Changeset 5804

Timestamp:

Jan 8, 2020, 11:28:31 AM (4 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:

• extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/grid/MipsDemuxJobCreator.java (modified) (2 diffs)

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

@@ -515 +515 @@
               {
                 libName = demuxName+".N";
-                // TODO - implement warnings, but levels need to be different
-                /*
-                if (passedFilterPct > MAX_UNMAPPED_PERCENT)
-                {
-                  sumDemux.addWarning("PF_NNNN_PCT is " + Values.formatNumber(passedFilterPct, 2) + "% on lane " + laneNo + " (" + poolName + ")");
-                }
-                */
               }
               else if ("IGNORED".equals(libName))
@@ -530 +523 @@
               {
                 libName = demuxName+".U";
-                /*
-                if (passedFilterPct > MAX_UNUSED_PERCENT)
-                {
-                  sumDemux.addWarning("Unused barcode '" + line.getString(barcodeCol) + "' (" + line.getString(barcodeNameCol) + ") has " + Values.formatNumber(passedFilterPct, 2) + "% PF_READS on lane " + laneNo + " (" + poolName + ")");
-                }
-                */
               }
               else
-              {
-                /*
-                if (passedFilterPct < MIN_LIBRARY_PERCENT)
-                {
-                  sumDemux.addWarning("Library '" + libName + "' (" + line.getString(barcodeNameCol) + ") has " +Values.formatNumber(passedFilterPct, 2) + "% PF_READS on lane " + laneNo + " (" + poolName + ")");
-                }
-                */
-              }
+              {}
               
               Reads sum = sumReads.get(libName);