Merge branch 'master' of https://github.com/imgag/ngs-bits

.github/workflows/linux_machine_gcc.yml

@@ -21,7 +21,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         submodules: recursive
     - name: Update OS repositories

.github/workflows/mac_machine.yml

@@ -7,7 +7,7 @@ jobs:
     runs-on: macos-13
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         submodules: recursive
     - name: Update submodules

.github/workflows/windows_machine.yml

@@ -9,7 +9,7 @@ jobs:
       run:
         shell: msys2 {0}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: msys2/setup-msys2@v2
         with:
           msystem: MINGW64

doc/GSvar/igv_integration.md

@@ -36,7 +36,8 @@ When IGV initialization was perfomed or when was skipped for the session, the in
 
 ### IGV gene track/genome
 
-To generate a custom gene track with all genes from the NGSD to display in IGV you can use the tool `NGSDExportIgvGeneTrack`. This tool will create two gene track text files (one with all genes and one containing only MANE + Clinical transcripts). These files then can be (bg)zipped and manually loaded into IGV. Much easier is it to create a custom IGV genome with our megSAP script [`create_igv_genome.php`](https://github.com/imgag/megSAP/blob/master/src/Tools/create_igv_genome.php) which contains the genes/transcripts from your NGSD, the masked GRCh38 genome and additional tracks. This geneome should then be set in your `GSvar.ini` and then will always be loaded when you use IGV through GSvar.
+To generate a custom genome for IGV with all Ensembl transcripts use the megSAP script [`create_igv_genome.php`](https://github.com/imgag/megSAP/blob/master/src/Tools/create_igv_genome.php).  
+The created JSON genome file must only be set as `igv_genome` in the `GSvar.ini` and then will always be loaded when you use IGV through GSvar.
 
 
 ## FAQ

doc/install_win.md

@@ -85,3 +85,10 @@ To make the tools executable outside *QtCreator* and portable, you have to copy
 		<td>libmysql.dll</td>
 	</tr>
 </table>
+
+## Building a custom genome for IGV
+
+To generate a custom genome for IGV with all Ensembl transcripts use the megSAP script [`create_igv_genome.php`](https://github.com/imgag/megSAP/blob/master/src/Tools/create_igv_genome.php).  
+The created JSON genome file must only be set as `igv_genome` in the `GSvar.ini` and then will always be loaded when you use IGV through GSvar.
+
+

src/GSvar/ImportDialog.cpp

@@ -333,7 +333,8 @@ void ImportDialog::addRow(SqlQuery& query, int r)
 	int c=0;
 	foreach (const QString& field, db_fields_)
 	{
-		QString value = ui_.table->item(r,c)->data(Qt::UserRole).toString();
+		QTableWidgetItem* item = ui_.table->item(r,c);
+		QString value = item==nullptr ? "" : item->data(Qt::UserRole).toString();
 		const TableFieldInfo& field_info = db_.tableInfo(db_table_).fieldInfo(field);
 		query.bindValue(c, value.isEmpty() && field_info.is_nullable ? QVariant() : value);
 		++c;

src/GSvar/MainWindow.cpp

@@ -467,10 +467,23 @@ void MainWindow::userSpecificDebugFunction()
 	}
 	else if (user=="ahschul1")
 	{
-		//Test sample sheet
-		QString run_id = NGSD().getValue("SELECT id FROM sequencing_run WHERE name='#03178'").toString();
+		//Extract MANE transcript names
+		const TranscriptList transcripts = NGSD().transcripts();
+		const auto matches = NGSHelper::transcriptMatches(GenomeBuild::HG38);
+
+
+		foreach(const Transcript& trans, transcripts)
+		{
+			if (!trans.isManeSelectTranscript()) continue;
+			QByteArray enst = trans.name();
+			QByteArrayList nm;
+			foreach (const QByteArray& match, matches[enst])
+			{
+				if (match.startsWith("NM_")) nm << match;
+			}
+			if (!nm.isEmpty()) qDebug() << enst << nm.join(",");
+		}
 
-		QMessageBox::information(this, "SampleSheet", NGSD().createSampleSheet(run_id.toInt()));
 	}
 	else if (user=="ahott1a1")
 	{

src/NGSDExportIgvGeneTrack/main.cpp

@@ -87,11 +87,24 @@ class ConcreteTool
 					//determine new offset:
 					cds_offset = (cds_offset + coding_region.length()) % 3;
 
+					//update cds status
+					cds_status = "cmpl";
+
+//					if (((trans.strand()==Transcript::MINUS && i==0) || (trans.strand()==Transcript::PLUS && i==(coding_regions.count()-1))) && exon_ranges.size()>0)
+//					{
+//						//on first iteration: check if utr and exon are connected
+//						if (exon_ranges.last()[1] == coding_region.start())
+//						{
+//							exon_ranges.last()[1] = coding_region.end();
+//							exon_ranges.last()[2] = phase;
+//							continue;
+//						}
+//					}
+
 					//add (exon) start, end and frame offset
 					exon_ranges.append(QList<int>() << coding_region.start() << coding_region.end() << phase);
 
-					//update cds status
-					cds_status = "cmpl";
+
 
 				}
 
@@ -100,6 +113,16 @@ class ConcreteTool
                 {
                     // 5prime UTR LINEs
                     const BedLine& reg = utr5prime[i];
+
+//					if (((trans.strand()==Transcript::MINUS && i==0) || (trans.strand()==Transcript::PLUS && i==(coding_regions.count()-1))) && exon_ranges.size()>0)
+//					{
+//						//on first iteration: check if utr and exon are connected
+//						if (exon_ranges.last()[1] == (reg.start()-1))
+//						{
+//							exon_ranges.last()[1] = reg.end();
+//							continue;
+//						}
+//					}
 					//add (exon) start, end and frame offset
 					exon_ranges.append(QList<int>() << reg.start() << reg.end() << -1);
                 }
@@ -116,11 +139,30 @@ class ConcreteTool
 
 			//sort exons by coordinate
 			std::sort(exon_ranges.begin(), exon_ranges.end(),[](const QList<int>& a, const QList<int>& b)->bool{return a.at(0)<b.at(0);});
+
+			//merge regions (and convert to 0-based)
+			QList<QList<int>> merged_exon_ranges;
+			foreach(QList<int> exon, exon_ranges)
+			{
+				if (merged_exon_ranges.size() > 0)
+				{
+					if (merged_exon_ranges.last()[1] == (exon[0]-1))
+					{
+						merged_exon_ranges.last()[1] = exon[1];
+						merged_exon_ranges.last()[2] = std::max(merged_exon_ranges.last()[2], exon[2]);
+						continue;
+					}
+				}
+				exon[0] -= 1; //convert to 0-based
+				merged_exon_ranges.append(exon);
+			}
+
+
 			//format for columns
 			QByteArray exon_starts, exon_ends, exon_frames;
-			foreach(const QList<int>& exon, exon_ranges)
+			foreach(const QList<int>& exon, merged_exon_ranges)
 			{
-				exon_starts += QByteArray::number(exon.at(0)-1) + ","; // convert to 0-based
+				exon_starts += QByteArray::number(exon.at(0)) + ",";
 				exon_ends += QByteArray::number(exon.at(1)) + ",";
 				exon_frames += QByteArray::number(exon.at(2)) + ",";
 			}
@@ -136,7 +178,7 @@ class ConcreteTool
 			line.append(QByteArray::number(trans.end()));
 			line.append(cds_start);
 			line.append(cds_end);
-			line.append(QByteArray::number(exon_ranges.size()));
+			line.append(QByteArray::number(merged_exon_ranges.size()));
 			line.append(exon_starts);
 			line.append(exon_ends);
 			line.append("0"); //score

src/cppREST/EndpointManager.cpp

@@ -90,7 +90,7 @@ HttpResponse EndpointManager::getUserTokenAuthStatus(const HttpRequest& request)
 		return HttpResponse(ResponseStatus::FORBIDDEN, HttpUtils::detectErrorContentType(request.getHeaderByName("User-Agent")), "You are not authorized with a valid user token");
 	}
 
-	if (SessionManager::isSessionExpired(getTokenIfAvailable(request)))
+    if (SessionManager::isSessionExpired(SessionManager::getSessionBySecureToken(getTokenIfAvailable(request))))
     {
         return HttpResponse(ResponseStatus::REQUEST_TIMEOUT, request.getContentType(), EndpointManager::formatResponseMessage(request, "Secure token has expired"));
 	}
@@ -105,7 +105,7 @@ HttpResponse EndpointManager::getDbTokenAuthStatus(const HttpRequest& request)
         return HttpResponse(ResponseStatus::FORBIDDEN, HttpUtils::detectErrorContentType(request.getHeaderByName("User-Agent")), EndpointManager::formatResponseMessage(request, "You are not authorized with a valid database token"));
 	}
 
-	if (SessionManager::isSessionExpired(request.getFormUrlEncoded()["dbtoken"]))
+    if (SessionManager::isSessionExpired(SessionManager::getSessionBySecureToken(request.getFormUrlEncoded()["dbtoken"])))
     {
         return HttpResponse(ResponseStatus::REQUEST_TIMEOUT, request.getContentType(), EndpointManager::formatResponseMessage(request, "Database token has expired"));
 	}

src/cppREST/SessionManager.cpp

@@ -56,31 +56,31 @@ void SessionManager::addNewSession(QString id, Session in)
 
 void SessionManager::removeSession(QString id)
 {
-	if (instance().session_store_.contains(id))
-	{
-		instance().mutex_.lock();
-		instance().session_store_.remove(id);
-		instance().mutex_.unlock();
-	}
+    instance().mutex_.lock();
+    if (instance().session_store_.contains(id))
+    {
+		instance().session_store_.remove(id);	
+    }
+    instance().mutex_.unlock();
 }
 
 Session SessionManager::getSessionBySecureToken(QString token)
 {
-	QMapIterator<QString, Session> i(instance().session_store_);
-	while (i.hasNext())
-	{
-		i.next();
-		if (i.key() == token)
-		{
-			return i.value();
-		}
-	}
-	return Session();
+    Session found_session = {};
+    instance().mutex_.lock();
+    if (instance().session_store_.contains(token))
+    {
+        found_session = instance().session_store_[token];
+    }
+    instance().mutex_.unlock();
+    return found_session;
 }
 
 bool SessionManager::isSessionExpired(Session in)
 {
-	// Session lifetime in seconds
+    if (in.isEmpty()) return false;
+
+    // Session lifetime in seconds
 	qint64 valid_period = ServerHelper::getNumSettingsValue("session_duration");
 	if (valid_period == 0) valid_period = DEFAULT_VALID_PERIOD; // default value, if not set in the config
 	if (in.login_time.addSecs(valid_period).toSecsSinceEpoch() < QDateTime::currentDateTime().toSecsSinceEpoch())
@@ -90,23 +90,16 @@ bool SessionManager::isSessionExpired(Session in)
 	return false;
 }
 
-bool SessionManager::isSessionExpired(QString token)
-{
-	return isSessionExpired(getSessionBySecureToken(token));
-}
-
 bool SessionManager::isTokenReal(QString token)
 {
-	QMapIterator<QString, Session> i(instance().session_store_);
-	while (i.hasNext())
-	{
-		i.next();
-		if (i.key() == token)
-		{
-			return true;
-		}
-	}
-	return false;
+    bool is_real = false;
+    instance().mutex_.lock();
+    if (instance().session_store_.contains(token))
+    {
+        is_real = true;
+    }
+    instance().mutex_.unlock();
+    return is_real;
 }
 
 QMap<QString, Session> SessionManager::removeExpiredSessions()

src/cppREST/SessionManager.h

@@ -49,8 +49,7 @@ class CPPRESTSHARED_EXPORT SessionManager
     static void addNewSession(QString id, Session in);
 	static void removeSession(QString id);	
 	static Session getSessionBySecureToken(QString token);
-	static bool isSessionExpired(Session in);
-	static bool isSessionExpired(QString token);
+    static bool isSessionExpired(Session in);
 
 	static bool isTokenReal(QString token);
     static QMap<QString, Session> removeExpiredSessions();

src/cppREST/UrlManager.cpp

@@ -56,36 +56,42 @@ void UrlManager::addNewUrl(QString id, UrlEntity in)
 
 void UrlManager::removeUrl(const QString& id)
 {
-	if (instance().url_storage_.contains(id))
-	{
-		instance().mutex_.lock();
-		instance().url_storage_.remove(id);
-		instance().mutex_.unlock();
+    instance().mutex_.lock();
+    if (instance().url_storage_.contains(id))
+    {
+        instance().url_storage_.remove(id);
     }
+    instance().mutex_.unlock();
 }
 
 bool UrlManager::isInStorageAlready(const QString& filename_with_path)
 {
-	QMapIterator<QString, UrlEntity> i(instance().url_storage_);
+    bool is_found = false;
+    instance().mutex_.lock();
+    QMapIterator<QString, UrlEntity> i(instance().url_storage_);
     while (i.hasNext())
     {
 		i.next();		
 		if (i.value().filename_with_path == filename_with_path)
 		{
-			return true;
+            is_found = true;
 		}
 	}
+    instance().mutex_.unlock();
 
-	return false;
+    return is_found;
 }
 
 UrlEntity UrlManager::getURLById(const QString& id)
 {
-	if (instance().url_storage_.contains(id))
+    UrlEntity found_entity = {};
+    instance().mutex_.lock();
+    if (instance().url_storage_.contains(id))
     {
-        return instance().url_storage_[id];
+        found_entity = instance().url_storage_[id];
 	}
-	return UrlEntity{};
+    instance().mutex_.unlock();
+    return found_entity;
 }
 
 bool UrlManager::isUrlExpired(UrlEntity in)

src/tools-TEST/data_out/NGSDExportIgvGeneTrack_out1.txt

@@ -1,5 +1,5 @@
-0	ENST00000352993	chr17	+	43044294	43125370	43045677	43124096	24	43044294,43045677,43047642,43049120,43051062,43057051,43063332,43063873,43067607,43070927,43074330,43076487,43082403,43090943,43095845,43097243,43099774,43104121,43104867,43106455,43115725,43124016,43124096,43125270,	43045677,43045802,43047703,43049194,43051117,43057135,43063373,43063951,43067695,43071238,43074521,43076614,43082575,43091032,43095922,43097289,43099880,43104261,43104956,43106533,43115779,43124096,43124115,43125370,	0	BRCA1	cmpl	cmpl	-1,0,2,0,2,0,0,2,2,0,2,1,2,0,2,1,2,0,2,1,1,1,-1,-1,
-0	ENST00000591534	chr17	+	43045562	43125329	43045677	43074478	13	43045562,43045677,43047642,43049120,43051062,43057051,43063332,43063873,43067607,43070927,43074330,43074478,43125270,	43045677,43045802,43047703,43049194,43051117,43057135,43063373,43063951,43067695,43071238,43074478,43074521,43125329,	0	BRCA1	cmpl	cmpl	-1,0,2,0,2,0,0,2,2,0,2,-1,-1,
+0	ENST00000352993	chr17	+	43044294	43125370	43045677	43124096	22	43044294,43047642,43049120,43051062,43057051,43063332,43063873,43067607,43070927,43074330,43076487,43082403,43090943,43095845,43097243,43099774,43104121,43104867,43106455,43115725,43124016,43125270,	43045802,43047703,43049194,43051117,43057135,43063373,43063951,43067695,43071238,43074521,43076614,43082575,43091032,43095922,43097289,43099880,43104261,43104956,43106533,43115779,43124115,43125370,	0	BRCA1	cmpl	cmpl	0,2,0,2,0,0,2,2,0,2,1,2,0,2,1,2,0,2,1,1,1,-1,
+0	ENST00000591534	chr17	+	43045562	43125329	43045677	43074478	11	43045562,43047642,43049120,43051062,43057051,43063332,43063873,43067607,43070927,43074330,43125270,	43045802,43047703,43049194,43051117,43057135,43063373,43063951,43067695,43071238,43074521,43125329,	0	BRCA1	cmpl	cmpl	0,2,0,2,0,0,2,2,0,2,-1,
 0	CCDS11459, ENST00000493795	chr17	+	43045677	43106526	43045677	43106526	20	43045677,43047642,43049120,43051062,43057051,43063332,43063873,43067607,43070927,43074330,43076487,43082403,43090943,43091434,43095845,43097243,43099774,43104121,43104867,43106455,	43045802,43047703,43049194,43051117,43057135,43063373,43063951,43067695,43071238,43074521,43076614,43082575,43091032,43094860,43095922,43097289,43099880,43104261,43104956,43106526,	0	BRCA1	cmpl	cmpl	0,2,0,2,0,0,2,2,0,2,1,2,0,2,2,1,2,0,2,1,
 0	CCDS11453, ENST00000357654	chr17	-	43045677	43124096	43045677	43124096	22	43045677,43047642,43049120,43051062,43057051,43063332,43063873,43067607,43070927,43074330,43076487,43082403,43090943,43091434,43095845,43097243,43099774,43104121,43104867,43106455,43115725,43124016,	43045802,43047703,43049194,43051117,43057135,43063373,43063951,43067695,43071238,43074521,43076614,43082575,43091032,43094860,43095922,43097289,43099880,43104261,43104956,43106533,43115779,43124096,	0	BRCA1	cmpl	cmpl	1,0,1,0,0,1,1,0,1,2,1,0,1,1,2,1,0,1,2,2,2,0,
-0	ENST00000354071	chr17	+	43091097	43125315	43091330	43124096	12	43091097,43091330,43095845,43097243,43099774,43104121,43104867,43106455,43115725,43124016,43124096,43125270,	43091330,43094860,43095922,43097289,43099880,43104261,43104956,43106533,43115779,43124096,43124115,43125315,	0	BRCA1	cmpl	cmpl	-1,0,2,1,2,0,2,1,1,1,-1,-1,
+0	ENST00000354071	chr17	+	43091097	43125315	43091330	43124096	10	43091097,43095845,43097243,43099774,43104121,43104867,43106455,43115725,43124016,43125270,	43094860,43095922,43097289,43099880,43104261,43104956,43106533,43115779,43124115,43125315,	0	BRCA1	cmpl	cmpl	0,2,1,2,0,2,1,1,1,-1,

