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

…artist

src/GSvar/ProcessingSystemWidget.cpp

@@ -50,12 +50,17 @@ void ProcessingSystemWidget::updateGUI()
 	//###target region infos###
 	try
 	{
-		BedFile roi = GlobalServiceProvider::database().processingSystemRegions(sys_id_, false);
+        BedFile roi = GlobalServiceProvider::database().processingSystemRegions(sys_id_, true);
 		if (!roi.isEmpty())
 		{
 			ui_.roi_bases->setText(QString::number(roi.baseCount(), 'f', 0));
 			ui_.roi_regions->setText(QString::number(roi.count(), 'f', 0));
 		}
+        else
+        {
+            ui_.roi_bases->setText("n/a");
+            ui_.roi_regions->setText("n/a");
+        }
 	}
 	catch (Exception& e)
 	{

src/cppNGSD-TEST/NGSD_Test.h

@@ -2897,7 +2897,7 @@ private slots:
 
 		somatic_report_settings.sbs_signature = TESTDATA("data_in/somatic/Somatic_DNA123456_01-NA12878_03/snv_signatures/De_Novo_map_to_COSMIC_SBS96.csv");
 		somatic_report_settings.dbs_signature = TESTDATA("data_in/somatic/Somatic_DNA123456_01-NA12878_03/snv_signatures/De_Novo_map_to_COSMIC_DBS78.csv");
-		somatic_report_settings.id_signature = TESTDATA("data_in/somatic/Somatic_DNA123456_01-NA12878_03/snv_signatures/De_Novo_map_to_COSMIC_ID83.csv");
+		somatic_report_settings.id_signature = TESTDATA("data_in/somatic/Somatic_DNA123456_01-NA12878_03/snv_signatures/De_Novo_map_to_COSMIC_ID83.tsv");
 		somatic_report_settings.cnv_signature = TESTDATA("data_in/somatic/Somatic_DNA123456_01-NA12878_03/cnv_signatures/De_Novo_map_to_COSMIC_CNV48.csv");
 
 		S_EQUAL(db.processedSampleId("DNA123456_01"), "4004");

src/cppNGSD-TEST/data_in/somatic/Somatic_DNA123456_01-NA12878_03/snv_signatures/De_Novo_map_to_COSMIC_ID83.tsv

@@ -0,0 +1,10 @@
+##L1 Error %: 64.56
+##L2 Error %: 24.87
+##KL Divergence: 0.947
+##Cosine Similarity: 0.97
+##Correlation: 0.97
+#type	signature	value
+De novo extracted	Signature 83-A	
+Global NMF Signatures	Signature ID1	15.04
+Global NMF Signatures	Signature ID2	47.28
+Global NMF Signatures	Signature ID12	37.68

src/cppNGSD-TEST/data_out/somatic_report_tumor_normal_2.rtf

@@ -4808,7 +4808,7 @@ Aetiologie
 \ql
 {
 \fs18
-F\u252;r die Mutationssignaturen des Typs SBS92 konnten keine COSMIC Signaturen identifieziert werden.
+F\u252;r die Mutationssignaturen des Typs SBS92 konnten keine COSMIC Signaturen identifiziert werden.
 }\cell}
 \row
 \trowd\trgraph180\trpaddb28\trpaddl28\trpaddr28\trpaddt28\clbrdrt\brdrw1\brdrhair\brdrcf4\clbrdrb\brdrw1\brdrhair\brdrcf4\clbrdrl\brdrw1\brdrhair\brdrcf4\clbrdrr\brdrw1\brdrhair\brdrcf4\cellx1500\clbrdrt\brdrw1\brdrhair\brdrcf4\clbrdrb\brdrw1\brdrhair\brdrcf4\clbrdrl\brdrw1\brdrhair\brdrcf4\clbrdrr\brdrw1\brdrhair\brdrcf4\cellx3000\clbrdrt\brdrw1\brdrhair\brdrcf4\clbrdrb\brdrw1\brdrhair\brdrcf4\clbrdrl\brdrw1\brdrhair\brdrcf4\clbrdrr\brdrw1\brdrhair\brdrcf4\cellx4500\clbrdrt\brdrw1\brdrhair\brdrcf4\clbrdrb\brdrw1\brdrhair\brdrcf4\clbrdrl\brdrw1\brdrhair\brdrcf4\clbrdrr\brdrw1\brdrhair\brdrcf4\cellx6500\clbrdrt\brdrw1\brdrhair\brdrcf4\clbrdrb\brdrw1\brdrhair\brdrcf4\clbrdrl\brdrw1\brdrhair\brdrcf4\clbrdrr\brdrw1\brdrhair\brdrcf4\cellx9922
@@ -4996,7 +4996,7 @@ Unknown
 \ql
 {
 \fs18
-F\u252;r die Mutationssignaturen des Typs DBS78 konnten keine COSMIC Signaturen identifieziert werden.
+F\u252;r die Mutationssignaturen des Typs DBS78 konnten keine COSMIC Signaturen identifiziert werden.
 }\cell}
 \row
 \trowd\trgraph180\trpaddb28\trpaddl28\trpaddr28\trpaddt28\clbrdrt\brdrw1\brdrhair\brdrcf4\clbrdrb\brdrw1\brdrhair\brdrcf4\clbrdrl\brdrw1\brdrhair\brdrcf4\clbrdrr\brdrw1\brdrhair\brdrcf4\cellx9922
@@ -5010,7 +5010,7 @@ F\u252;r die Mutationssignaturen des Typs DBS78 konnten keine COSMIC Signaturen
 \ql
 {
 \fs18
-F\u252;r die Mutationssignaturen des Typs CNV48 konnten keine COSMIC Signaturen identifieziert werden.
+F\u252;r die Mutationssignaturen des Typs CNV48 konnten keine COSMIC Signaturen identifiziert werden.
 }\cell}
 \row
 \trowd\trgraph180\trpaddb28\trpaddl28\trpaddr28\trpaddt28\cellx9922

src/cppNGSD/SomaticReportHelper.cpp

@@ -1556,55 +1556,90 @@ void SomaticReportHelper::signatureTableHelper(RtfTable &table, QString file, co
 {
 	VersatileFile stream(file);
 
