Merge branch 'master' into qt6_switch

imgag · Feb 20, 2025 · fe4d524 · fe4d524
2 parents c154634 + 1bf3f21
commit fe4d524
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Showing 4 changed files with 12 additions and 44 deletions.
diff --git a/bin/GSvar_filters.ini b/bin/GSvar_filters.ini
@@ -157,7 +157,7 @@ Trio	types=de-novo,recessive,LOH,comp-het,x-linked	build=hg38
 Allele frequency	max_af=1.0
 Allele frequency (sub-populations)	max_af=1.0
 Count NGSD	max_count=20	ignore_genotype=false
-Variant quality	qual=20	depth=0	mapq=40	strand_bias=-1	allele_balance=-1	min_occurences=0
+Variant quality	qual=20	depth=5	mapq=40	strand_bias=-1	allele_balance=-1	min_occurences=0
 Annotated pathogenic	action=KEEP	sources=HGMD,ClinVar	also_likely_pathogenic=true
 Allele frequency	max_af=3.0
 Classification NGSD	action=REMOVE	classes=1,2

diff --git a/doc/GSvar/changelog.md b/doc/GSvar/changelog.md
@@ -1,5 +1,9 @@
 # GSvar change log
 
+## 2025_01-41 (20.02.25)
+
+- trio: adapted mendelian error rate calculation to Dragen 4.3 output
+
 ## 2025_01-22 (06.02.25)
 
 - sequencing run tab: added settings dialog for NovaSeqX sample sheet creation

diff --git a/src/GSvar/ExpressionExonWidget.cpp b/src/GSvar/ExpressionExonWidget.cpp
@@ -65,7 +65,7 @@ void ExpressionExonWidget::loadExpressionFile()
 	try
 	{
 		QApplication::setOverrideCursor(Qt::BusyCursor);
-        QElapsedTimer timer;
+		QTime timer;
 		timer.start();
 
 		//load TSV file
@@ -142,7 +142,7 @@ void ExpressionExonWidget::initTable()
 	{
 		QApplication::setOverrideCursor(Qt::BusyCursor);
 		ui_->tw_expression_table->setEnabled(false);
-        QElapsedTimer timer;
+		QTime timer;
 		timer.start();
 
 		column_names_.clear();
@@ -196,10 +196,7 @@ void ExpressionExonWidget::applyFilters()
 
 		filter_result_.reset(true);
 
-        //debug:
-        //int filtered_lines = expression_data_.count();
-
-        QElapsedTimer timer;
+		QTime timer;
 		timer.start();
 
 
@@ -226,10 +223,6 @@ void ExpressionExonWidget::applyFilters()
 						filter_result_.flags()[row_idx] = variant_gene_set_.contains(expression_data_[row_idx].at(gene_idx).toUtf8().trimmed());
 					}
 				}
-
-				//debug:
-				//qDebug() << "\t removed: " << (filtered_lines - filter_result_.countPassing()) << Helper::elapsedTime(timer);
-                //filtered_lines = filter_result_.countPassing();
 			}
 
 			//filter by genes
@@ -276,10 +269,6 @@ void ExpressionExonWidget::applyFilters()
 						}
 					}
 				}
-
-				//debug:
-				//qDebug() << "\t removed: " << (filtered_lines - filter_result_.countPassing()) << Helper::elapsedTime(timer);
-                //filtered_lines = filter_result_.countPassing();
 			}
 		}
 
@@ -321,10 +310,6 @@ void ExpressionExonWidget::applyFilters()
 					QMessageBox::warning(this, "Invalid rpb value", "Couldn't convert given rpb value to number!\n" + e.message());
 				}
 			}
-
-			//debug:
-			//qDebug() << "\t removed: " << (filtered_lines - filter_result_.countPassing()) << Helper::elapsedTime(timer);
-            //filtered_lines = filter_result_.countPassing();
 		}
 
 		//filter by srpb value
@@ -363,10 +348,6 @@ void ExpressionExonWidget::applyFilters()
 					QMessageBox::warning(this, "Invalid srpb value", "Couldn't convert given srpb value to number!\n" + e.message());
 				}
 			}
-
-			//debug:
-			//qDebug() << "\t removed: " << (filtered_lines - filter_result_.countPassing()) << Helper::elapsedTime(timer);
-            //filtered_lines = filter_result_.countPassing();
 		}
 
 		//filter by biotype
@@ -399,11 +380,6 @@ void ExpressionExonWidget::applyFilters()
 			}
 		}
 
-
-		//debug:
-		///qDebug() << "\t removed (file based): " << (filtered_lines - filter_result_.countPassing()) << Helper::elapsedTime(timer);
-        //filtered_lines = filter_result_.countPassing();
-
 		//filter by statistical data
 
 		//filter by low expression srpb value
@@ -494,10 +470,6 @@ void ExpressionExonWidget::applyFilters()
 					QMessageBox::warning(this, "Invalid cohort mean value", "Couldn't convert given cohort mean value to number!\n" + e.message());
 				}
 			}
-
-			//debug:
-			//qDebug() << "\t removed: " << (filtered_lines - filter_result_.countPassing()) << Helper::elapsedTime(timer);
-            //filtered_lines = filter_result_.countPassing();
 		}
 
 		//filter by log2fc
@@ -536,10 +508,6 @@ void ExpressionExonWidget::applyFilters()
 					QMessageBox::warning(this, "Invalid log2fc value", "Couldn't convert given log2fc value to number!\n" + e.message());
 				}
 			}
-
-			//debug:
-			//qDebug() << "\t removed: " << (filtered_lines - filter_result_.countPassing()) << Helper::elapsedTime(timer);
-            //filtered_lines = filter_result_.countPassing();
 		}
 
 		//filter by zscore
@@ -578,10 +546,6 @@ void ExpressionExonWidget::applyFilters()
 					QMessageBox::warning(this, "Invalid zscore value", "Couldn't convert given zscore value to number!\n" + e.message());
 				}
 			}
-
-			//debug:
-			//qDebug() << "\t removed: " << (filtered_lines - filter_result_.countPassing()) << Helper::elapsedTime(timer);
-            //filtered_lines = filter_result_.countPassing();
 		}
 
 
@@ -706,7 +670,7 @@ void ExpressionExonWidget::updateTable()
 	{
 		//fill table widget with expression data
 		QApplication::setOverrideCursor(Qt::BusyCursor);
-        QElapsedTimer timer;
+		QTime timer;
 		timer.start();
 
 		//disable sorting

diff --git a/src/GSvar/MainWindow.ui b/src/GSvar/MainWindow.ui
@@ -326,10 +326,10 @@
                 <bool>false</bool>
                </property>
                <attribute name="horizontalHeaderVisible">
-                <bool>false</bool>
+                <bool>true</bool>
                </attribute>
                <attribute name="verticalHeaderVisible">
-                <bool>false</bool>
+                <bool>true</bool>
                </attribute>
                <attribute name="verticalHeaderCascadingSectionResizes">
                 <bool>false</bool>
@@ -369,7 +369,7 @@
      <x>0</x>
      <y>0</y>
      <width>1100</width>
-     <height>20</height>
+     <height>21</height>
     </rect>
    </property>
    <widget class="QMenu" name="menuFile">