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Qualimap: BamQC: add percentage on target #2020

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merged 9 commits into from
Sep 14, 2023
Merged

Qualimap: BamQC: add percentage on target #2020

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4d37b05
qualimap bamqc: add percentage on target
FerriolCalvet Aug 31, 2023
2c25211
Update multiqc/modules/qualimap/QM_BamQC.py
vladsavelyev Aug 31, 2023
2a68767
Update multiqc/modules/qualimap/QM_BamQC.py
vladsavelyev Aug 31, 2023
08cdc6e
rename the regions_mapped_reads metric
FerriolCalvet Sep 1, 2023
a34588b
Merge branch 'ewels:master' into master
FerriolCalvet Sep 1, 2023
87cc5f4
Merge branch 'master' into master
vladsavelyev Sep 1, 2023
9b68d22
Review tweaks
ewels Sep 14, 2023
ae435cd
Merge branch 'master' into master
ewels Sep 14, 2023
726fb06
Changelog
ewels Sep 14, 2023
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12 changes: 11 additions & 1 deletion multiqc/modules/qualimap/QM_BamQC.py
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Original file line number Diff line number Diff line change
Expand Up @@ -141,6 +141,8 @@ def parse_genome_results(self, f):
self.general_stats_data[s_name]["mean_coverage"] = d["mean_coverage"]
self.general_stats_data[s_name]["regions_size"] = d["regions_size"]
self.general_stats_data[s_name]["regions_mapped_reads"] = d["regions_mapped_reads"]
d["percentage_aligned_on_target"] = (d["regions_mapped_reads"] / d["mapped_reads"]) * 100
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self.general_stats_data[s_name]["percentage_aligned_on_target"] = d["percentage_aligned_on_target"]
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except KeyError:
pass

Expand Down Expand Up @@ -622,12 +624,20 @@ def general_stats_headers(self):
"hidden": True,
}
self.general_stats_headers["regions_mapped_reads"] = {
"title": "{} Aligned".format(config.read_count_prefix),
"title": "{} On target".format(config.read_count_prefix),
"description": "Number of mapped reads on target region ({})".format(config.read_count_desc),
"scale": "RdYlGn",
"shared_key": "read_count",
"hidden": True,
}
self.general_stats_headers["percentage_aligned_on_target"] = {
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"title": "% On target",
"description": "% mapped reads on target region",
"max": 100,
"min": 0,
"suffix": "%",
"scale": "YlGn",
}


def _calculate_bases_within_thresholds(bases_by_depth, total_size, depth_thresholds):
Expand Down