d_count > 0
-        && sample.d_count >= params.deletions_count_limit
-    ) {
-        // if( params.clear_filtered ) {
-        //     sample.clear();
-        // }
-
-        sample.status.set( SampleCountsFilterTag::kAboveDeletionsCountLimit );
-        ++stats[SampleCountsFilterTag::kAboveDeletionsCountLimit];
-        return false;
-    }
-
     // -------------------------------------------
     //     SNP vs Invariant
     // -------------------------------------------

diff --git a/lib/genesis/population/filter/sample_counts_filter_numerical.hpp b/lib/genesis/population/filter/sample_counts_filter_numerical.hpp
@@ -140,6 +140,17 @@ struct SampleCountsFilterNumericalParams
      */
     size_t max_count = 0;
 
+    /**
+     * @brief Maximum number of deletions at a position before being filtered out.
+     *
+     * If this is set to a value greater than 0, and the number of deletions at the position
+     * (determined by the SampleCounts::d_count) is equal to or greater than this value,
+     * the sample is filtered out by setting its status accordingly.
+     *
+     * @see SampleCountsFilterTag::kAboveDeletionsCountLimit
+     */
+    size_t deletions_count_limit = 0;
+
     /**
      * @brief Minimum coverage expected for a SampleCounts to be considered covered.
      *
@@ -162,17 +173,6 @@ struct SampleCountsFilterNumericalParams
      */
     size_t max_coverage = 0;
 
-    /**
-     * @brief Maximum number of deletions at a position before being filtered out.
-     *
-     * If this is set to a value greater than 0, and the number of deletions at the position
-     * (determined by the SampleCounts::d_count) is equal to or greater than this value,
-     * the sample is filtered out by setting its status accordingly.
-     *
-     * @see SampleCountsFilterTag::kAboveDeletionsCountLimit
-     */
-    size_t deletions_count_limit = 0;
-
     // -------------------------------------------
     //     SNP vs Invariant
     // -------------------------------------------