Fixed FastqCheckUMI

imgag · Feb 21, 2025 · 9098079 · 9098079
1 parent b98be03
commit 9098079
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Showing 4 changed files with 7 additions and 9 deletions.
diff --git a/src/FastqCheckUMI/main.cpp b/src/FastqCheckUMI/main.cpp
@@ -84,11 +84,11 @@ class ConcreteTool
 
 	bool isValidSequence(QByteArray barcode, int& length)
 	{
-        QRegularExpression seq("[ATCGN]*");
-		barcode = barcode.trimmed().toUpper();
-		length = barcode.length();
+        QRegularExpression seq(QRegularExpression::anchoredPattern("[ATCGN]*"));
+        barcode = barcode.trimmed().toUpper();
+        length = barcode.length();
         if(seq.match(barcode).hasMatch()) return true;
-		return false;
+        return false;
 	}
 };
 

diff --git a/src/GSvar/RepeatExpansionWidget.cpp b/src/GSvar/RepeatExpansionWidget.cpp
@@ -199,7 +199,6 @@ void RepeatExpansionWidget::showContextMenu(QPoint pos)
 	}
 	else if (action==a_omim)
     {
-        Log::info("RE!!!!!");
         QRegularExpression mim_exp("([0-9]{6})");
         QString text = getCell(row, "OMIM disease IDs");
 
@@ -208,7 +207,6 @@ void RepeatExpansionWidget::showContextMenu(QPoint pos)
         {
             QRegularExpressionMatch match = it.next();
             QDesktopServices::openUrl(QUrl("https://www.omim.org/entry/" + match.captured(1)));
-            Log::info(match.captured(1));
         }
 	}
 	else if (action==a_stripy)

diff --git a/src/GSvar/VariantOpenDialog.cpp b/src/GSvar/VariantOpenDialog.cpp
@@ -76,7 +76,7 @@ void VariantOpenDialog::parseVariant(QString format, QString text, const FastaFi
 			//1	55056267	.	CGGGCTTCTTGTGGCACGT	C	.	.
 			text = text.replace("\t", " ");
 
-			QStringList parts = text.split(QRegExp("\\s+"));
+            QStringList parts = text.split(QRegularExpression("\\s+"));
 			if (parts.count()<5) THROW(ArgumentException, "Invalid VCF variant '" + text + "': less than 5 parts found!");
 
 			//parse parts

diff --git a/src/GSvarServer-TEST/Controller-Test.h b/src/GSvarServer-TEST/Controller-Test.h
@@ -223,7 +223,7 @@ private slots:
 		IS_TRUE(response.getStatusLine().split('\n').first().contains("404"));
 		IS_TRUE(response.getPayload().isNull());
 
-		QRegExp rx("(length:)(?:\\s*)(\\d+)");
+        QRegularExpression rx("(length:)(?:\\s*)(\\d+)");
 		rx.setCaseSensitivity(Qt::CaseInsensitive);
 		int pos = rx.indexIn(response.getHeaders());
 
@@ -265,7 +265,7 @@ private slots:
 		IS_TRUE(response.getStatusLine().split('\n').first().contains("200"));
 		IS_TRUE(response.getPayload().isNull());
 
-		QRegExp rx("(length:)(?:\\s*)(\\d+)");
+        QRegularExpression rx("(length:)(?:\\s*)(\\d+)");
 		rx.setCaseSensitivity(Qt::CaseInsensitive);
 		int pos = rx.indexIn(response.getHeaders());