Merge remote-tracking branch 'remotes/origin/master' into lrGS_Methyl…

…artist

README.md

@@ -124,7 +124,7 @@ The default output format of the quality control tools is [qcML](https://pubmed.
 
 ### VCF tools (small variants)
 
-* [VcfAdd](doc/tools/VcfAdd.md) - Appends variants from a VCF file to another VCF file.
+* [VcfAdd](doc/tools/VcfAdd.md) - Merges several VCF files into one VCF by appending one to the other.
 * [VcfAnnotateConsequence](doc/tools/VcfAnnotateConsequence.md) - Adds transcript-specific consequence predictions to a VCF file (similar to Ensembl VEP).
 * [VcfAnnotateFromBed](doc/tools/VcfAnnotateFromBed.md) - Annotates the INFO column of a VCF with data from a BED file.
 * [VcfAnnotateFromBigWig](doc/tools/VcfAnnotateFromBigWig.md) - Annotates the INFO column of a VCF with data from a BED file.
@@ -137,7 +137,6 @@ The default output format of the quality control tools is [qcML](https://pubmed.
 * [VcfExtractSamples](doc/tools/VcfExtractSamples.md) - Extract one or several samples from a VCF file. Can also be used to re-order sample columns.
 * [VcfFilter](doc/tools/VcfFilter.md) - Filters a VCF based on the given criteria.
 * [VcfLeftNormalize](doc/tools/VcfLeftNormalize.md) - Normalizes all variants and shifts indels to the left in a VCF file.
-* [VcfMerge](doc/tools/VcfMerge.md) - Merges several VCF files into one VCF.
 * [VcfSort](doc/tools/VcfSort.md) - Sorts variant lists according to chromosomal position.
 * [VcfSplit](doc/tools/VcfSplit.md) - Splits a VCF into several chunks.
 * [VcfStrip](doc/tools/VcfStrip.md) - Removes unwanted information from a VCF file

bin/GSvar_filters.ini

@@ -8,7 +8,7 @@ Annotated pathogenic	action=KEEP	sources=HGMD,ClinVar	also_likely_pathogenic=tru
 Allele frequency	max_af=3.0
 Filter columns	action=REMOVE	entries=low_mappability,mosaic
 Classification NGSD	action=REMOVE	classes=1,2
-Classification NGSD	action=KEEP	classes=3,4,5,M,R*
+Classification NGSD	action=KEEP	classes=3,4,5,M,R
 
 #rare variants (non-coding, predicted splicing change)
 Allele frequency	max_af=1

doc/GSvar/changelog.md

@@ -1,5 +1,12 @@
 # GSvar change log
 
+## 2024_11-86 (20.01.25)
+
+- general: renamed class 'R*' to 'R' (changed in HerediCare and HerediVar)
+- general: improved opening QC files from GSvarServer
+- variant details: updated allOfUs variant URL
+- NGSD: Added device type 'Revio'
+
 ## 2024_11-50 (07.01.25)
 
 - general: added sample counts dialog (NGSD > Sample counts)

doc/tools/TsvSlice.md

@@ -1,5 +1,5 @@
 ### TsvSlice tool help
-	TsvSlice (2024_08-113-g94a3b440)
+	TsvSlice (2024_11-86-g94c45dea)
 
 	Extracts/reorders columns of a TSV file.
 
@@ -13,6 +13,8 @@
 	                    Default value: ''
 	  -numeric          If set, column names are interpreted as 1-based column numbers.
 	                    Default value: 'false'
+	  -rm               If set, the columns given in 'cols' are removed instead of extracted.
+	                    Default value: 'false'
 
 	Special parameters:
 	  --help            Shows this help and exits.
@@ -22,6 +24,6 @@
 	  --settings [file] Settings override file (no other settings files are used).
 
