GSvar: replaced context menu link to gnomAD 2.1 by link to gnomAD 4.0

imgag · Nov 7, 2023 · a8a3461 · a8a3461
1 parent 57284e7
commit a8a3461
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Showing 4 changed files with 9 additions and 19 deletions.
diff --git a/src/GSvar/GSvarHelper.cpp b/src/GSvar/GSvarHelper.cpp
@@ -288,7 +288,7 @@ Variant GSvarHelper::liftOverVariant(const Variant& v, bool hg19_to_hg38)
 	return v2;
 }
 
-QString GSvarHelper::gnomADLink(const Variant& v, GenomeBuild build)
+QString GSvarHelper::gnomADLink(const Variant& v, bool open_in_v4)
 {
 	QString url = "https://gnomad.broadinstitute.org/variant/" + v.chr().strNormalized(false) + "-";
 
@@ -298,12 +298,7 @@ QString GSvarHelper::gnomADLink(const Variant& v, GenomeBuild build)
 	}
 	else
 	{
-		QString genome_key = "reference_genome";
-		if (GSvarHelper::build()==GenomeBuild::HG38 && build==GenomeBuild::HG19) //GSvar for HG38, but link for HG19 > use special genome key
-		{
-			genome_key = "reference_genome_hg19";
-		}
-		FastaFileIndex idx(Settings::string(genome_key));
+		FastaFileIndex idx(Settings::string("reference_genome"));
 
 		if (v.obs()=="-") //deletion
 		{
@@ -319,10 +314,7 @@ QString GSvarHelper::gnomADLink(const Variant& v, GenomeBuild build)
 		}
 	}
 
-	//genome build
-	if (build==GenomeBuild::HG38) url += "?dataset=gnomad_r3";
-
-	return url;
+	return url + "?dataset=" + (open_in_v4 ? "gnomad_r4" : "gnomad_r3");
 }
 
 QString GSvarHelper::clinVarSearchLink(const Variant& v, GenomeBuild build)

diff --git a/src/GSvar/GSvarHelper.h b/src/GSvar/GSvarHelper.h
@@ -42,7 +42,7 @@ class GSvarHelper
 	static Variant liftOverVariant(const Variant& v, bool hg19_to_hg38);
 
 	//Returns gnomAD link for a variant
-	static QString gnomADLink(const Variant& v, GenomeBuild build);
+	static QString gnomADLink(const Variant& v, bool open_in_v4);
 	//Returns ClinVar search link for a variant
 	static QString clinVarSearchLink(const Variant& v, GenomeBuild build);
 

diff --git a/src/GSvar/VariantDetailsDockWidget.cpp b/src/GSvar/VariantDetailsDockWidget.cpp
@@ -882,7 +882,7 @@ QString VariantDetailsDockWidget::nobr()
 void VariantDetailsDockWidget::gnomadClicked(QString variant_string)
 {
 	Variant v = Variant::fromString(variant_string);
-	QString link = GSvarHelper::gnomADLink(v, GSvarHelper::build());
+	QString link = GSvarHelper::gnomADLink(v, false);
 	QDesktopServices::openUrl(QUrl(link));
 }
 
@@ -1031,16 +1031,14 @@ void VariantDetailsDockWidget::gnomadContextMenu(QPoint pos)
 	if (GSvarHelper::build()!=GenomeBuild::HG38) return;
 
 	QMenu menu;
-	QAction* a_v2 = menu.addAction("Lift-over to gnomAD 2.1");
+	QAction* a_v4 = menu.addAction("Open in gnomAD 4.0");
 
 	QAction* action = menu.exec(ui->gnomad->mapToGlobal(pos));
-	if (action==nullptr) return;
 
-	if (action==a_v2)
+	if (action==a_v4)
 	{
 		Variant v = Variant::fromString(variant_str);
-		Variant v2 = GSvarHelper::liftOverVariant(v, false);
-		QString link = GSvarHelper::gnomADLink(v2, GenomeBuild::HG19);
+		QString link = GSvarHelper::gnomADLink(v, true);
 		QDesktopServices::openUrl(QUrl(link));
 	}
 }

diff --git a/src/GSvar/VariantWidget.cpp b/src/GSvar/VariantWidget.cpp
@@ -394,7 +394,7 @@ void VariantWidget::gnomadClicked(QString var_id)
 {
 	NGSD db;
 	Variant v = db.variant(var_id);
-	QString link = GSvarHelper::gnomADLink(v, GSvarHelper::build());
+	QString link = GSvarHelper::gnomADLink(v, false);
 	QDesktopServices::openUrl(QUrl(link));
 }