Changeset 5736


Ignore:
Timestamp:
Nov 19, 2019, 3:43:51 PM (3 years ago)
Author:
Nicklas Nordborg
Message:

References #1199: Implement Variant calling pipeline

Fixed some documentation and changes the auto-confirmation from Hisat to start raw-only variant calling.

Location:
extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie
Files:
2 edited

Legend:

Unmodified
Added
Removed
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/autoconfirm/HisatAlignAutoConfirmer.java

    r5713 r5736  
    285285          VariantCallingJobCreator jobCreator = new VariantCallingJobCreator();
    286286          jobCreator.setSkipRaw(false);
    287           jobCreator.setRawOnly(false);
     287          // TODO - to begin with we only do raw variant calling
     288          jobCreator.setRawOnly(true);
    288289          jobCreator.setSoftware(software);
    289290          jobCreator.setAutoConfirm(true);
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/grid/VariantCallingJobCreator.java

    r5725 r5736  
    397397        script.newLine();
    398398     
    399         script.comment("Calculate GC content and DNA strengt using custom script");
     399        script.comment("Calculate GC content and DNA strength using custom script");
    400400        script.comment("We need to get the reference sequence within 50 base-pairs of each entry in the VCF");
    401401        script.comment("and run that through gc_stat.py which produces a VCF file that vcfanno can use");
     
    499499  /**
    500500    Job completion handler for Variant call jobs. The handler downloads the
    501     'files.out' file and create links to the files and ....
    502     TODO
     501    'files.out' and 'stats.out' files. Links are created to the listed files
     502    and some information is added as annotations to either the alignment or
     503    raw bioassay.
    503504  */
    504505  public static class VariantCallJobCompletionHandler
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