 ### TsvSlice changelog
-	TsvSlice 2024_08-113-g94a3b440
+	TsvSlice 2024_11-86-g94c45dea
 
 [back to ngs-bits](https://github.com/imgag/ngs-bits)

doc/tools/VariantFilterAnnotations.md

@@ -1,5 +1,5 @@
 ### VariantFilterAnnotations tool help
-	VariantFilterAnnotations (2024_11-59-ge0a7288e)
+	VariantFilterAnnotations (2024_11-86-g94c45dea)
 
 	Filter a variant list in GSvar format based on variant annotations.
 
@@ -27,7 +27,7 @@
 	                                     action - Action to perform [default=KEEP] [valid=KEEP,FILTER]
 	Classification NGSD                Filter for variant classification from NGSD.
 	                                   Parameters:
-	                                     classes - NGSD classes [default=4,5] [valid=1,2,3,4,5,M,R*] [non-empty]
+	                                     classes - NGSD classes [default=4,5] [valid=1,2,3,4,5,M,R] [non-empty]
 	                                     action - Action to perform [default=KEEP] [valid=KEEP,FILTER,REMOVE]
 	Column match                       Filter that matches the content of a column against a perl-compatible regular expression.
 	                                   For details about regular expressions, see http://perldoc.perl.org/perlretut.html
@@ -183,7 +183,7 @@
 	  --settings [file] Settings override file (no other settings files are used).
 
 ### VariantFilterAnnotations changelog
-	VariantFilterAnnotations 2024_11-59-ge0a7288e
+	VariantFilterAnnotations 2024_11-86-g94c45dea
 
 	2018-07-30 Replaced command-line parameters by INI file and added many new filters.
 	2017-06-14 Refactoring of genotype-based filters: now also supports multi-sample filtering of affected and control samples.

doc/tools/VcfAdd.md

@@ -1,23 +1,22 @@
 ### VcfAdd tool help
-	VcfAdd (2024_08-110-g317f43b9)
+	VcfAdd (2024_11-86-g94c45dea)
 
-	Appends variants from a VCF file to another VCF file.
+	Merges several VCF files into one VCF by appending one to the other.
 
-	VCF header lines are taken from 'in' only.
+	Variant lines from all other input files are appended to the first input file.
+	VCF header lines are taken from the first input file only.
 
 	Mandatory parameters:
-	  -in2 <file>           Input VCF file that is added to 'in'.
+	  -in <filelist>        Input VCF ro VCG.GZ files to merge.
 
 	Optional parameters:
-	  -in <file>            Input VCF file to add 'in2' to.
+	  -out <file>           Output VCF file with all variants.
 	                        Default value: ''
-	  -out <file>           Output VCF file with variants from 'in' and 'in2'.
-	                        Default value: ''
-	  -filter <string>      Tag variants from 'in2' with this filter entry.
+	  -filter <string>      Tag variants from all but the first input file with this filter entry.
 	                        Default value: ''
 	  -filter_desc <string> Description used in the filter header - use underscore instead of spaces.
 	                        Default value: ''
-	  -skip_duplicates      Skip variants from  'in2' which are also contained in 'in'.
+	  -skip_duplicates      Skip variants if they occur more than once.
 	                        Default value: 'false'
 
 	Special parameters:
@@ -28,7 +27,8 @@
 	  --settings [file]     Settings override file (no other settings files are used).
 
 ### VcfAdd changelog
-	VcfAdd 2024_08-110-g317f43b9
+	VcfAdd 2024_11-86-g94c45dea
 
+	2025-01-17 Added support for gzipped VCFs and removing duplicates if there is only one input file.
 	2022-12-08 Initial implementation.
 [back to ngs-bits](https://github.com/imgag/ngs-bits)

src/GSvar/ClinvarUploadDialog.cpp

@@ -3048,7 +3048,7 @@ QString ClinvarUploadDialog::convertClassification(QString classification, bool
 		}
 		if (classification=="Established risk allele")
 		{
-			return "R*";
+			return "R";
 		}
 	}
 	else
@@ -3073,7 +3073,7 @@ QString ClinvarUploadDialog::convertClassification(QString classification, bool
 		{
 			return "Benign";
 		}
-		if (classification=="R*")
+		if (classification=="R")
 		{
 			return "Established risk allele";
 		}

