Constant Field Values


Contents
uk.ac.*

uk.ac.sanger.cgp.standalonecsa.beans.AmplimerBean
public static final java.lang.String VALID_RESIDUES "ACGTNRYKMBDHV"

uk.ac.sanger.cgp.standalonecsa.beans.Constants.PreFlagging
public static final int FAIL 4
public static final int PASS 1
public static final int USEFUL 2
public static final int USELESS 3

uk.ac.sanger.cgp.standalonecsa.beans.Constants.TraceStatus
public static final int BAD_AB1_BASE_CALL 18
public static final int BAD_COMMENT_BLOCK 17
public static final int BAD_TRACE 11
public static final int FAILED_MOB_CORR 13
public static final int OVERLOADED 7
public static final int UNDERLOADED 6
public static final int UNKNOWN_CHROMAT_FORMAT 16

uk.ac.sanger.cgp.standalonecsa.beans.Constants.VariantType
public static final int COMPLEX_INDEL 4
public static final int DEL 3
public static final int GERM_SUB 10
public static final int INS 2
public static final int REF_SUB 5
public static final int SPEC_INDEL 6
public static final int SUB 1
public static final int TRACE_HOLE 7

uk.ac.sanger.cgp.standalonecsa.beans.Constants.Zygosity
public static final int HETEROZYGOUS 2
public static final int HETEROZYGOUS_TO_CHANGE 3
public static final int HOMOZYGOUS 1
public static final int UNKNOWN 4

uk.ac.sanger.cgp.standalonecsa.util.CsaConfig
public static final java.lang.String CONFIG_LOC "standaloneCsa.properties"
public static final java.lang.String CSA_ANALYSIS_LOC "./resources/csa_analysis.properties"
public static final java.lang.String DEFAULT_AMPLIMER_CONFIG_LOC "amplimer.properties"
protected static final java.lang.String DEFAULT_PROP_LOC "/default.properties"
protected static final java.lang.String STATUS_LOC "/status.properties"

uk.ac.sanger.cgp.standalonecsa.util.SetupUtils
public static final java.lang.String ALPHA_NUMERIC ".*"
public static final java.lang.String CHAR_ONLY "^[A-Za-z_\\-]$"
public static final java.lang.String DIGITS_ONLY "^[0-9]+$"