Changeset 5770


Ignore:
Timestamp:
Dec 3, 2019, 9:40:36 AM (3 years ago)
Author:
Nicklas Nordborg
Message:

References #1208: Implement wizard for building database of variant frequencies in SCAN-B samples

Progress reporting is now supported by the python script.

File:
1 edited

Legend:

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

    r5768 r5770  
    123123    String statCmd = "./mut_stats.py";
    124124    statCmd += " ${WD}/vcflist.txt";
     125    statCmd += " ${WD}/progress";
    125126    statCmd += " > mut_stats.vcf";
    126127    script.cmd(statCmd);
     
    155156    int total = alignments.size();
    156157    Pattern specimenName = Pattern.compile("(\\d+\\.\\d+)\\..*"); // Extract specimen name by taking first part of alignment name
     158
    157159    for (DerivedBioAssay alignment : alignments)
    158160    {
     
    179181      String patient = patients.get(0).getName();
    180182      String dataFolder = ScriptUtil.checkValidPath((String)Annotationtype.DATA_FILES_FOLDER.getAnnotationValue(dc, manager, alignment), true, true);
    181       tw.tablePrintData(patient, projectRoot + dataFolder+"/variants-raw.vcf.gz");
     183      tw.tablePrintData(patient, projectRoot+dataFolder+"/variants-raw.vcf.gz", alignment.getName());
    182184    }
    183185    tw.flush();
Note: See TracChangeset for help on using the changeset viewer.