src/GSvar/MainWindow.cpp

@@ -218,6 +218,7 @@ MainWindow::MainWindow(QWidget *parent)
 	ui_.splitter_2->setStretchFactor(0, 10);
 	ui_.splitter_2->setStretchFactor(1, 1);
 	connect(ui_.tabs, SIGNAL(tabCloseRequested(int)), this, SLOT(closeTab(int)));
+	connect(ui_.tabs, SIGNAL(customContextMenuRequested(QPoint)), this, SLOT(tabContextMenu(QPoint)));
 
 	// add rna menu
 	rna_menu_btn_ = new QToolButton();
@@ -2242,7 +2243,7 @@ void MainWindow::openProcessedSampleFromNGSD(QString processed_sample_name, bool
 			analyses << GlobalServiceProvider::database().secondaryAnalyses(processed_sample_name + "-" + normal_sample, "somatic");
 		}
 		//check for germline trio/multi analyses
-		else if (search_multi)
+		if (search_multi)
 		{
 			analyses << GlobalServiceProvider::database().secondaryAnalyses(processed_sample_name, "trio");
 			analyses << GlobalServiceProvider::database().secondaryAnalyses(processed_sample_name, "multi sample");
@@ -2387,10 +2388,7 @@ void MainWindow::openProcessedSampleTab(QString ps_name)
 		connect(widget, SIGNAL(clearMainTableSomReport(QString)), this, SLOT(clearSomaticReportSettings(QString)));
 		connect(widget, SIGNAL(addModelessDialog(QSharedPointer<QDialog>, bool)), this, SLOT(addModelessDialog(QSharedPointer<QDialog>, bool)));
 		int index = openTab(QIcon(":/Icons/NGSD_sample.png"), ps_name, type, widget);
-		if (Settings::boolean("debug_mode_enabled"))
-		{
-			ui_.tabs->setTabToolTip(index, "NGSD ID: " + ps_id);
-		}
+		ui_.tabs->tabBar()->setTabData(index, ps_id);
 	}
 	catch (Exception& e)
 	{
@@ -2417,10 +2415,7 @@ void MainWindow::openRunTab(QString run_name)
 	SequencingRunWidget* widget = new SequencingRunWidget(this, QStringList() << run_id);
 	connect(widget, SIGNAL(addModelessDialog(QSharedPointer<QDialog>, bool)), this, SLOT(addModelessDialog(QSharedPointer<QDialog>, bool)));
 	int index = openTab(QIcon(":/Icons/NGSD_run.png"), run_name, type, widget);
-	if (Settings::boolean("debug_mode_enabled"))
-	{
-		ui_.tabs->setTabToolTip(index, "NGSD ID: " + run_id);
-	}
+	ui_.tabs->tabBar()->setTabData(index, run_id);
 }
 
 void MainWindow::openRunBatchTab(const QStringList& run_names)
@@ -2466,10 +2461,7 @@ void MainWindow::openGeneTab(QString symbol)
 
 	GeneWidget* widget = new GeneWidget(this, symbol.toUtf8());
 	int index = openTab(QIcon(":/Icons/NGSD_gene.png"), symbol, type, widget);
-	if (Settings::boolean("debug_mode_enabled"))
-	{
-		ui_.tabs->setTabToolTip(index, "NGSD ID: " + QString::number(NGSD().geneId(symbol.toUtf8())));
-	}
+	ui_.tabs->tabBar()->setTabData(index, QString::number(NGSD().geneId(symbol.toUtf8())));
 }
 
 void MainWindow::openVariantTab(Variant variant)
@@ -2487,12 +2479,7 @@ void MainWindow::openVariantTab(Variant variant)
 		//open tab
 		VariantWidget* widget = new VariantWidget(variant, this);
 		int index = openTab(QIcon(":/Icons/NGSD_variant.png"), name, type, widget);
-
-		//add database id
-		if (Settings::boolean("debug_mode_enabled"))
-		{
-			ui_.tabs->setTabToolTip(index, "NGSD ID: " + v_id);
-		}
+		ui_.tabs->tabBar()->setTabData(index, v_id);
 	}
 	catch(Exception& e)
 	{
@@ -2516,10 +2503,7 @@ void MainWindow::openProcessingSystemTab(QString system_name)
 
