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Samtools: Stats: fix "Percent Mapped" plot when samtools was run with read filtering #1972

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merged 5 commits into from
Aug 24, 2023
Merged

Samtools: Stats: fix "Percent Mapped" plot when samtools was run with read filtering #1972

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b1a424c
Update stats.py
lindenb Aug 9, 2023
d51cead
Update CHANGELOG.md
lindenb Aug 9, 2023
18312ae
Update stats.py
lindenb Aug 9, 2023
eed088a
Merge branch 'master' into pl_samtools_stats
vladsavelyev Aug 23, 2023
f339a97
Merge branch 'master' into pl_samtools_stats
vladsavelyev Aug 24, 2023
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -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

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2 changes: 1 addition & 1 deletion multiqc/modules/samtools/stats.py
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Expand Up @@ -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:
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