Samtools: Stats: fix "Percent Mapped" plot when samtools was run with…

… read filtering (#1972) * Update stats.py fix for #1971 * Update CHANGELOG.md * Update stats.py forgot an underspace... --------- Co-authored-by: Vlad Savelyev <vladislav.sav@gmail.com>
MultiQC · Aug 24, 2023 · 965fbc0 · 965fbc0
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -22,6 +22,8 @@
   - Fix a bug happening when both `region` and `global` coverage histograms for a sample are available (i.e. when mosdepth was run with `--by`, see [mosdepth docs](https://github.com/brentp/mosdepth#usage)). In this case, data was effectively merged. Instead, summarise it separately and add a separate report section for the region-based coverage data.
 - **RSeQC**
   - Fix "max() arg is an empty sequence" error ([#1985](https://github.com/ewels/MultiQC/issues/1985))
+- **Samtools**
+  - Stats: fix "Percent Mapped" plot when samtools was run with read filtering ([#1971](https://github.com/ewels/MultiQC/issues/1971))
 
 ## [MultiQC v1.15](https://github.com/ewels/MultiQC/releases/tag/v1.15) - 2023-08-04
 

diff --git a/multiqc/modules/samtools/stats.py b/multiqc/modules/samtools/stats.py
@@ -183,7 +183,7 @@ def alignment_section(self, samples_data):
         bedgraph_data = {}
         for sample_id, data in samples_data.items():
             expected_total = data["raw_total_sequences"]
-            read_sum = data["reads_mapped"] + data["reads_unmapped"]
+            read_sum = data["reads_mapped"] + data["reads_unmapped"] + data["filtered_sequences"]
             if read_sum == expected_total:
                 bedgraph_data[sample_id] = data
             else: