Changeset 5477

Timestamp:

Jun 10, 2019, 10:44:47 AM (3 years ago)

Author:

Nicklas Nordborg

Message:

References #1142: Create MIPs flow cell and start/end/confirm sequencing

Sequencing ended can now be detected also for HiSeq sequencing, but the picard step for checking data files will fail since the read-string is not generated correctly when there are four groups in the sequencing-cycles (read1-index1-index2-read2).

Location:

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie

Files:

• extensions/HiSeqSignalHandler.java (modified) (1 diff)
• servlet/SequencingRunServlet.java (modified) (2 diffs)

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/extensions/HiSeqSignalHandler.java

@@ -242 +242 @@
         // when completed. Lets say that the sequencing step start at 25% and go to 90%
         int finalBclCount = laneCount * surfaceCount * swathCount * tileCount * numReads;
-        if (finalBclCount >= bclCount)
+        if (bclCount >= finalBclCount)
         {
           // There is about 90 minutes between the last BCL file and

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/SequencingRunServlet.java

@@ -865 +865 @@
         Document dom = XmlUtil2.getXml(stdout[2], null, false);
         XmlConfig runParameters = new XmlConfig(dom.getRootElement(), "");
-        
-        Date startDate = Reggie.CONVERTER_STRING_TO_DATE.convert("20"+runParameters.getConfig("RunStartDate"));
-        String flowCellBarcode = runParameters.getConfig("FlowCellSerial");
-        String sequencingCycles = runParameters.getConfig("Setup/Read1") + 
-            "-" + runParameters.getConfig("Setup/Index1Read") + 
-            "-" + runParameters.getConfig("Setup/Read2");
-        int runNumber = Values.getInt(runParameters.getConfig("RunNumber"));
-        String dataFilesFolder = runParameters.getConfig("RunID");
-        String hiSeqPosition = "A";
-        
+
         dc = sc.newDbControl();
         
@@ -881 +872 @@
         FlowCell fc = FlowCell.getBySequencingRun(dc, sr);
         PhysicalBioAssay flowCell = fc.getPhysicalBioAssay();
+        
+        String flowCelltype = (String)Annotationtype.FLOWCELL_TYPE.getAnnotationValue(dc, flowCell);
+        String sequencingCycles = (String)Annotationtype.SEQUENCING_CYCLES.getAnnotationValue(dc, flowCell);
+        int readGroups = sequencingCycles == null ? 3 : sequencingCycles.split("\\-").length; // 3 or 4 depending on if we have 1 or 2 index reads
+
+        Date startDate = null;
+        String flowCellBarcode = null;
+        String hiSeqPosition = "A";
+        String dataFilesFolder = null;
+        int runNumber = 0;
+        if ("HiSeq".equals(flowCelltype))
+        {
+          startDate = Reggie.CONVERTER_STRING_TO_DATE.convert("20"+runParameters.getConfig("Setup/RunStartDate"));
+          flowCellBarcode = runParameters.getConfig("Setup/Barcode");
+          if (readGroups == 3)
+          {
+            sequencingCycles = runParameters.getConfig("Setup/Read1") + 
+                "-" + runParameters.getConfig("Setup/IndexRead1") + 
+                "-" + runParameters.getConfig("Setup/Read2");
+          }
+          else
+          {
+            sequencingCycles = runParameters.getConfig("Setup/Read1") + 
+                "-" + runParameters.getConfig("Setup/IndexRead1") + 
+                "-" + runParameters.getConfig("Setup/IndexRead2") +
+                "-" + runParameters.getConfig("Setup/Read2");
+          }
+          runNumber = Values.getInt(runParameters.getConfig("Setup/ScanNumber"));
+          dataFilesFolder = runParameters.getConfig("Setup/RunID");
+          hiSeqPosition = runParameters.getConfig("Setup/FCPosition");
+        }
+        else
+        {
+          startDate = Reggie.CONVERTER_STRING_TO_DATE.convert("20"+runParameters.getConfig("RunStartDate"));
+          flowCellBarcode = runParameters.getConfig("FlowCellSerial");
+          if (readGroups == 3)
+          {
+            sequencingCycles = runParameters.getConfig("Setup/Read1") + 
+                "-" + runParameters.getConfig("Setup/Index1Read") + 
+                "-" + runParameters.getConfig("Setup/Read2");
+          }
+          else
+          {
+            sequencingCycles = runParameters.getConfig("Setup/Read1") + 
+                "-" + runParameters.getConfig("Setup/Index1Read") + 
+                "-" + runParameters.getConfig("Setup/Index2Read") +
+                "-" + runParameters.getConfig("Setup/Read2");
+          }
+          runNumber = Values.getInt(runParameters.getConfig("RunNumber"));
+          dataFilesFolder = runParameters.getConfig("RunID");
+        }
         
         // Update flow cell