Changeset 5477


Ignore:
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:
2 edited

Legend:

Unmodified
Added
Removed
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/extensions/HiSeqSignalHandler.java

    r5475 r5477  
    242242        // when completed. Lets say that the sequencing step start at 25% and go to 90%
    243243        int finalBclCount = laneCount * surfaceCount * swathCount * tileCount * numReads;
    244         if (finalBclCount >= bclCount)
     244        if (bclCount >= finalBclCount)
    245245        {
    246246          // 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

    r5475 r5477  
    865865        Document dom = XmlUtil2.getXml(stdout[2], null, false);
    866866        XmlConfig runParameters = new XmlConfig(dom.getRootElement(), "");
    867        
    868         Date startDate = Reggie.CONVERTER_STRING_TO_DATE.convert("20"+runParameters.getConfig("RunStartDate"));
    869         String flowCellBarcode = runParameters.getConfig("FlowCellSerial");
    870         String sequencingCycles = runParameters.getConfig("Setup/Read1") +
    871             "-" + runParameters.getConfig("Setup/Index1Read") +
    872             "-" + runParameters.getConfig("Setup/Read2");
    873         int runNumber = Values.getInt(runParameters.getConfig("RunNumber"));
    874         String dataFilesFolder = runParameters.getConfig("RunID");
    875         String hiSeqPosition = "A";
    876        
     867
    877868        dc = sc.newDbControl();
    878869       
     
    881872        FlowCell fc = FlowCell.getBySequencingRun(dc, sr);
    882873        PhysicalBioAssay flowCell = fc.getPhysicalBioAssay();
     874       
     875        String flowCelltype = (String)Annotationtype.FLOWCELL_TYPE.getAnnotationValue(dc, flowCell);
     876        String sequencingCycles = (String)Annotationtype.SEQUENCING_CYCLES.getAnnotationValue(dc, flowCell);
     877        int readGroups = sequencingCycles == null ? 3 : sequencingCycles.split("\\-").length; // 3 or 4 depending on if we have 1 or 2 index reads
     878
     879        Date startDate = null;
     880        String flowCellBarcode = null;
     881        String hiSeqPosition = "A";
     882        String dataFilesFolder = null;
     883        int runNumber = 0;
     884        if ("HiSeq".equals(flowCelltype))
     885        {
     886          startDate = Reggie.CONVERTER_STRING_TO_DATE.convert("20"+runParameters.getConfig("Setup/RunStartDate"));
     887          flowCellBarcode = runParameters.getConfig("Setup/Barcode");
     888          if (readGroups == 3)
     889          {
     890            sequencingCycles = runParameters.getConfig("Setup/Read1") +
     891                "-" + runParameters.getConfig("Setup/IndexRead1") +
     892                "-" + runParameters.getConfig("Setup/Read2");
     893          }
     894          else
     895          {
     896            sequencingCycles = runParameters.getConfig("Setup/Read1") +
     897                "-" + runParameters.getConfig("Setup/IndexRead1") +
     898                "-" + runParameters.getConfig("Setup/IndexRead2") +
     899                "-" + runParameters.getConfig("Setup/Read2");
     900          }
     901          runNumber = Values.getInt(runParameters.getConfig("Setup/ScanNumber"));
     902          dataFilesFolder = runParameters.getConfig("Setup/RunID");
     903          hiSeqPosition = runParameters.getConfig("Setup/FCPosition");
     904        }
     905        else
     906        {
     907          startDate = Reggie.CONVERTER_STRING_TO_DATE.convert("20"+runParameters.getConfig("RunStartDate"));
     908          flowCellBarcode = runParameters.getConfig("FlowCellSerial");
     909          if (readGroups == 3)
     910          {
     911            sequencingCycles = runParameters.getConfig("Setup/Read1") +
     912                "-" + runParameters.getConfig("Setup/Index1Read") +
     913                "-" + runParameters.getConfig("Setup/Read2");
     914          }
     915          else
     916          {
     917            sequencingCycles = runParameters.getConfig("Setup/Read1") +
     918                "-" + runParameters.getConfig("Setup/Index1Read") +
     919                "-" + runParameters.getConfig("Setup/Index2Read") +
     920                "-" + runParameters.getConfig("Setup/Read2");
     921          }
     922          runNumber = Values.getInt(runParameters.getConfig("RunNumber"));
     923          dataFilesFolder = runParameters.getConfig("RunID");
     924        }
    883925       
    884926        // Update flow cell
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