src/tools-TEST/data_out/NGSDExportIgvGeneTrack_out2.txt

@@ -1,2 +1,2 @@
-0	ENST00000591534	chr17	+	43045562	43125329	43045677	43074478	13	43045562,43045677,43047642,43049120,43051062,43057051,43063332,43063873,43067607,43070927,43074330,43074478,43125270,	43045677,43045802,43047703,43049194,43051117,43057135,43063373,43063951,43067695,43071238,43074478,43074521,43125329,	0	BRCA1	cmpl	cmpl	-1,0,2,0,2,0,0,2,2,0,2,-1,-1,
-0	ENST00000354071	chr17	+	43091097	43125315	43091330	43124096	12	43091097,43091330,43095845,43097243,43099774,43104121,43104867,43106455,43115725,43124016,43124096,43125270,	43091330,43094860,43095922,43097289,43099880,43104261,43104956,43106533,43115779,43124096,43124115,43125315,	0	BRCA1	cmpl	cmpl	-1,0,2,1,2,0,2,1,1,1,-1,-1,
+0	ENST00000591534	chr17	+	43045562	43125329	43045677	43074478	11	43045562,43047642,43049120,43051062,43057051,43063332,43063873,43067607,43070927,43074330,43125270,	43045802,43047703,43049194,43051117,43057135,43063373,43063951,43067695,43071238,43074521,43125329,	0	BRCA1	cmpl	cmpl	0,2,0,2,0,0,2,2,0,2,-1,
+0	ENST00000354071	chr17	+	43091097	43125315	43091330	43124096	10	43091097,43095845,43097243,43099774,43104121,43104867,43106455,43115725,43124016,43125270,	43094860,43095922,43097289,43099880,43104261,43104956,43106533,43115779,43124115,43125315,	0	BRCA1	cmpl	cmpl	0,2,1,2,0,2,1,1,1,-1,