Qualimap: BamQC: add percentage on target (#2020)

* qualimap bamqc: add percentage on target * Update multiqc/modules/qualimap/QM_BamQC.py * Update multiqc/modules/qualimap/QM_BamQC.py * rename the regions_mapped_reads metric * Review tweaks * Changelog --------- Co-authored-by: Vlad Savelyev <vladislav.sav@gmail.com> Co-authored-by: Phil Ewels <phil.ewels@seqera.io>
MultiQC · Sep 14, 2023 · d601907 · d601907
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -65,6 +65,8 @@ This idea goes way back to [issue #290](https://github.com/ewels/MultiQC/issues/
   - fix `UnicodeDecodeError` when parsing `fastqc_data.txt`: try latin-1 or fail gracefully ([#2024](https://github.com/ewels/MultiQC/issues/2024))
 - **Kaiju**:
   - Fix `UnboundLocalError` on outputs when Kanju was run with the `-e` flag ([#2023](https://github.com/ewels/MultiQC/pull/2023))
+- **Qualimap**
+  - BamQC: Include `% On Target` in General Stats table ([#2019](https://github.com/ewels/MultiQC/issues/2019))
 
 ## [MultiQC v1.15](https://github.com/ewels/MultiQC/releases/tag/v1.15) - 2023-08-04
 

diff --git a/multiqc/modules/qualimap/QM_BamQC.py b/multiqc/modules/qualimap/QM_BamQC.py
@@ -135,12 +135,17 @@ def parse_genome_results(self, f):
     try:
         self.general_stats_data[s_name]["total_reads"] = d["total_reads"]
         self.general_stats_data[s_name]["mapped_reads"] = d["mapped_reads"]
-        d["percentage_aligned"] = (d["mapped_reads"] / d["total_reads"]) * 100
-        self.general_stats_data[s_name]["percentage_aligned"] = d["percentage_aligned"]
-        self.general_stats_data[s_name]["general_error_rate"] = d["general_error_rate"] * 100
+        self.general_stats_data[s_name]["general_error_rate"] = d["general_error_rate"] * 100.0
         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"]
+        try:
+            d["percentage_aligned"] = (d["mapped_reads"] / d["total_reads"]) * 100.0
+            self.general_stats_data[s_name]["percentage_aligned"] = d["percentage_aligned"]
+            d["percentage_aligned_on_target"] = (d["regions_mapped_reads"] / d["mapped_reads"]) * 100.0
+            self.general_stats_data[s_name]["percentage_aligned_on_target"] = d["percentage_aligned_on_target"]
+        except ZeroDivisionError:
+            pass
     except KeyError:
         pass
 
@@ -582,25 +587,25 @@ def general_stats_headers(self):
         "suffix": "X",
         "scale": "BuPu",
     }
-    self.general_stats_headers["percentage_aligned"] = {
-        "title": "% Aligned",
-        "description": "% mapped reads",
+    self.general_stats_headers["percentage_aligned_on_target"] = {
+        "title": "% On target",
+        "description": "% mapped reads on target region",
         "max": 100,
         "min": 0,
         "suffix": "%",
         "scale": "YlGn",
     }
-    self.general_stats_headers["mapped_reads"] = {
-        "title": "{} Aligned".format(config.read_count_prefix),
-        "description": "Number of mapped reads ({})".format(config.read_count_desc),
-        "scale": "RdYlGn",
-        "shared_key": "read_count",
+    self.general_stats_headers["regions_size"] = {
+        "title": "{} Region size".format(config.read_count_prefix),
+        "description": "Size of target region",
+        "suffix": " bp",
+        "scale": "PuBuGn",
         "hidden": True,
     }
-    self.general_stats_headers["total_reads"] = {
-        "title": "{} Total reads".format(config.read_count_prefix),
-        "description": "Number of reads ({})".format(config.read_count_desc),
-        "scale": "Blues",
+    self.general_stats_headers["regions_mapped_reads"] = {
+        "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,
     }
@@ -614,20 +619,28 @@ def general_stats_headers(self):
         "format": "{0:.2f}",
         "hidden": True,
     }
-    self.general_stats_headers["regions_size"] = {
-        "title": "{} Region size".format(config.read_count_prefix),
-        "description": "Size of target region",
-        "suffix": " bp",
-        "scale": "PuBuGn",
-        "hidden": True,
+    self.general_stats_headers["percentage_aligned"] = {
+        "title": "% Aligned",
+        "description": "% mapped reads",
+        "max": 100,
+        "min": 0,
+        "suffix": "%",
+        "scale": "YlGn",
     }
-    self.general_stats_headers["regions_mapped_reads"] = {
+    self.general_stats_headers["mapped_reads"] = {
         "title": "{} Aligned".format(config.read_count_prefix),
-        "description": "Number of mapped reads on target region ({})".format(config.read_count_desc),
+        "description": "Number of mapped reads ({})".format(config.read_count_desc),
         "scale": "RdYlGn",
         "shared_key": "read_count",
         "hidden": True,
     }
+    self.general_stats_headers["total_reads"] = {
+        "title": "{} Total reads".format(config.read_count_prefix),
+        "description": "Number of reads ({})".format(config.read_count_desc),
+        "scale": "Blues",
+        "shared_key": "read_count",
+        "hidden": True,
+    }
 
 
 def _calculate_bases_within_thresholds(bases_by_depth, total_size, depth_thresholds):