Changeset 6468


Ignore:
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:
1 edited

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

    r6467 r6468  
    455455        if (m.matches())
    456456        {
    457           metrics.passedFilter = Values.getLong(m.group(1), -1);
     457          metrics.reads = Values.getLong(m.group(1), -1);
     458          metrics.passedFilter = metrics.reads;
    458459        }
    459460      }
     
    506507        int bowtie_fragment_count_limit = Values.getInt(cfg.getConfig("demux/bowtie-fragment-count-limit", mergeParameterSet, "20000"));
    507508 
    508         // We may have READS from the JSON import, but if not we should do the best and use the PF_READS value
    509         Long reads = (Long)Annotationtype.READS.getAnnotationValue(dc, merged);
    510         if (reads == null)
    511         {
    512           metrics.reads = metrics.passedFilter;
    513           Annotationtype.READS.setAnnotationValue(dc, merged, metrics.reads);
    514         }
    515         else
    516         {
    517           metrics.reads = reads;
    518         }
     509        Annotationtype.READS.setAnnotationValue(dc, merged, metrics.reads);
    519510        Annotationtype.PF_READS.setAnnotationValue(dc, merged, metrics.passedFilter);
    520511        Annotationtype.ADAPTER_READS.setAnnotationValue(dc, merged, metrics.passedFilter - metrics.passedTrimmomatic[0]);
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