-	if (file != "" && stream.exists() && stream.open(QIODevice::ReadOnly))
+	try
 	{
+		//file not present or cannot be opened
+		if (file=="" || !stream.exists() || !stream.open(QIODevice::ReadOnly)) THROW(Exception, "could not open file "+file);
+
+		//init
 		QList<int> cell_widths = {1500, 1500, 1500, 2000, 3422};
+		QByteArray cos_similarity;
+		QByteArray correlation;
+		QList<KeyValuePair> signatures;
 
-		QByteArray content = stream.readAll();
-		QByteArrayList lines = content.split('\n');
-		if (lines.count() < 2) return;
+		//parse content
+		QByteArrayList lines = stream.readAll().split('\n');
+		if (lines[0].startsWith("##")) //TSV format
+		{
+			foreach(QByteArray line, lines)
+			{
+				line = line.trimmed();
+				if (line.isEmpty()) continue;
 
-//		QByteArray header = lines[0];
-		QByteArray values = lines[1];
+				//header
+				if (line.startsWith("##Cosine Similarity:")) cos_similarity = line.mid(21).trimmed();
+				if (line.startsWith("##Correlation:")) correlation = line.mid(15).trimmed();
+				if (line.startsWith("#")) continue;
 
-		QByteArrayList parts = values.split(',');
+				//content
+				QByteArrayList parts = line.split('\t');
+				if (parts.count()!=3) continue;
 
-		QByteArray cos_similarity = parts[5];
-		QByteArray correlation = parts[6];
+				QByteArray sig_name = parts[1].replace("Signature ", "");
+				QByteArray sig_perc = parts[2];
+				signatures.append(KeyValuePair(sig_name, sig_perc));
 
-		//if there is only a single resulting signature it has no percentage after it.
-		if (parts[0].trimmed() == parts[1].trimmed())
-		{
-			RtfTableRow row;
-			row.addCell(doc_.maxWidth(), "Für die Mutationssignaturen des Typs " + type + " konnten keine COSMIC Signaturen identifieziert werden.");
-			table.addRow(row);
-			return;
+			}
 		}
+		else //CSV format
+		{
+			if (lines.count() < 2) THROW(Exception, "CNV format: not two lines");
+			QByteArrayList parts = lines[1].split(',');
 
-		QByteArrayList signatures = (parts[1] + "&").split('&');
+			cos_similarity = parts[5];
+			correlation = parts[6];
 
-		foreach (auto sig, signatures)
-		{
-			sig = sig.trimmed();
-			if (sig == "") continue;
-			sig.replace("Signature ", "");
+			//if there is only a single resulting signature it has no percentage after it.
+			if (parts[0].trimmed() != parts[1].trimmed())
+			{
+				foreach(QByteArray entry, parts[1].split('&'))
+				{
+					entry = entry.replace("Signature ", "").trimmed();
+					if (entry.isEmpty() || !entry.contains(' ')) continue;
 
-			QByteArray sig_name = sig.split(' ')[0];
-			QByteArray sig_perc = sig.split(' ')[1];
-			sig_perc.replace("(", "");
-			sig_perc.replace("%)", "");
+					QByteArray sig_name = entry.split(' ')[0];
+					QByteArray sig_perc = entry.split(' ')[1];
+					sig_perc.replace("(", "");
+					sig_perc.replace("%)", "");
 
-			RtfTableRow row;
-			row.addCell(cell_widths[0], sig_name);
-			row.addCell(cell_widths[1], sig_perc.replace(".", ",").trimmed());
-			row.addCell(cell_widths[2], correlation.replace(".", ",").trimmed());
-			row.addCell(cell_widths[3], cos_similarity.replace(".", ",").trimmed());
-			row.addCell(cell_widths[4], descriptions[sig_name]);
+					signatures.append(KeyValuePair(sig_name, sig_perc));
+				}
+			}
+		}
 
+		//create output table
+		if (signatures.isEmpty())
+		{
+			RtfTableRow row;
+			row.addCell(doc_.maxWidth(), "Für die Mutationssignaturen des Typs " + type + " konnten keine COSMIC Signaturen identifiziert werden.");
 			table.addRow(row);
 		}
+		else
+		{
+			foreach (auto sig, signatures)
+			{
+				RtfTableRow row;
+				row.addCell(cell_widths[0], sig.key.toLatin1());
+				row.addCell(cell_widths[1], sig.value.toLatin1().replace(".", ",").trimmed());
+				row.addCell(cell_widths[2], correlation.replace(".", ",").trimmed());
+				row.addCell(cell_widths[3], cos_similarity.replace(".", ",").trimmed());
+				row.addCell(cell_widths[4], descriptions[sig.key.toLatin1()]);
+
+				table.addRow(row);
+			}
+		}
 	}
-	else
+	catch (Exception& /*e*/)
 	{
 		RtfTableRow row;
 		row.addCell(doc_.maxWidth(), "Die Mutationssignaturen des Typs " + type + " konnten nicht berechnet werden.");