Changeset 6476


Ignore:
Timestamp:
Nov 5, 2021, 11:24:48 AM (15 months ago)
Author:
Nicklas Nordborg
Message:

References #1346: Implement support for OncoArray? SNP data

Added more annotation types for GenotypeCall items for storing data extracted from the GTC files.

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/dao/Annotationtype.java

    r6461 r6476  
    17121712    new Annotationtype("QC_GenoTypeComment", Type.STRING, false, Item.DERIVEDBIOASSAY);
    17131713 
     1714 
     1715  /**
     1716    The "CallDate" annotation type, used for derived bioassays (GenotypeCall).
     1717    @since 4.34
     1718  */
     1719  public static final Annotationtype CALL_DATE =
     1720    new Annotationtype("CallDate", Type.TIMESTAMP, false, Item.DERIVEDBIOASSAY);
     1721
     1722  /**
     1723    The "NumCalls" annotation type, used for derived bioassays (GenotypeCall).
     1724    @since 4.34
     1725  */
     1726  public static final Annotationtype NUM_CALLS =
     1727    new Annotationtype("NumCalls", Type.INT, false, Item.DERIVEDBIOASSAY);
     1728 
     1729  /**
     1730    The "NumNoCalls" annotation type, used for derived bioassays (GenotypeCall).
     1731    @since 4.34
     1732  */
     1733  public static final Annotationtype NUM_NO_CALLS =
     1734    new Annotationtype("NumNoCalls", Type.INT, false, Item.DERIVEDBIOASSAY);
     1735
     1736  /**
     1737    The "CallRate" annotation type, used for derived bioassays (GenotypeCall).
     1738    @since 4.34
     1739  */
     1740  public static final Annotationtype CALL_RATE =
     1741    new Annotationtype("CallRate", Type.FLOAT, false, Item.DERIVEDBIOASSAY);
     1742
     1743  /**
     1744    The "GC10" annotation type, used for derived bioassays (GenotypeCall).
     1745    @since 4.34
     1746  */
     1747  public static final Annotationtype GC10 =
     1748    new Annotationtype("GC10", Type.FLOAT, false, Item.DERIVEDBIOASSAY);
     1749 
     1750  /**
     1751    The "GC50" annotation type, used for derived bioassays (GenotypeCall).
     1752    @since 4.34
     1753  */
     1754  public static final Annotationtype GC50 =
     1755    new Annotationtype("GC50", Type.FLOAT, false, Item.DERIVEDBIOASSAY);
     1756
     1757  /**
     1758    The "LogRDev" annotation type, used for derived bioassays (GenotypeCall).
     1759    @since 4.34
     1760  */
     1761  public static final Annotationtype LOG_R_DEV =
     1762    new Annotationtype("LogRDev", Type.FLOAT, false, Item.DERIVEDBIOASSAY);
     1763   
    17141764  /**
    17151765    The "mBAF_SNPCount" annotation, used for derived bioassays (AlignedSequences).
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/InstallServlet.java

    r6475 r6476  
    626626        jsonChecks.add(checkAnnotationType(dc, Annotationtype.BEADCHIP_POSITION, 1, null, createIfMissing, effectivePermissionsUse));
    627627        jsonChecks.add(checkAnnotationType(dc, Annotationtype.SCAN_DATE, 1, null, createIfMissing, effectivePermissionsUse));
     628
     629        jsonChecks.add(checkAnnotationType(dc, Annotationtype.CALL_DATE, 1, null, createIfMissing, effectivePermissionsUse));
     630        jsonChecks.add(checkAnnotationType(dc, Annotationtype.NUM_CALLS, 1, null, createIfMissing, effectivePermissionsUse));
     631        jsonChecks.add(checkAnnotationType(dc, Annotationtype.NUM_NO_CALLS, 1, null, createIfMissing, effectivePermissionsUse));
     632        jsonChecks.add(checkAnnotationType(dc, Annotationtype.CALL_RATE, 1, null, createIfMissing, effectivePermissionsUse));
     633        jsonChecks.add(checkAnnotationType(dc, Annotationtype.GC10, 1, null, createIfMissing, effectivePermissionsUse));
     634        jsonChecks.add(checkAnnotationType(dc, Annotationtype.GC50, 1, null, createIfMissing, effectivePermissionsUse));
     635        jsonChecks.add(checkAnnotationType(dc, Annotationtype.LOG_R_DEV, 1, null, createIfMissing, effectivePermissionsUse));
    628636       
    629637        jsonChecks.add(checkAnnotationType(dc, Annotationtype.SEQUENCING_START, 1, null, createIfMissing, effectivePermissionsUse));
     
    10661074
    10671075        jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.GENOTYPE_CALL, createIfMissing,
    1068             Annotationtype.DATA_FILES_FOLDER,
    1069             Annotationtype.ANALYSIS_RESULT,
    1070             Annotationtype.PIPELINE
     1076            Annotationtype.CALL_DATE, Annotationtype.NUM_CALLS, Annotationtype.NUM_NO_CALLS,
     1077            Annotationtype.CALL_RATE, Annotationtype.GC10, Annotationtype.GC50,
     1078            Annotationtype.LOG_R_DEV, Annotationtype.DATA_FILES_FOLDER,
     1079            Annotationtype.ANALYSIS_RESULT, Annotationtype.PIPELINE
    10711080          ));
    10721081       
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