 	ProcessingSystemWidget* widget = new ProcessingSystemWidget(this, sys_id);
 	int index = openTab(QIcon(":/Icons/NGSD_processing_system.png"), name, type, widget);
-	if (Settings::boolean("debug_mode_enabled"))
-	{
-		ui_.tabs->setTabToolTip(index, "NGSD ID: " + QString::number(sys_id));
-	}
+	ui_.tabs->tabBar()->setTabData(index, QString::number(sys_id));
 }
 
 void MainWindow::openProjectTab(QString name)
@@ -2529,10 +2513,7 @@ void MainWindow::openProjectTab(QString name)
 
 	ProjectWidget* widget = new ProjectWidget(this, name);
 	int index = openTab(QIcon(":/Icons/NGSD_project.png"), name, type, widget);
-	if (Settings::boolean("debug_mode_enabled"))
-	{
-		ui_.tabs->setTabToolTip(index, "NGSD ID: " + NGSD().getValue("SELECT id FROM project WHERE name=:0", true, name).toString());
-	}
+	ui_.tabs->tabBar()->setTabData(index, NGSD().getValue("SELECT id FROM project WHERE name=:0", true, name).toString());
 }
 
 int MainWindow::openTab(QIcon icon, QString name, TabType type, QWidget* widget)
@@ -2600,6 +2581,37 @@ bool MainWindow::focusTab(TabType type, QString name)
 	return false;
 }
 
+void MainWindow::tabContextMenu(QPoint pos)
+{
+	int index = ui_.tabs->tabBar()->tabAt(pos);
+	QString data = ui_.tabs->tabBar()->tabData(index).toString();
+
+	// create menu
+	QMenu menu(ui_.tabs);
+	QAction* a_copy_text = menu.addAction("Copy text");
+	a_copy_text->setEnabled(index!=-1);
+	QAction* a_copy_id = menu.addAction("Copy NGSD id");
+	a_copy_id->setEnabled(index!=-1 && !data.isEmpty());
+
+	// execute menu
+	QAction* action = menu.exec(ui_.tabs->mapToGlobal(pos));
+	if (action == nullptr) return;
+
+	// execute
+	if (action==a_copy_text)
+	{
+		QApplication::clipboard()->setText(ui_.tabs->tabText(index));
+	}
+	else if (action==a_copy_id)
+	{
+		QApplication::clipboard()->setText(data);
+	}
+	else
+	{
+		THROW(ProgrammingException, "Invalid menu action in context menu selected!")
+	}
+}
+
 void MainWindow::on_actionChangeLog_triggered()
 {
 	QDesktopServices::openUrl(QUrl("https://github.com/imgag/ngs-bits/tree/master/doc/GSvar/changelog.md"));

src/GSvar/MainWindow.h

@@ -440,6 +440,8 @@ public slots:
 	void closeTab(int index);
 	///Focus tab based on type and name. Returns if a tab was found and focused.
 	bool focusTab(TabType type, QString name);
+	///Show context menu of tab
+	void tabContextMenu(QPoint pos);
 
 	///Edits the variant configuration for the variant with the given index
 	void editVariantReportConfiguration(int index);

src/GSvar/MainWindow.ui

@@ -42,6 +42,9 @@
     </property>
     <item>
      <widget class="QTabWidget" name="tabs">
+      <property name="contextMenuPolicy">
+       <enum>Qt::CustomContextMenu</enum>
+      </property>
       <property name="currentIndex">
        <number>0</number>
       </property>