Changeset 6468

Timestamp:

Nov 4, 2021, 8:47:01 AM (15 months ago)

Author:

Nicklas Nordborg

Message:

References #1347: Updates to registration of specimen handled by external lab

Use the number of reads in the FASTQ files to set the READS annotation.

File:

• extensions/net.sf.basedb.reggie/branches/4.33-stable/src/net/sf/basedb/reggie/grid/ImportFastqJobCreator.java (modified) (2 diffs)

extensions/net.sf.basedb.reggie/branches/4.33-stable/src/net/sf/basedb/reggie/grid/ImportFastqJobCreator.java

@@ -455 +455 @@
         if (m.matches())
         {
-          metrics.passedFilter = Values.getLong(m.group(1), -1);
+          metrics.reads = Values.getLong(m.group(1), -1);
+          metrics.passedFilter = metrics.reads;
         }
       }
@@ -506 +507 @@
         int bowtie_fragment_count_limit = Values.getInt(cfg.getConfig("demux/bowtie-fragment-count-limit", mergeParameterSet, "20000"));
   
-        // We may have READS from the JSON import, but if not we should do the best and use the PF_READS value
-        Long reads = (Long)Annotationtype.READS.getAnnotationValue(dc, merged);
-        if (reads == null)
-        {
-          metrics.reads = metrics.passedFilter;
-          Annotationtype.READS.setAnnotationValue(dc, merged, metrics.reads);
-        }
-        else
-        {
-          metrics.reads = reads;
-        }
+        Annotationtype.READS.setAnnotationValue(dc, merged, metrics.reads);
         Annotationtype.PF_READS.setAnnotationValue(dc, merged, metrics.passedFilter);
         Annotationtype.ADAPTER_READS.setAnnotationValue(dc, merged, metrics.passedFilter - metrics.passedTrimmomatic[0]);