Changeset 5804


Ignore:
Timestamp:
Jan 8, 2020, 11:28:31 AM (2 years ago)
Author:
Nicklas Nordborg
Message:

References #1216: Finalize the "Confirm MIPs demux" wizard

The MIPs demux should not generate any warnings related to the number of reads since it is better if the pipeline runs to completion before checking quality and results.

File:
1 edited

Legend:

Unmodified
Added
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  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/grid/MipsDemuxJobCreator.java

    r5800 r5804  
    515515              {
    516516                libName = demuxName+".N";
    517                 // TODO - implement warnings, but levels need to be different
    518                 /*
    519                 if (passedFilterPct > MAX_UNMAPPED_PERCENT)
    520                 {
    521                   sumDemux.addWarning("PF_NNNN_PCT is " + Values.formatNumber(passedFilterPct, 2) + "% on lane " + laneNo + " (" + poolName + ")");
    522                 }
    523                 */
    524517              }
    525518              else if ("IGNORED".equals(libName))
     
    530523              {
    531524                libName = demuxName+".U";
    532                 /*
    533                 if (passedFilterPct > MAX_UNUSED_PERCENT)
    534                 {
    535                   sumDemux.addWarning("Unused barcode '" + line.getString(barcodeCol) + "' (" + line.getString(barcodeNameCol) + ") has " + Values.formatNumber(passedFilterPct, 2) + "% PF_READS on lane " + laneNo + " (" + poolName + ")");
    536                 }
    537                 */
    538525              }
    539526              else
    540               {
    541                 /*
    542                 if (passedFilterPct < MIN_LIBRARY_PERCENT)
    543                 {
    544                   sumDemux.addWarning("Library '" + libName + "' (" + line.getString(barcodeNameCol) + ") has " +Values.formatNumber(passedFilterPct, 2) + "% PF_READS on lane " + laneNo + " (" + poolName + ")");
    545                 }
    546                 */
    547               }
     527              {}
    548528             
    549529              Reads sum = sumReads.get(libName);
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